Patent Analysis

Weber JL 1990 GENOMICS Aug: 7(4): 524-530 (corresponding to US Patent 5,075,217)

Abbott CM, McMahon CJ, Whitehouse DB, Povey S.
Prenatal diagnosis of alpha-1-antitrypsin deficiency using polymerase chain reaction.
Lancet 1988 Apr 2: 1(8588): 763-4.

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Abu-Hadid MM, Fuji H, Sood AK. Department of Molecular Immunology, Roswell Park Memorial Institute, Buffalo, NY 14263.

Identification of an alternatively spliced Kd and the Qa-6d mRNAs by using amplified cDNA.
Mol Immunol. 1988 Aug: 25(8): 739-49.

We have employed the primer chain reaction method for direct sequencing of H-2 mRNAs. This approach is highly sensitive and permits quantitation and sequencing of the canonical as well as alternatively spliced mRNAs that may be expressed at 5-10% level in comparison to the major H-2 species. Using this technique, we have identified a novel species of alternatively spliced Kd mRNA expressed in L1210 lymphoma and in the spleen and liver of DBA/2 mice. Similarly, we found a previously described alternatively spliced species of H-2Dd mRNA to be expressed in L1210 lymphoma and have determined the sequence of the cytoplasmic domain of Ld mRNA. In addition, we have identified a Class I MHC transcript presumably encoded by a gene allelic to Q6 gene of BALB/c mice.

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Ahrens P, Kruse TA, Schwartz M, Rasmussen PB, Din N.
A new HindIII restriction fragment length polymorphism in the hemophilia A locus.
Hum Genet. 1987 Jun: 76(2): 127-8.

Using a fragment of the cDNA for human coagulation factor VIII as a hybridization probe, we have detected a new polymorphic HindIII site in intron 19 of the factor VIII gene. The frequency of the minor allele is 0.30. This polymorphism shows strong linkage disequilibrium with a previously described BclI polymorphism in intron 18.

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Akeson AL, Wiginton DA, Dusing MR, States JC, Hutton JJ. Children's Hospital Research Foundation, Cincinnati, Ohio.

Mutant human adenosine deaminase alleles and their expression by transfection into fibroblasts.
J Biol Chem. 1988 Nov 5: 263(31): 16291-6.

Adenosine deaminase (ADA) deficiency in humans is one cause of severe combined immunodeficiency disease. Single base mutations affecting the ADA protein have been identified for both alleles of the ADA-deficient cell line GM2606 and for one allele of the ADA-deficient cell line GM2825A. One allele of GM2606 has a mutation altering amino acid 101 from Arg to Trp, and the other allele has a mutation altering amino acid 211 from Arg to His. As previously reported, one ADA allele of GM2825A has a single base mutation changing Ala-329 to Val-329, and the other allele has a mutation which eliminates exon 4 from the mature mRNA. Sequence analysis of polymerase chain reaction-amplified GM2825A DNA showed a single base change of A to G within the invariant bases of the 3' splice site of intron 3 that can account for the mis-splicing of exon 4. To test the effect on ADA catalytic activity of these mutations and the mutations previously found in the ADA-deficient line GM2756, expression vectors containing normal and mutant ADA-coding sequences under transcriptional regulation of the Rous sarcoma virus long terminal repeat were constructed and transfected into human fibroblasts. All transfected cells had levels of ADA mRNA 15-25 times higher than the endogenous ADA message. Yet, cells transfected with the normal ADA-coding sequences had ADA enzymatic levels 40 times higher than cells transfected with any of the mutant ADA sequences. This analysis demonstrates that while the mutant ADA-coding sequences are transcribed, they do not encode a functional ADA protein.

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Allen RC, Graves G, Budowle B. Dept. of Pathology and Laboratory Medicine, Medical University of South Carolina, Children's Hospital, Charleston 29425.
Polymerase chain reaction amplification products separated on rehydratable polyacrylamide gels and stained with silver.
Biotechniques. 1989 Jul-Aug: 7(7): 736-44.

Separation of polymerase chain reaction (PCR) amplification of specific fragment length polymorphisms was carried out on rehydratable polyacrylamide gels on a horizontal flat slab system. A discontinuous sulfate-borate buffer system was employed on 5-8% T gels crosslinked with 3.5% C. Samples were diluted in leading sulfate ion buffer at 1/10 the ionic strength of the separating gel buffer and placed directly onto the surface of the rehydrated gels in 0.5-10 microliters volumes. The trailing ion and counterion were contained in a gel plug and placed directly onto the anodal and cathodal ends of the gel, and the electrodes placed directly onto the surface of the gel plugs. Filter paper wicks, soaked in diluted leading ion buffer, were placed along each side to lower the ionic strength of the edges, thereby increasing mobility at the edge and thus preventing smile effects. The gel-gel contact of the plug and separating gel prevent the production of a junction potential which occurs between dissimilar materials such as a paper wick and the gel. Ten- to 20-cm separations were carried out from 2-5 h, respectively, and resolution in the 20 cm system was 1.6-4 bp (base pairs) between 100 and 500 bp, 4-7 bp between 500 and 1000 bp, 12-20 bp between 1000 and 2000 bp and about 50 bp between 2000 and 3000 bp. Between 3000 and 4000 bp, resolution fell off to +/- 100 bp. Sensitivity, using a silver stain, indicated that one could readily distinguish less than 10 pg of DNA per mm width on the gels.

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Amselem S, Nunes V, Vidaud M, Estivill X, Wong C, d'Auriol L, Vidaud D, Galibert F, Baiget M, Goossens M. INSERM U.91 Hopital Henri Mondor, Creteil, France.
Determination of the spectrum of beta-thalassemia genes in Spain by use of dot-blot analysis of amplified beta-globin DNA.
Am J Hum Genet. 1988 Jul: 43(1): 95-100.

We have delineated the molecular lesions causing beta-thalassemia in Spain, a country that has witnessed the passage of different Mediterranean populations over the centuries, in order to evaluate the extent of heterogeneity of these mutations and to make possible simplified prenatal diagnosis of the disorder in that country. The use of the polymerase chain-reaction (PCR) technique to preferentially amplify beta-globin DNA sequences that contain the most frequent beta-thalassemia mutations in Mediterraneans enabled us to rapidly analyze 58 beta-thalassemia alleles in a dot-blot format either by hybridization with allele-specific radiolabeled oligonucleotide probes or by direct sequence analysis of the amplification product. The Spanish population carries seven different beta-thalassemia mutations; the nonsense codon 39 is predominant (64%), whereas the IVS1 position 110 mutation, the most common cause of beta-thalassemia in the eastern part of the Mediterranean basin, is underrepresented (8.5%). The IVS1 mutation at position 6 accounts for 15% of the defects and leads to a more severe form of beta+-thalassemia than originally described in most of the patients we studied. In this study, we demonstrate further the usefulness of the dot-blot hybridization of PCR-amplified genomic DNA in both rapid population surveys and prenatal diagnosis of beta-thalassemia.

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Angelini G, de Preval C, Gorski J, Mach B.
High-resolution analysis of the human HLA-DR polymorphism by hybridization with sequence-specific oligonucleotide probes.
Proc Natl Acad Sci U S A. 1986 Jun: 83(12): 4489-93. Erratum in: Proc Natl Acad Sci U S A 1986 Sep: 83(17): 6664.

The human major histocompatibility complex class II antigens of the HLA-D are highly polymorphic, surface proteins essential in the cellular interactions necessary for an immune response. The analysis of this polymorphism is crucial for (i) histocompatibility matching for transplantation and (ii) understanding the association between HLA-D and certain important diseases. The polymorphism of certain HLA-D haplotypes may escape detection by current methodologies. Analysis at the genomic level of the polymorphism of one of the HLA-D subregions HLA-DR, using oligonucleotide probes specific for the polymorphic regions, is capable of distinguishing single nucleotide differences. The DRw6 haplotype was analyzed in view of the lack of DRw6 specific sera. On the basis of nucleotide sequence analysis, the DRw6 haplotype consists of at least two subtypes. When analyzed with oligonucleotide probes, this split identifies new polymorphic groups that differ from the DRw6 serological subgroups.

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By using probes for

-, Yβ₁-, and β-globin genes, we found four additional polymorphic restriction sites that have frequencies >0.1 in persons of Mediterranean area origin, Asian Indians, and American Blacks. Three of these (HincII sites) and the two previously described polymorphic HindIII sites [one in intervening sequence (IVS) II of each γ-globin gene] are distributed over 32 kilobases (kb) of DNA located 5′ to the δ-globin gene. This region of DNA comprises two-thirds of the β-globin gene cluster. Since each of these five polymorphic sites can be present (+) or absent (-), in theory there exist 32 possible combinations of sites (haplotypes). However, in Italians, Greeks, Indians, and Turks, 3 of the 32 haplotypes, (+----), (-+-++), and (-++-+), account for 92% of 89 β^A chromosomes examined. The observed frequencies for these haplotypes are 0.64, 0.15, and 0.13 in the populations studied, in contrast to expected frequencies (based on the observed gene frequencies at each of the five sites) of 0.20, 0.006, and 0.005, respectively. In American Blacks, a fourth haplotype, (----+), which is rare in non-Black populations, has a frequency of 0.37 in contrast to its expected frequency of 0.05. These results suggest a nonrandom association of DNA sequences over 32 kb 5′ to the δ-globin gene in all populations studied. Two other polymorphic sites 3′ to the δ gene (the newly discovered Ava II site in IVS II of the β-globin gene and the BamHI site 3′ to it) are nonrandomly associated with each other but randomly distributed with respect to the above haplotypes. This suggests that randomization of sequences has occurred within 12 kb of DNA between these two nonrandomly associated sequence clusters. Nonrandom association of polymorphic restriction sites has practical consequences in that it limits the usefulness of these additional HincII sites for prenatal diagnosis of hemoglobinopathies by linkage analysis. These sites provide little additional information for detection of β-thalassemia, while the polymorphic Ava II site, which lies outside the nonrandomly associated sequences 5′ to the δ gene, improves the test applicability from 52% to 70% of couples at risk.

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Antonarakis SE, Phillips JA 3rd, Kazazian HH Jr.
Genetic diseases: diagnosis by restriction endonuclease analysis.
J Pediatr. 1982 Jun: 100(6): 845-56.

We have summarized a number of different genetic disorders which can be diagnosed at the DNA level using restriction endonuclease fragment analysis. A whole spectrum of defects can be recognized: point mutations, deletions, additions, and crossing-over products or hybrid genes. These same restriction endonuclease techniques can enable different genes to be marked by polymorphism patterns. Thus, abnormal genes can be identified even if their exact DNA lesion is unknown or cannot be directly detected. The progress that has been made with the hemoglobinopathies and the experience from this group of single gene disorders should find application to other diseases as soon as specific probes become available.

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Antonarakis SE, Orkin SH, Kazazian HH Jr, Goff SC, Boehm CD, Waber PG, Sexton JP, Ostrer H, Fairbanks VF, Chakravarti A.

Evidence for multiple origins of the beta E-globin gene in Southeast Asia.
Proc Natl Acad Sci U S A. 1982 Nov: 79(21): 6608-11.

To investigate whether recurrent mutation has contributed to the high frequency of the beta E-globin gene in Southeast Asia, we used the haplotypes at three polymorphic restriction sites within and to the 3' side of the beta-globin gene to predict the framework of 23 beta E-globin genes. These haplotypes suggested that beta E-globin genes are present in two different beta-globin gene frameworks. DNA sequence determination of one gene representing each framework demonstrated that the same mutation (GAG leads to AAG at codon 26) was present in both frameworks. Moreover, the frameworks differed at three nucleotide positions known to be polymorphic in Mediterraneans. These polymorphic sites are located 70 nucleotides to the 5' side of the beta E mutation and 382 and 1032 nucleotides to the 3' side of it. The existence of the beta E mutation in these two beta-globin gene frameworks can be explained by (i) recurrent mutation giving rise to beta E-globin, (ii) a double crossing-over event, or (iii) two single crossing-over events. Mathematical analysis suggests that the first alternative, recurrent mutation of G leads to A at the first nucleotide of codon 26, is most likely.

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Analysis of DNA haplotypes suggests a genetic predisposition to trisomy 21 associated with DNA sequences on chromosome 21.
Proc Natl Acad Sci U S A. 1985 May: 82(10): 3360-4.

To test the hypothesis that there is a genetic predisposition to nondisjunction and trisomy 21 associated with DNA sequences on chromosome 21, we used DNA polymorphism haplotypes for chromosomes 21 to examine the distribution of different chromosomes 21 in Down syndrome and control families from the same ethnic group. The chromosomes 21 from 20 Greek families with a Down syndrome child and 27 control Greek families have been examined for DNA polymorphism haplotypes by using four common polymorphic sites adjacent to two closely linked single-copy DNA sequences (namely pW228C and pW236B), which map somewhere near the proximal long arm of chromosome 21. Three haplotypes, +, +---, and - with respective frequencies of 43/108, 24/108, and 23/108, account for the majority of chromosomes 21 in the control families. However, haplotype - was found to be much more commonly associated with chromosomes 21 that underwent nondisjunction in the Down syndrome families (frequency of 21/50; X2 for the two distributions is 9.550; P = 0.023; degrees of freedom, 3). The two populations (control and trisomic families) did not differ in the distribution of haplotypes for two DNA polymorphisms on chromosome 17. The data from this initial study suggest that the chromosome 21, which is marked in Greeks with haplotype - for the four above described polymorphic sites, is found more commonly in chromosomes that participate in nondisjunction than in controls. We propose an increased tendency for nondisjunction due to DNA sequences associated with a subset of chromosomes 21 bearing this haplotype.

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Antonarakis SE, Copeland KL, Carpenter RJ Jr, Carta CA, Hoyer LW, Caskey CT, Toole JJ, Kazazian HH Jr.

Prenatal diagnosis of haemophilia A by factor VIII gene analysis.
Lancet. 1985 Jun 22: 1(8443): 1407-9.

Cloned factor VIII deoxyribose nucleic acid (DNA) sequences were used as probes in the prenatal diagnosis of haemophilia A. Fetal DNA from cultured amniotic fluid cells was examined for a DNA polymorphism within the factor VIII gene which marked the haemophilia A gene in the pregnant obligate carrier. The fetus was predicted to be an affected male, and the diagnosis of haemophilia A was confirmed both in utero and after termination of the pregnancy.

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Antonarakis SE, Waber PG, Kittur SD, Patel AS, Kazazian HH Jr, Mellis MA, Counts RB, Stamatoyannopoulos G, Bowie EJ, Fass DN, et al.

Hemophilia A. Detection of molecular defects and of carriers by DNA analysis.
N Engl J Med. 1985 Oct 3: 313(14): 842-8.

To understand the molecular basis of hemophilia A and to provide heterozygote detection and prenatal diagnosis by DNA analysis, we used cloned factor VIII:C DNA fragments to study 10 affected families. In four of these families, inhibitors of factor VIII:C had developed in affected persons. In one such family a deletion of approximately 80 kb within the factor VIII:C gene was identified. Carriers of the deletion were identified through detection of an abnormal DNA fragment located at the deletion end points. In another family a single nucleotide change in the coding region of the factor VIII:C gene produced a nonsense codon leading to premature termination of factor VIII:C synthesis. Carrier detection was performed in eight female members of this four-generation family. In a third family a small change in the size of a restriction-endonuclease fragment correlated with the presence of the mutant gene, and in the other seven families the molecular defect has not yet been identified. In addition, we used two common polymorphic sites in the factor VIII:C gene to differentiate the normal from the defective gene in four of six obligate female carriers from families with patients in whom inhibitors did not develop. Carrier detection was possible in other members of these families. These data suggest that DNA analysis of the factor VIII:C gene provides an accurate method of carrier detection and, potentially, of prenatal diagnosis in at least 50 per cent of the pedigrees affected by hemophilia A.

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Antonarakis SE, Oettgen P, Chakravarti A, Halloran SL, Hudson RR, Feisee L, Karathanasis SK.
Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.

DNA polymorphism haplotypes of the human apolipoprotein APOA1-APOC3-APOA4 gene cluster.
Hum Genet. 1988 Nov: 80(3): 265-73.

The genes coding for apolipoproteins A1, C3, and A4 (APOA1, APOC3, APOA4) are closely linked and tandemly organized within a 15-kilobase (kb) DNA segment on the long arm of human chromosome 11. The nucleotide variability of a 61-kb DNA segment containing these genes and their flanking sequences was studied by restriction analysis of a sample of 18 unrelated Northern Europeans using seven different genomic DNA probes. Eleven restriction site polymorphisms located within this DNA segment were used for haplotype analysis of 129 Mediterranean and 67 American black chromosomes. Estimation of the extent of nonrandom association between these polymorphisms indicated considerable linkage disequilibrium within the APOA1-APOC3-APOA4 gene cluster. Several haplotypes arose by recombination, and the rate of recombination within this gene cluster was estimated to be at least 4 times greater than that expected based on uniform recombination. The polymorphism information content of each of these polymorphisms, taken individually, ranges between 0.053 and 0.375, while that of their haplotypes ranges between 0.858 and 0.862. Therefore, DNA polymorphism haplotypes in the APOA1-APOC3-APOA4 gene cluster constitute a highly informative genetic marker on the long arm of human chromosome 11.

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Antonarakis SE, Kang J, Lam VM, Tam JW, Li AM.
Department of Paediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205.

Molecular characterization of beta-globin gene mutations in patients with beta-thalassaemia intermedia in south China.
Br J Haematol. 1988 Nov: 70(3): 357-61.

We have studied the spectrum of mutations producting beta-thalassaemia intermedia in South China. The methods of mutation detection include oligonucleotide analysis, polymerase chain reaction amplification of the beta-globin gene and direct genomic sequencing. The mutations have been identified in 22 beta-globin genes from the patients in 11 unrelated families. Seven different mutations have been identified and the A to G substitution in the TATA box of the beta-globin gene accounts for 42% of these mutant beta-globin genes. Most patients have a beta(+) thalassaemia and one copy of the TATA box mutation. In two patients with beta(0) thalassaemia intermedia the mild phenotype may be explained in one by the presence of the - + - + + 5' beta-globin gene cluster haplotype which contains the Xmn I site -158 nt to the G gamma-globin gene or in the other by the number of alpha-globin genes present.

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Arai K, Madison J, Huss K, Ishioka N, Satoh C, Fujita M, Neel JV, Sakurabayashi I, Putnam FW. Department of Biology, Indiana University, Bloomington 47405.

Point substitutions in Japanese alloalbumins.
Proc Natl Acad Sci U S A. 1989 Aug: 86(16): 6092-6.

We have completed the structural study of five rare types of inherited albumin variants (alloalbumins) discovered in the Biochemical Genetics Study of 15,581 unrelated children in Hiroshima and Nagasaki. We have also identified the structural change in five other alloalbumin specimens detected during clinical electrophoresis of sera from Japanese living near Tokyo. Each of the five albumin variants from Nagasaki and Hiroshima has a single amino acid substitution. All of these substitutions differ, and none has been reported in non-Japanese populations. No instances of proalbumin variants or of albumin B (the most frequent alloalbumins in Caucasians) were detected in the children in Hiroshima and Nagasaki. However, one instance of a variant proalbumin and two examples of albumin B occurred in Japanese from the vicinity of Tokyo. In addition a previously unreported point substitution was found in albumin Tochigi, which is present in two unrelated persons from Tochigi prefecture. Four of the point mutations in the Japanese alloalbumins are in close proximity in a short segment of the polypeptide chain (residues 354-382) in which three additional point substitutions have been reported in diverse populations. These results, combined with earlier data, suggest that point substitutions are grouped in certain segments of the albumin molecule.

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Use of pooled DNA samples to detect linkage disequilibrium of polymorphic restriction fragments and human disease: studies of the HLA class II loci.
Proc Natl Acad Sci U S A. 1985 Oct: 82(20): 6970-4.

A rapid method has been developed and used to search for restriction fragment length polymorphisms (RFLPs) that are in linkage disequilibrium with disease-associated loci. By using genomic blot-hybridization analysis with DQ beta-chain and DR beta-chain cDNA probes, we examined DNA polymorphisms within the HLA class II loci associated with susceptibility to insulin-dependent mellitus (IDDM). To facilitate the search for informative RFLPs, we compared pooled DNA samples from IDDM patients with pooled DNA samples from randomly selected control individuals, instead of using the conventional approach of examining DNA samples from individuals in two groups. (The conditions under which this approach is useful are treated theoretically in the Appendix.) Several specific polymorphic restriction fragments associated with IDDM were revealed by using this economical and rapid approach. The restriction enzymes and probes identified as informative in this screening were then used to analyze HLA-DR-typed IDDM families, homozygous typing cells, and unrelated individuals to determine the association of the specific restriction fragments with HLA-DR serological type and the frequency in control and IDDM populations. Some individual polymorphic fragments for which the IDDM population was enriched correlated strongly with HLA-DR3, whereas others correlated strongly with HLA-DR4. Some fragments (e.g., a 10-kilobase Taq I fragment detected with the DR beta probe) that were more prevalent in the IDDM population subdivided the serologically defined HLA-DR type and may be informative markers for IDDM susceptibility.

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Arpaia E, Dumbrille-Ross A, Maler T, Neote K, Tropak M, Troxel C, Stirling JL, Pitts JS, Bapat B, Lamhonwah AM, et al. Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.

Identification of an altered splice site in Ashkenazi Tay-Sachs disease.
Nature. 1988 May 5: 333(6168): 85-6.

Tay-Sachs disease is an autosomal recessive genetic disorder resulting from mutation of the HEXA gene encoding the alpha-subunit of the lysosomal enzyme, beta-N-acetylhexosaminidase A (ref. 1). A relatively high frequency of carriers (1/27) of a lethal, infantile form of the disease is found in the Ashkenazi Jewish population, but it is not yet evident whether this has resulted from a founder effect and random genetic drift or from a selective advantage of heterozygotes. We have identified a single-base mutation in a cloned fragment of the HEXA gene from an Ashkenazi Jewish patient. This change, the substitution of a C for G in the first nucleotide of intron 12 is expected to result in defective splicing of the messenger RNA. A test for the mutant allele based on amplification of DNA by the 'polymerase chain rection and cleavage of a DdeI restriction site generated by the mutation revealed that this case and two other cases of the Ashkenazi, infantile form of Tay-Sachs disease are heterozygous for two different mutations. The occurrence of multiple mutant alleles warrants further examination of the selective advantage hypothesis.

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Bahnak BR, Lavergne JM, Verweij CL, Rothschild C, Pannekoek H, Larrieu MJ, Meyer D. INSERM U.143, Hopital de Bicetre, Paris, France.

Carrier detection in severe (type III) von Willebrand disease using two intragenic restriction fragment length polymorphisms.

DNA from a family with a female member affected with severe (type III) vWD was analysed using three restriction enzymes and a partial vWF cDNA probe. Two restriction fragment length polymorphisms (RFLPs) detected with the enzymes Bgl II and Xba I proved to be informative in this family. A 36.0 Kb allele demonstrated with the enzyme Xba I was rare in the general population but very important in this family for segregation analysis of the alleles and their association with the putative defective chromosome. The propositus was homozygous for the 36.0 Kb Xba I polymorphic band and heterozygous for the Bgl II polymorphism. She was the only member of the family showing this allelic pattern. The linkage of the alleles could be determined because her mother was homozygous for the 9.0 Kb Bgl II polymorphism but heterozygous for the Xba I polymorphism. The segregation of the alleles could be traced to the proband's son and a niece. The genotypic analysis revealed that her niece could be considered as carrying a defective gene for severe vWD.

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Baxter-Lowe LA, Hunter JB, Casper JT, Gorski J. Blood Center of Southeastern Wisconsin, Inc., Milwaukee 53233.

HLA gene amplification and hybridization analysis of polymorphism. HLA matching for bone marrow transplantation of a patient with HLA-deficient severe combined immunodeficiency syndrome.
J Clin Invest. 1989 Aug: 84(2): 613-8.

The treatment of choice for certain immunodeficiency syndromes and hematological disorders is bone marrow transplantation (BMT). The success of BMT is influenced by the degree of HLA compatibility between recipient and donor. However, aberrant expression of HLA sometimes makes it difficult, if not impossible, to determine the patient's HLA type by standard serological and cellular techniques. We describe here the application of new molecular biological techniques to perform high resolution HLA typing independent of HLA expression. A patient with HLA-deficient severe combined deficiency was HLA typed using in vitro amplification of the HLA genes and sequence-specific oligonucleotide probe hybridization (SSOPH). Two major advances provided by this technology are:detection of HLA polymorphism at the level of single amino acid differences; and elimination of a requirement for HLA expression. Although the patient's lymphocytes lacked class II HLA proteins, polymorphism associated with DR7,w53;DQw2;DRw11a (a split of DR5), w52b (a split of DRw52);DQw7 were identified. The patient's class I expression was partially defective, and typing was accomplished by a combination of serological (HLA-A and -C) and SSOPH analysis (HLA-B). Complete patient haplotypes were predicted after typing of family members [A2;B35(w6); Cw4; DRw11a(w52b);DQw7 and A2;B13(w4); Cw6;DR7(w53); DQw2]. Potential unrelated donors were typed and a donor was selected for BMT.

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Beaudet AL, Spence JE, Montes M, O'Brien WE, Estivill X, Farrall M, Williamson R.

Experience with new DNA markers for the diagnosis of cystic fibrosis.
N Engl J Med. 1988 Jan 7: 318(1): 50-1.

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Bellis M, Jubier-Maurin V, Dod B, Vanlerberghe F, Laurent AM, Senglat C, Bonhomme F, Roizes G. Centre National de la Recherche Scientifique, Institut de Biologie, Montpellier, France.

Distributions of two recently inserted long interspersed elements of the L1 repetitive family at the Alb and beta h3 loci in wild mice populations.
Mol Biol Evol. 1987 Jul;4(4):351-63.

The presence of the L1 sequences, L1Md4 next to the pseudogene beta h3 and I12 found in the twelfth intron of the albumin gene, in certain strains of laboratory mice but not of others has led to the suggestion that these sequences were recent insertions into the Mus mus domesticus genome. To be sure that they are really recent insertions and not relics of an ancestral chromosome, we investigated the presence or absence of these sequences in populations of wild mice belonging to the semispecies M. m. domesticus and M. m. musculus as well as in other species of the genus Mus and in related murids. The sequence I12 in the albumin gene was found in 34% of the chromosomes of the wild mice belonging to M. m. domesticus and to a lesser extent (6%) in M. m. musculus. Of 114 M. m. domesticus chromosomes, L1Md4 was found in only nine, seven of which came from the same locality. Its presence was associated with the haplotype Hbbp, which is relatively rare in European populations of M. musculus. Since there was no evidence for the presence of these two L1 sequences in more distantly related species, we conclude that they are recent insertions in the M. musculus genome.

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Bidwell JL, Bidwell EA, Savage DA, Middleton D, Klouda PT, Bradley BA. Molecular Genetics Laboratory, United Kingdom Transplant Service, Bristol, England.

A DNA-RFLP typing system that positively identifies serologically well-defined and ill-defined HLA-DR and DQ alleles, including DRw10.
Transplantation. 1988 Mar;45(3):640-6.

A single enzyme/multiple probe system of HLA-DR and DQ typing using restriction fragment-length polymorphism (RFLP) analysis is presented. TaqI-digested genomic DNAs are hybridized sequentially with short DR beta, DQ beta, and DQ alpha cDNA probes. The DR beta probe discriminates between the DR allelic specificities DR1 to DRw14, with the two exceptions of some DR3/DRw13 and some DR7/DRw9 combinations. We describe the positive identification of a DRw10-specific RFLP and demonstrate its segregation in families. The DQ beta probe defines an allelic system that identifies the alleles DQw1, DQw2, and DQw3. This permits the resolution of DR3/DRw13 and DR7/DRw9 alleles by defining the DR/DQ association caused by linkage disequilibrium. The DQ alpha probe defines another allelic series interrelated with, but independent from, the DQ beta series. Specific DQ beta/DQ alpha RFLP combinations correlate with known Dw splits of DR2, DRw6, and DR7. Combined use of the three probes permits the identification of HLA-DR, DQ, and certain Dw specificities and provides an effective and easily interpretable system for major histocompatibility complex class II allogenotyping.

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Boehm CD. Johns Hopkins University School of Medicine, Department of Pediatrics, Baltimore, MD 21205.

Use of polymerase chain reaction for diagnosis of inherited disorders.
Clin Chem. 1989 Sep: 35(9): 1843-8.

The polymerase chain reaction (PCR) is a rapid method for generating a 10(6)- to 10(7)-fold increase in the number of copies of a discrete DNA or RNA sequence. The technique is being used for rapid prenatal diagnosis and carrier testing of several inherited disorders. After PCR, mutations producing single-gene disorders can be detected by several different methods, including endonuclease digestion and gel electrophoresis (applicable when a mutation affects an endonuclease recognition site), gel electrophoresis (used for detection of deletions), and hybridization to an oligonucleotide probe specific for a mutation. Less often, gene sequencing of a PCR product is used to rapidly identify a mutation. In addition, the PCR technique can be applied to polymorphism analysis to provide diagnosis by linkage analysis. In other areas, PCR is being used to detect and characterize microbial pathogens and to characterize mutations associated with carcinogenesis. The PCR method is useful in situations in which the amount of DNA sample is limited, such as in forensics and prenatal testing, or in which the quality of the DNA sample is poor.

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Boehnke M, Arnheim N, Li H, Collins FS. Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor 48109.

Fine-structure genetic mapping of human chromosomes using the polymerase chain reaction on single sperm: experimental design considerations.

The polymerase chain reaction (PCR) makes it possible to rapidly generate a very large number of copies of a specific region of DNA. Application of PCR to individual human sperm cells permits the typing of a large number of independent male meiotic events. If the donor male is heterozygous at three loci, sperm typing using PCR will permit ordering of loci in a manner analogous to classical methods of experimental genetics. Sequential analysis of trios of loci by sperm typing will provide a very accurate means of ordering any number of tightly linked loci. Here, we describe experimental design and sample-size issues raised by the application of sperm typing by PCR for mapping human chromosomes, and we demonstrate that sperm typing will be an efficient method for generating fine-structure human genetic maps.

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Construction of a genetic linkage map in man using restriction fragment length polymorphisms.
Am J Hum Genet. 1980 May: 32(3): 314-31.

We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci." Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.

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Bouhassira EE, Lachman H, Krishnamoorthy R, Labie D, Nagel RL.
Division of Hematology, Albert Einstein College of Medicine, Bronx, NY 10461.

A gene conversion located 5' to the A gamma gene in linkage disequilibrium with the Bantu haplotype in sickle cell anemia.
J Clin Invest. 1989 Jun: 83(6): 2070-3.

Cloning and sequencing of the gamma-globin gene of a sickle cell anemia patient homozygous for the Bantu haplotype has revealed a gene conversion that involves the replacement of an A gamma sequence by a G gamma sequence in the promoter area of the A gamma gene. This event is similar to another gene conversion believed to be responsible for the very high homology between gamma-globin genes, suggesting that the promoter area of these genes is prone to this type of genetic rearrangement. Further analysis demonstrated that the chromosome bearing this gene conversion has a very high frequency among Bantu chromosomes and a very low or nil frequency in other haplotypes linked to the beta s gene. No correlation was found between the G gamma/A gamma ratio and the presence of the gene conversion among Bantu haplotype patients, thus excluding a portion of the gamma gene sequence in the determination of this ratio.

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Familial hypercholesterolemia in South African Afrikaners. PvuII and StuI DNA polymorphisms in the LDL-receptor gene consistent with a predominating founder gene effect.
Hum Genet. 1987 Sep: 77(1): 32-5.

Familial hypercholesterolemia (FH), at a prevalence of more than 1 in 100, is at least five times more common in one South African population group than in populations in North America and Europe. Fourteen homozygotic familial hypercholesterolemic subjects from this South African group were genotyped for two intragenic DNA restriction fragment length polymorphisms (RFLPs) in the LDL-receptor gene. A StuI polymorphism is located in exon 8, and a PvuII polymorphism, in intron 15. Of ten unrelated FH homozygotes genotyped for both RFLPs, nine were homozygous for an S + P- haplotype, and one was heterozygous for an S + P-/S-P + haplotype. The remaining four were genotyped for PvuII only and were homozygous for P-. Compared with a previously determined population frequency for the latter, this represents an association (P less than 0.05) between the frequency for the P- allele and FH in this population, and this finding is consistent with the "founder gene effect" previously postulated to be present on genealogical and biochemical evidence.

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Brinster RL, Allen JM, Behringer RR, Gelinas RE, Palmiter RD. Laboratory of Reproductive Physiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia 19104.

Introns increase transcriptional efficiency in transgenic mice.
Proc Natl Acad Sci U S A. 1988 Feb: 85(3): 836-40.

Experiments were designed to test the effect of introns on gene expression in transgenic mice. Four different pairs of gene constructs, which were identical except that one member of each pair lacked all introns, were compared for expression of mRNA after introduction into the murine germ line by microinjection of fertilized eggs. The expression of two chimeric genes, made by fusing either the mouse metallothionein I or the rat elastase 1 promoter/enhancer to the rat growth hormone gene, was assayed in fetal liver or pancreas, respectively, while two natural genes, an oligonucleotide-marked mouse metallothionein I gene and the human beta-globin gene, were assayed in fetal liver. In each case there was, on average, 10- to 100-fold more mRNA produced from the intron-containing construct. Moreover, mRNA levels were proportional to the relative rates of transcription that were measured in isolated nuclei. However, when the expression of the two mouse metallothionein I gene-based constructs was tested after transfection into cultured cells, little difference was observed. These observations suggest that introns play a role in facilitating transcription of microinjected genes and that this effect may be manifest only on genes exposed to developmental influences.

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Brocker-Vriends AH, Briet E, Quadt R, Dreesen JC, Bakker E, Claassen-Tegelaar R, Kanhai HH, van de Kamp JJ, Pearson PL.

Genotype assignment of haemophilia A by use of intragenic and extragenic restriction fragment length polymorphisms.
Thromb Haemost. 1987 Apr 7: 57(2): 131-6.

We performed DNA analysis in 20 families with haemophilia A in order to evaluate its usefulness for carrier detection and prenatal diagnosis. The polymorphic BclI site within intron 18 of the factor VIII gene and the extragenic TaqI and BglII polymorphic sites which are detected by the random DNA probes designated St14 and DX13, respectively, were investigated for. Two events of recombination were found between the St14 and the haemophilia A locus in 51 informative meioses. In one of these recombinant meioses crossing over had also occurred between the DX13 and the haemophilia A locus. No further crossovers between the DX13 and the haemophilia A locus were found in 20 informative meioses. Segregation analysis of the polymorphic markers and the deleterious mutation within the families allowed a diagnosis at the gene level for 52 out of 57 potential carriers. The new method considerably decreased the uncertainty about carriership for seventeen of the nineteen women with a probability of carriership between 5% and 95% based on pedigree analysis and factor VIII assays. In seven cases chromosome and DNA analysis of a chorionic villus biopsy was carried out. Three of the fetuses were female, four were male. Three of the male fetuses had inherited the normal maternal X-chromosome and were, therefore, not affected. For another male fetus no diagnosis at the gene level was possible since the mother was homozygous for all the known restriction fragment length polymorphisms within or closely linked with the haemophilia A locus.

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Buchman VL, Chumakov PM, Ninkina NN, Samarina OP, Georgiev GP.
Institute of Molecular Biology, U.S.S.R. Academy of Sciences, Moscow.

A variation in the structure of the protein-coding region of the human p53 gene.
Gene. 1988 Oct 30: 70(2): 245-52.

An extensive analysis of genomic DNA preparations from a number of normal and malignant tissues revealed BglII site polymorphism of the human p53 gene. Approximately 10% of p53 gene alleles were found to contain an additional BglII site localized in a region of intron I. This allelic form of p53 gene was also responsible for p53 protein having altered electrophoretic mobility. Molecular cloning and sequencing of both the alleles of p53 gene revealed a base-pair change in codon 72 causing arginine----proline substitution in the allele with the additional BglII site. Both variants of the p53 gene may occur in homozygous state and are therefore functional.

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Four restriction fragment length polymorphisms revealed by probes from a single cosmid map to chromosome 19.
Am J Hum Genet. 1986 Apr: 38(4): 447-60.

We have discovered and characterized a compound polymorphic locus on chromosome 19, defined by an arbitrary genomic DNA segment cloned into a cosmid vector. Four different restriction fragment length polymorphisms with minor allele frequencies equal to or greater than 10% are revealed by Southern hybridization of subclones of cosmid 1-13 with TaqI, MspI, BamHI, and HindIII digests of human DNAs. Seventy-two percent of unrelated individuals are heterozygous at one or more loci, and seven of the 24 possible haplotypes occur with frequencies of 3%-38%. Using a somatic cell hybrid panel, we have mapped this locus to 19p13.2----19q13.3, whereas in situ hybridization suggests the probe is on 19p. Taken together, these results suggest localization to 19p13.2----19cen. The locus revealed by probes from cosmid 1-13 has been designated D19S11.

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Bugawan TL, Horn GT, Long CM, Mickelson E, Hansen JA, Ferrara GB, Angelini G, Erlich HA. Department of Human Genetics, Cetus Corporation, Emeryville, CA 94608.

Analysis of HLA-DP allelic sequence polymorphism using the in vitro enzymatic DNA amplification of DP-alpha and DP-beta loci.
J Immunol. 1988 Dec 1: 141(11): 4024-30.

Allelic sequence variation of the HLA DP-alpha and DP-beta genes has been analyzed in a panel of 34 DP-typed cell lines. The polymorphic second exon of these genes was specifically amplified in vitro by the polymerase chain reaction method, using the thermostable DNA polymerase of Thermus, aquaticus. The analysis of M13 clones containing the amplified DP-beta sequences revealed a total of 14 allelic variants. In general, specific allelic DP-beta sequences were associated with each of the defined DPw1-w6 types, with beta allele subtypes revealed for the DPw2 and DPw4 specificities. An additional six DP-beta alleles which did not correlate with any of the T cell-defined specificities (DP "blanks") were also identified. Only the two previously characterized alleles of DP-alpha were detected. These observations suggest that the T cell-defined DP specificities are determined by polymorphic residues on the beta-chain. The sequence polymorphisms in DP-beta are clustered in a few specific regions, and can be detected using sequence-specific oligonucleotide probes and polymerase chain reaction amplified DNA in a rapid dot-blot format. This approach provides a simple and informative method of DP typing. The DP-beta sequences derived from four DP-typed celiac disease patients were compared with the distribution of DP-beta alleles in control individuals.

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Cai SP, Chang CA, Zhang JZ, Saiki RK, Erlich HA, Kan YW.
Department of Medicine, University of California, San Francisco 94143-0724.

Rapid prenatal diagnosis of beta thalassemia using DNA amplification and nonradioactive probes.
Blood. 1989 Feb: 73(2): 372-4.

We used in vitro DNA amplification by the polymerase chain reaction and nonradioactive probes for prenatal diagnosis of beta thalassemia in Chinese from the Guangdong province. Exact molecular diagnoses were made in all 20 fetuses studied over a 6-month period. We conclude that this method of prenatal diagnosis for beta thalassemia is a viable approach in many parts of the world where this disease is common.

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Camerino G, Grzeschik KH, Jaye M, De La Salle H, Tolstoshev P, Lecocq JP, Heilig R, Mandel JL.

Regional localization on the human X chromosome and polymorphism of the coagulation factor IX gene (hemophilia B locus).
Proc Natl Acad Sci U S A. 1984 Jan: 81(2): 498-502.

Hemophilia B is an X-linked disease caused by a functional deficiency in coagulation factor IX. A cDNA clone corresponding to factor IX has been used to detect homologous sequences in the human genome. All DNA fragments hybridizing to the probe, under medium- or high-stringency conditions, are X-linked, and the patterns obtained suggest that a single large (greater than or equal to 20 kilobases) gene is detected. The gene has been mapped to the q26-q27 region of the long arm of the X chromosome by hybridization to DNA from a panel of human-mouse hybrid cell lines. A search for restriction fragment length polymorphisms using seven restriction enzymes has led to the detection of a Taq I polymorphism, with allelic frequencies of about 0.71 and 0.29. This genetic marker should be useful for the detection of carriers of the hemophilia B trait and for prenatal diagnosis in informative families and, more generally, for the establishment of a linkage map of the human X chromosome.

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A new MspI restriction fragment length polymorphism in the hemophilia B locus.
Hum Genet. 1985: 71(1): 79-81.

Using a partial cDNA probe for human coagulation factor IX, we have detected a new restriction fragment length polymorphism in human DNA digested with MspI. The frequency of the minor allele is 0.20 +/- 0.05 and average heterozygosity is about 0.32. The MspI RFLP is in strong linkage disequilibrium with the TaqI RFLP previously described, but should nevertheless be useful in segregation analysis in case of homozygosity for the TaqI minor allele.

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Cavalli-Sforza LL. Department of Genetics, Stanford University, CA 94305-5120.

Opinion: how can one study individual variation for 3 billion nucleotides of the human genome?
Am J Hum Genet. 1990 Apr: 46(4): 649-51.

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Chamberlain JS, Gibbs RA, Ranier JE, Nguyen PN, Caskey CT. Institute for Molecular Genetics, Baylor College of Medicine, Houston, TX 77030.

Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification.
Nucleic Acids Res. 1988 Dec 9: 16(23): 11141-56.

The application of recombinant DNA technology to prenatal diagnosis of many recessively inherited X-linked diseases is complicated by a high frequency of heterogeneous, new mutations (1). Partial gene deletions account for more than 50% of Duchenne muscular dystrophy (DMD) lesions, and approximately one-third of all cases result from a new mutation (2-5). We report the isolation and DNA sequence of several deletion prone exons from the human DMD gene. We also describe a rapid method capable of detecting the majority of deletions in the DMD gene. This procedure utilizes simultaneous genomic DNA amplification of multiple widely separated sequences and should permit deletion scanning at any hemizygous locus. We demonstrate the application of this multiplex reaction for prenatal and postnatal diagnosis of DMD.

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Chebloune Y, Pagnier J, Trabuchet G, Faure C, Verdier G, Labie D, Nigon V.
Departement de Biologie Generale et Appliquee Unite Associee 92, Universite Claude Bernard-Lyon, Villeurbane.
Structural analysis of the 5' flanking region of the beta-globin gene in African sickle cell anemia patients: further evidence for three origins of the sickle cell mutation in Africa.

Haplotype analysis of the beta-globin gene cluster shows two regions of DNA characterized by nonrandom association of restriction site polymorphisms. These regions are separated by a variable segment containing the repeated sequences (ATTTT)n and (AT)xTy, which might be involved in recombinational events. Studies of haplotypes linked to the sickle cell gene in Africa provide strong argument for three origins of the mutation: Benin, Senegal, and the Central African Republic. Nevertheless, the haplotype determination does not give any information about the variable segment and does not totally exclude the possibility of recombination leading to different haplotypes linked to the mutation. The structure of the variable segment in the three African populations was studied by S1 nuclease mapping of genomic DNA, which allows a comparison of several samples. A 1080-base-pair DNA segment was sequenced for one sample from each population. S1 nuclease mapping confirmed the homogeneity of each population with regard to both (ATTTT)n and (AT)xTy repeats. We found three additional structures for (AT)xTy correlating with the geographic origin of the patients. Ten other nucleotide positions, 5' and 3' to the (AT)xTy copies, were found to be variable when compared to homologous sequences from human and monkey DNAs. These results allow us to propose an evolutionary scheme for the polymorphisms in the 5' flanking region of the beta-globin gene. The results strongly support the hypothesis of three origins for the sickle mutation in Africa.

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Nature. 1987 Sep 24-30: 329(6137): 293-4. Erratum in: Nature 1987 Oct 22-28: 329(6141): 678.

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Chelly J, Concordet JP, Kaplan JC, Kahn A. Unite de Recherches en Genetique et Pathologie Moleculaires, Unite 129, Institut National de la Sante et de la Recherche Medicale, CHU Cochin, Paris, France.
Illegitimate transcription: transcription of any gene in any cell type.

Using in vitro amplification of cDNA by the polymerase chain reaction, we have detected spliced transcripts of various tissue-specific genes (genes for anti-Mullerian hormone, beta-globin, aldolase A, and factor VIIIc) in human nonspecific cells, such as fibroblasts, hepatoma cells, and lymphoblasts. In rats, erythroid- and liver-type pyruvate kinase transcripts were also detected in brain, lung, and muscle. The abundance of these "illegitimate" transcripts is very low; yet, their existence and the possibility of amplifying them by the cDNA polymerase chain reaction provide a powerful tool to analyze pathological transcripts of any tissue-specific gene by using any accessible cell.

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Chow CM, Metzenberg RL, Rajbhandary UL. Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Nuclear gene for mitochondrial leucyl-tRNA synthetase of Neurospora crassa: isolation, sequence, chromosomal mapping, and evidence that the leu-5 locus specifies structural information.
Mol Cell Biol. 1989 Nov: 9(11): 4631-44.

We have isolated and characterized the nuclear gene for the mitochondrial leucyl-tRNA synthetase (LeuRS) of Neurospora crassa and have established that a defect in this structural gene is responsible for the leu-5 phenotype. We have purified mitochondrial LeuRS protein, determined its N-terminal sequence, and used this sequence information to identify and isolate a full-length genomic DNA clone. The 3.7-kilobase-pair region representing the structural gene and flanking regions has been sequenced. The 5' ends of the mRNA were mapped by S1 nuclease protection, and the 3' ends were determined from the sequence of cDNA clones. The gene contains a single short intron, 60 base pairs long. The methionine-initiated open reading frame specifies a 52-amino-acid mitochondrial targeting sequence followed by a 942-amino-acid protein. Restriction fragment length polymorphism analyses mapped the mitochondrial LeuRS structural gene to linkage group V, exactly where the leu-5 mutation had been mapped before. We show that the leu-5 strain has a defect in the structural gene for mitochondrial LeuRS by restoring growth under restrictive conditions for this strain after transformation with a wild-type copy of the mitochondrial LeuRS gene. We have cloned the mutant allele present in the leu-5 strain and identified the defect as being due to a Thr-to-Pro change in mitochondrial LeuRS. Finally, we have used immunoblotting to show that despite the apparent lack of mitochondrial LeuRS activity in leu-5 extracts, the leu-5 strain contains levels of mitochondrial LeuRS protein to similar to those of the wild-type strain.

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Clark AG. Department of Biology, Pennsylvania State University, University Park 16802.
Inference of haplotypes from PCR-amplified samples of diploid populations.

Direct sequencing of genomic DNA from diploid individuals leads to ambiguities on sequencing gels whenever there is more than one mismatching site in the sequences of the two orthologous copies of a gene. While these ambiguities cannot be resolved from a single sample without resorting to other experimental methods (such as cloning in the traditional way), population samples may be useful for inferring haplotypes. For each individual in the sample that is homozygous for the amplified sequence, there are no ambiguities in the identification of the allele's sequence. The sequences of other alleles can be inferred by taking the remaining sequence after "subtracting off" the sequencing ladder of each known site. Details of the algorithm for extracting allelic sequences from such data are presented here, along with some population-genetic considerations that influence the likelihood for success of the method. The algorithm also applies to the problem of inferring haplotype frequencies of closely linked restriction-site polymorphisms.

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Claustres M, Bellet H, Desgeorges M, Kjellberg P, Toueri MF, Rollin B, Bonnet H.
DNA amplification in the study of polymorphisms linked to the cystic fibrosis gene

The highly specific polymerase chain reaction recently described can be used to amplify selectively several polymorphic regions of DNA genetically close to the cystic fibrosis gene. This method, providing automated, revolutionizes the classical methods of prenatal diagnosis and carrier detection.

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Cohen JB, Levinson AD. Department of Cell Genetics, Genentech Inc., South San Francisco, California 94080.
A point mutation in the last intron responsible for increased expression and transforming activity of the c-Ha-ras oncogene.

The T24/EJ allele of the Ha-ras proto-oncogene owes its powerful oncogenic activity not merely to the well documented mutation that perturbs the structure of the encoded polypeptide, but in addition to a second single nucleotide alteration in an intron that causes a tenfold increase in expression. This effect on expression is maintained upon transfer of the surrounding DNA to a heterologous gene, and as such defines a novel regulatory element.

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Coleman RT, Gonzalez PA, Funke H, Assmann G, Levy-Wilson B, Frossard PM.
Polymorphisms in the apolipoprotein AI-CIII gene complex.

We report the presence of five restriction fragment length polymorphisms in the apolipoprotein AI-CIII (apo AI-CIII) gene complex as well as their respective allelic frequencies in a German population (pi) that we studied: an SstI (BanII) polymorphism in the 3' non-coding region of apo CIII q1(pi) = 0.13); an MspI polymorphism in the third intron of apo AI (q2(pi) = 0.12); a PvuII polymorphism in the first intron of apo CIII (q3(pi) = 0.30); and two XmnI polymorphisms in the 5' side of apo AI (q4(pi) = 0.20 and q5(pi) = 0.05).

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Coleman RT, Malloy MJ, Kane JP, Frossard PM. California Biotechnology, Inc., Mountain View 94043.

NcoI dimorphic site located 8kb 3' to the human apolipoprotein AIV (APOA4) gene.

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DNA restriction fragment length polymorphisms and heterozygosity in the human genome.
Hum Genet. 1984: 66(1): 1-16.

A list is presented of published reports of DNA polymorphisms found in the human genome by restriction enzyme analysis. While the list indicates the large number of restriction fragment length polymorphisms (RFLPs) detected to date, the information collated is insufficient to permit an estimate of heterozygosity for the genome as a whole. Data from our laboratory are therefore also presented on RFLPs detected using a random sample of cloned DNA segments. Such an analysis has permitted a first unbiassed estimate of heterozygosity for the human genome. Since this figure is an order of magnitude higher than previous estimates derived from protein data, the majority of polymorphic variation present in the human genome must, by implication, occur in noncoding sequences. In addition it was confirmed that enzymes containing the dinucleotide CpG in their recognition sequences detect more polymorphic variation than those that do not contain a CpG. Also presented are the clinical applications of DNA polymorphisms in the diagnosis of human genetic disease.

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Cooper DN, Smith BA, Cooke HJ, Niemann S, Schmidtke J.
An estimate of unique DNA sequence heterozygosity in the human genome.

Fifteen different restriction fragment length polymorphisms (RFLPs) were detected in the human genome using 19 cloned DNA segments, derived from flow-sorted metaphase chromosomes or total genomic DNA, as hybridization probes. Since these clones were selected at random with respect to their coding potential, their analysis permitted an unbiased estimate of single-copy DNA sequence heterozygosity in the human genome. Since our estimate (h = 0.0037) is an order of magnitude higher than previous estimates derived from protein data, most of the polymorphic variation present in the genome must occur in non-coding sequences. In addition, it was confirmed that enzymes containing the dinucleotide CpG in their recognition sequence detect more polymorphic variation than those that do not contain CpG.

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Cox DW, Billingsley GD, Mansfield T. Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.
DNA restriction-site polymorphisms associated with the alpha 1-antitrypsin gene.

Restriction-site variation in and around the alpha 1-antitrypsin gene has been studied using two genomic probes. With use of restriction enzymes SstI, MspI, and AvaII, three polymorphic sites have been described with a 4.6-kb probe in the 5' portion of the gene. With use of a 6.5-kb probe, polymorphisms in the coding and 3' regions of the gene have been detected with AvaII, MaeIII, and TaqI. All of these polymorphisms are of sufficiently high frequency to be useful in genetic mapping studies. The polymorphisms with AvaII and MaeIII (6.5-kb probe) are particularly useful for prenatal diagnosis. PI types and M subtypes tend to be associated with specific DNA haplotypes; there are two different types of DNA haplotypes associated with PI M1. The extent of linkage disequilibrium differs throughout the region of the alpha 1-antitrypsin gene.

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Cremer T, Lichter P, Borden J, Ward DC, Manuelidis L. Section of Neuropathology, Yale University School of Medicine, New Haven, CT 06510.

Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes.

Chromosome aberrations in two glioma cell lines were analyzed using biotinylated DNA library probes that specifically decorate chromosomes 1, 4, 7, 18 and 22 from pter to qter. Numerical changes, deletions and rearrangements of these chromosomes were readily visualized in metaphase spreads, as well as in early prophase and interphase nuclei. Complete chromosomes, deleted chromosomes and segments of translocated chromosomes were rapidly delineated in very complex karyotypes. Simultaneous hybridizations with additional subregional probes were used to further define aberrant chromosomes. Digital image analysis was used to quantitate the total complement of specific chromosomal DNAs in individual metaphase and interphase cells of each cell line. In spite of the fact that both glioma lines have been passaged in vitro for many years, an under-representation of chromosome 22 and an over-representation of chromosome 7 (specifically 7p) were observed. These observations agree with previous studies on gliomas. In addition, sequences of chromosome 4 were also found to be under-represented, especially in TC 593. These analyses indicate the power of these methods for pinpointing chromosome segments that are altered in specific types of tumors.

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Davies KE, Pearson PL, Harper PS, Murray JM, O'Brien T, Sarfarazi M, Williamson R.
Linkage analysis of two cloned DNA sequences flanking the Duchenne muscular dystrophy locus on the short arm of the human X chromosome.

The inheritance of two restriction fragment length polymorphisms (RFLPs) on the short arm of the human X chromosome has been studied relative to Duchenne muscular dystrophy. This provides a partial genetic map of the short arm of the human X chromosome between Xp110 and Xp223. The data were derived from the segregation between a RFLP located at Xp21-Xp223, the DMD locus, and a RFLP located at Xp110-Xp113. The genetic distance from Xp110 to Xp223 was found to be approximately 40 centimorgans (cM). This provides experimental confirmation that 1cM corresponds to approximately 1,000 kilobase pairs of DNA for this region of the human X chromosome. Our data confirm that the DMD mutation lies between Xp223 and Xp110. The availability of flanking probes surrounding the DMD locus will assist in the ordering of further DNA sequences relative to the mutation.

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Delpech M, Deburgrave N, Baudis M, Maissonneuve P, Bardin JM, Sultan Y, Kaplan JC.
De novo mutation in hemophilia A established by DNA haplotype analysis and precluding prenatal diagnosis.

In a family with a single case of hemophilia A genetic counselling was requested by the pregnant aunt of the propositus. The haplotypes generated by two extra-genic RFLPs, at DXS52 (St14/Taq1) and DXS15 (DX13/BglII), and one intragenic RFLP in F8C (647/BclI) indicated that: she was not a carrier; the case of hemophilia resulted from a de novo mutation in a grandfather's gamete.

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de Preval C, Angelini G, Boogh B, Ferrara GB, Mach B. Department of Microbiology, School of Medicine, University of Geneva, Switzerland.

DNA typing of HLA-DR beta chain genes can discriminate between undetected alleles and real homozygotes.

Immunogenetics. 1987: 26(4-5): 249-57.

The polymorphism of HLA-DR antigens has been studied by Southern blot hybridization under conditions specific for the detection of the DR beta chain genes. Haplotype-specific patterns were defined with DNA from DR1, 2, 3, 4, 7, w8, w11, w12, and W13 homozygous typing cells, with restriction enzymes Eco RI, Bgl I, and Pvu II. Certain serological specificities, such as DR2, DR3, and DR7, can be encoded by distinct allelic forms of DR beta chain genes. The procedure of "DNA typing" was applied to family analysis of individuals expressing only a single DR specificity upon serological typing. Three cases are described here: (1) in family GR, phenotypic DR 7 homozygotes correspond to genomic heterozygotes, and a novel DR7 allele is described: (2) in family RU, the genes corresponding to a serologically undetected (blank) DR allele were identified by restriction fragment length polymorphism (RFLP); this novel DR haplotype has an RFLP pattern similar to those of the DRw52 family, even though this specificity was not expressed on the DR-blank lymphocytes; (3) in family RG, there is no blank allele, but a homozygote RFLP situation at the DR subregion.

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A sensitive non-radioactive PCR-RFLP analysis for detecting point mutations at 12th codon of oncogene c-Ha-ras in DNAs of gastric cancer.

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Deng TL, Li Y, Johnson LF. Department of Biochemistry, Ohio State University, Columbus 43210.
Thymidylate synthase gene expression is stimulated by some (but not all) introns.

We previously described the construction of an intronless mouse thymidylate synthase (TS) minigene that has the normal 5' and 3' flanking regions of the gene linked to full length TS cDNA. Transfection of the minigene into ts- hamster V79 cells led to low level expression of normal mouse TS mRNA and protein. In the present study we analyzed the effect of introns on the expression of the TS minigene in transient transfection assays. Inclusion of introns 5 and 6 at their normal locations in the coding region led to an 8-9-fold stimulation of the level of TS and TS mRNA. Almost all of introns 5 and 6 could be deleted without diminishing the stimulatory effect. Inclusion of intron 3 also stimulated the expression of the minigene, although to a lesser extent than introns 5 and 6. However, inclusion of intron 4 had no stimulatory effect. Analysis of minigenes that contained various combinations of introns revealed that the stimulatory effects of the introns were not additive.

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Denton PH, Fowlkes DM, Lord ST, Reisner HM. Department of Microbiology and Immunology, University of North Carolina, Chapel Hill 27599.
Hemophilia B Durham: a mutation in the first EGF-like domain of factor IX that is characterized by polymerase chain reaction.
Blood. 1988 Oct: 72(4): 1407-11.

Two men with factor IX (FIX)antigen-positive (CRM+) hemophilia B were selected for study because of their abnormal expression of an immunologically defined epitope previously localized to the EGF-like domains of the molecule. Exons IV and V (coding for the first and second EGF-like domains) of FIX were amplified 10(7) times from the patients' genomic DNA by using polymerase chain reaction (PCR) technology and sequenced. Both patients had identical mutations which resulted in the highly conserved Gly 60 residue being changed to Ser. PCR-amplified exon IV from six normal males had the previously defined canonic sequence. The correlation between the mutation and defective epitope expression in the two patients suggests that a change in the tertiary structure of the EGF-like domain is likely to cause the mild hemophilia B.

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Dennis ES, Sachs MM, Gerlach WL, Beach L, Peacock WJ. CSIRO, Division of Plant Industry, Canberra ACT, Australia.
The Ds1 transposable element acts as an intron in the mutant allele Adh1-Fm335 and is spliced from the message.

The Ds-induced maize Adh1 allele Adh1-Fm335 retains its anaerobic regulation and normal transcription start site despite the presence of the 405 bp Ds element in the 5' untranslated leader region of the gene. The steady state level of Adh1-specific transcript is reduced to about 1% that of the progenitor or revertant alleles. Run-on transcription studies show that the reduced level of Adh1 specific mRNA is not attributable to a decreased transcription rate. S1 mapping indicates that the Ds element is spliced from the Adh1-Fm335 transcript using a donor site 14 bp into the Ds element and an acceptor site at the 3' junction of the Ds element with the flanking genome DNA.

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(Free Full Text)
Detera-Wadleigh SD, Coffman D, Shimada T. Clinical Neurogenetics Branch, National Institute of Mental Health, Bethesda, MD 20892.

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Dicker AP, Volkenandt M, Adamo A, Barreda C, Bertino JR. Cornell University Graduate School of Medical Sciences, Memorial Sloan-Kettering Cancer Center.
Sequence analysis of a human gene responsible for drug resistance: a rapid method for manual and automated direct sequencing of products generated by the polymerase chain reaction.

We developed a system for rapid, manual and automated sequence analysis by utilizing and modifying methods used in conjunction with the polymerase chain reaction (PCR). We are using these techniques to detect single base mutations in the dihydrofolate reductase (DHFR) gene giving rise to methotrexate (MTX) resistance of tumor cells obtained from patients with malignancies. Amplifying in vitro both genomic DNA and transcripts of the human DHFR we are able to reproducibly generate single-stranded templates. Utilizing [alpha-35S]dATP and both the universal and reverse sequencing primers we obtain sequence information from either strand. The methods described have been successfully used for automated sequencing with the Applied Biosystems Model 370A Sequencer using both modified T7 DNA polymerase and Taq I. DNA polymerase for dideoxy-termination sequencing. The use of this methodology to detect a single base change in a human colon carcinoma cell line, HCT-8, is illustrated.

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Tight linkage between a splicing mutation and a specific DNA haplotype in phenylketonuria.
Nature. 1986 Aug 28-Sep 3: 322(6082): 799-803.

The first phenylketonuria mutation identified in the human phenylalanine hydroxylase gene is a single base substitution (GT----AT) in the canonical 5'-splice donor site of intron 12. Direct hybridization analysis using specific oligonucleotide probes demonstrates that the mutation is tightly associated with a specific restriction fragment-length polymorphism haplotype among mutant alleles. The splicing mutation is the most prevalent phenylketonuria allele among Caucasians, and the results suggest the possibility of detecting carriers of the genetic trait who have no family history of phenylketonuria.

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DiLella AG, Huang WM, Woo SL. Howard Hughes Medical Institute, Department of Cell Biology, Baylor College of Medicine, Houston, Texas.

Screening for phenylketonuria mutations by DNA amplification with the polymerase chain reaction.

Single base substitutions have been identified in two mutant phenylalanine hydroxylase (PAH) alleles that cause phenylketonuria (PKU). The two mutant alleles are common among caucasians of northern European ancestry; detection in genomic DNA samples of patients and carriers by hybridisation with oligonucleotides specific for the respective mutant alleles requires fractionation of restriction-enzyme-digested genomic DNA samples by gel electrophoresis. This method is too cumbersome for mass screening of PKU carriers. Identification of carriers of the mutant alleles was achieved by direct analysis of their genomic DNA samples after specific amplification of a sub-genomic DNA fragment containing both mutation sites by polymerase chain reaction. The results suggest that it is technically feasible to develop a programme for carrier detection of the genetic trait in the population for individuals without a family history of PKU.

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Di Marzo R, Dowling CE, Wong C, Maggio A, Kazazian HH Jr. Department of Hematology, V. Cervello Hospital, Palermo, Italy.
The spectrum of beta-thalassaemia mutations in Sicily.

To characterize beta-thalassaemia genes among the Sicilian population we have previously determined the DNA haplotypes in the beta-globin gene cluster of 99 beta-thal chromosomes. We found seven haplotypes, although 95 of 99 beta-thal chromosomes contained framework 1 and framework 3 beta genes. We have now determined the mutation in all 99 of these beta-thal genes by the use of oligonucleotide hybridization. PCR-amplification and direct genomic sequencing, and direct restriction analysis. Our results indicate that (1) the beta (0)-39 mutation is most frequent (35%); (2) beta(0)-39, IVS-1 nt 110 and IVS-1 nt 6 mutations account for 90% of beta-thal genes: (3) the IVS-1 nt 6 mutation is more frequent in thalassaemia intermedia (77%) than in Cooley's disease (34%): (4) the association between haplotypes and specific mutations is imperfect, but mutation spread has occurred within haplotypes containing the same beta-gene framework: (5) the beta(0)-39 and the IVS-1 nt 6 mutations, with a mutation spread to two major haplotypes, may be older than the IVS-1 nt 110 mutation: (6) these data make possible first-trimester prenatal diagnosis in many families (85%) in Sicily using only three pairs of oligonucleotides. In addition, a new mutation, a frameshift at codon 76 due to loss of a C residue, was found in a single beta-thal chromosome.

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Din N, Schwartz M, Kruse T, Vestergaard SR, Ahrens P, Caput D, Hartog K, Quiroga M.

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Dorsett D, Viglianti GA, Rutledge BJ, Meselson M. Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138.

Alteration of hsp82 gene expression by the gypsy transposon and suppressor genes in Drosophila melanogaster.

Genes Dev. 1989 Apr: 3(4): 454-68.

Several mutations in Drosophila result from insertion of the gypsy retrotransposon. Gypsy insertion mutagenesis and its modulation by allele-specific modifier genes were investigated by inserting gypsy or fragments of it into the intron of the Drosophila hsp82 heat shock gene. With gypsy in the parallel orientation, nearly all transcripts in transfected cells and transformed pupae were truncated in the 5' long terminal repeat (LTR). Truncation also occurred in or near the 3' LTR. The 5' LTR polyadenylation signal was strongly potentiated by a downstream 326-bp internal gypsy segment in either orientation. Anti-parallel gypsy reduced the amount of normal transcript to a much smaller extent, and a low level of truncation occurred within gypsy. No evidence was found for effects of the gypsy insertions on the hsp82 promoter. Mutations in the allelespecific modifier genes su(f) and su(w alpha) had effects on the amounts of readthrough transcripts consistent with their genetic behavior, whereas the effects of mutations in su(Hw) were only partly in accord with genetic expectations.

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Drayna D, Davies K, Hartley D, Mandel JL, Camerino G, Williamson R, White R.

Genetic mapping of the human X chromosome by using restriction fragment length polymorphisms.

Proc Natl Acad Sci U S A. 1984 May: 81(9): 2836-9.

Using a human X chromosome-specific DNA library, we have found arbitrary single-copy DNA sequences that reveal useful restriction fragment length polymorphisms. The inheritance of these and other available polymorphic DNA markers has been studied in a series of unrelated three-generation families with large sibships. These families reveal parental phase and allow determination of recombination frequencies by counting recombinant and nonrecombinant chromosomes. The resulting genetic map indicates that the minimal distance from Xp22 to Xqter is 215 recombination units. The spacing of the marker loci is such that the majority of the loci on the X chromosome, including disease loci, will lie within 20 centimorgans of at least one of these loci.

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Driscoll MC, Dispenzieri A, Tobias E, Miller CH, Aledort LM. Department of Pediatrics, Mount Sinai School of Medicine, NY.

A second BamHI DNA polymorphism and haplotype association in the factor IX gene.
Blood. 1988 Jul: 72(1): 61-5.

A second BamHI DNA polymorphism has been identified in the factor IX gene in an American black population at an allelic frequency of 0.13. This site has been localized within 500 basepairs (bp) 5' to the XmnI intron 3 polymorphic site and increases the heterozygosity of black females at the factor IX gene locus. In addition, haplotype analysis of factor IX genes at five polymorphic loci indicates that although there is conservation of sequences between the races, factor IX genes show more heterogeneity in an American black population and thus more heterozygosity is observed in black females compared with whites. This increased heterogeneity is due to DNA polymorphisms unique to black populations and to linkage equilibrium between the most 5' and 3' polymorphic sites in factor IX genes in blacks.

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Duceman BW, Ness D, Rende R, Chorney MJ, Srivastava R, Greenspan DS, Pan J, Weissman SM, Grumet FC.

HLA-JY328: mapping studies and expression of a polymorphic HLA class I gene.

Immunogenetics. 1986: 23(2): 90-9.

The JY328 clone was identified in a human genomic library using cDNA corresponding to mRNA for HLA-B7 as a probe. The L/328 cell line was established by cotransformation of mouse Ltk- cells with the herpes thymidine kinase gene and clone JY328. On Northern blots, RNA from L/328 strongly hybridized to an HLA class I probe, and an antigen was recognized by an anti-HLA class I framework antibody on the cell surface. A DNA probe corresponding to a segment of intron 7 was developed by comparing the nucleotide sequence of clone JY328 with that of other HLA class I-type genes. Using the radiolabeled probe to screen Southern blots of DNA from families with siblings exhibiting intra-HLA recombinations, a restriction fragment length polymorphism was revealed--a 1.4 kb BstE II band not present in all individuals. A corresponding fragment was apparent in the base sequence of clone JY328. The occurrence of this band on Southern blots established that JY328 maps distinct from and centromeric to the HLA-C locus and near to the HLA-B locus. Antibody absorption studies and cytotoxicity tests indicated that the JY328 gene product was not an HLA-B antigen but that it did specifically absorb CW7-specific antibody. In sum, these results suggest a novel, polymorphic HLA class I gene which expresses a product serologically similar to HLA-Cw7 but which does not map within the corresponding locus.

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Duyk GM, Kim SW, Myers RM, Cox DR. Department of Pediatrics, University of California, San Francisco 94143-0554.
Exon trapping: a genetic screen to identify candidate transcribed sequences in cloned mammalian genomic DNA.

Identification and recovery of transcribed sequences from cloned mammalian genomic DNA remains an important problem in isolating genes on the basis of their chromosomal location. We have developed a strategy that facilitates the recovery of exons from random pieces of cloned genomic DNA. The basis of this "exon trapping" strategy is that, during a retroviral life cycle, genomic sequences of nonviral origin are correctly spliced and may be recovered as a cDNA copy of the introduced segment. By using this genetic assay for cis-acting sequences required for RNA splicing, we have screened approximately 20 kilobase pairs of cloned genomic DNA and have recovered all four predicted exons.

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Rapid prenatal diagnosis of sickle cell anemia by a new method of DNA analysis.
N Engl J Med. 1987 Mar 12: 316(11): 656-61.

We have used a new method of DNA analysis for the rapid prenatal diagnosis of sickle cell anemia in two fetuses at risk for this disease. This method of detecting the sickle gene is a modification of standard restriction-enzyme techniques and requires only a small amount of DNA. The first step involves a 200,000-fold enzymatic amplification of the specific beta-globin DNA sequences that may carry the sickle mutation. This provides a sufficient quantity of DNA for the analysis. Next, a short radiolabeled synthetic DNA sequence homologous to normal beta A-globin gene sequences is hybridized to the amplified target sequences. The hybrid "duplexes" are then digested sequentially with two restriction endonucleases. The presence of beta A- or beta S-globin gene sequences in the amplified target DNA from the patient determines whether the beta A-hybridization probe anneals perfectly or with a single nucleotide mismatch. This difference affects the restriction-enzyme digestion of the DNA and the size of the resulting radiolabeled digestion products, which can be distinguished by electrophoresis followed by autoradiography. This method is sufficiently sensitive and rapid that the prenatal diagnosis of sickle cell anemia can be made on the same day that the fetal DNA is made available. It can also be applied to the diagnosis of hemoglobin C disease.

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Emrie PA, Jones C, Hofmann T, Fisher JH. University of Colorado Health Sciences Center, Department of Medicine, Denver 80206.

The coding sequence for the human 18,000-dalton hydrophobic pulmonary surfactant protein is located on chromosome 2 and identifies a restriction fragment length polymorphism.

Somat Cell Mol Genet. 1988 Jan: 14(1): 105-10.

The 18-kd hydrophobic pulmonary surfactant protein (PSP-B) is a developmentally regulated protein which is important for normal lung function. A complementary DNA probe for 221 NH2 terminal amino acids of PSP-B was used to determine the chromosomal location of this gene and identify a restriction fragment length polymorphism (RFLP). Southern blot hybridization to genomic DNA isolated from a panel of human-CHO somatic cell hybrids unambiguously maps this gene to chromosome 2. Human DNA cut with BamHI yields a RFLP with variable bands at 2.8 and 2.6 kb. Since there is a relative lack of polymorphic markers for chromosome 2, this sequence may be useful in linkage analysis.

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Estivill X, Scambler PJ, Wainwright BJ, Hawley K, Frederick P, Schwartz M, Baiget M, Kere J, Williamson R, Farrall M. Department of Biochemistry and Molecular Genetics, St. Mary's Hospital Medical School, University of London, England.

Patterns of polymorphism and linkage disequilibrium for cystic fibrosis.
Genomics. 1987 Nov: 1(3): 257-63.

Four polymorphic markers that map within 80 kb of an HTF island which is genetically very close to the cystic fibrosis locus have been identified. We have analyzed the linkage disequilibrium between each of these markers and the cystic fibrosis mutation in 89 families from four European countries, Denmark, Finland, Spain, and Great Britain. Strong linkage disequilibrium between three polymorphic sites and cystic fibrosis was observed. The markers on the J3.11 (D7S8) side of the HTF island show stronger disequilibrium than those on the met side. Linkage disequilibrium between markers and disease alters the probability that a person of a given haplotype is a carrier in some populations and helps to identify regions of a sequence that are most likely to contain the cystic fibrosis mutation.

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Farrall M, Law HY, Rodeck CH, Warren R, Stanier P, Super M, Lissens W, Scambler P, Watson E, Wainwright B, et al.
First-trimester prenatal diagnosis of cystic fibrosis with linked DNA probes.

Linkage analysis with cloned gene probes has shown that the mutation causing cystic fibrosis is located in the middle of the long arm of chromosome 7. First-trimester diagnosis of cystic fibrosis is reported in four informative families and second-trimester diagnosis in one family with fetal DNA prepared from chorionic villi, hybridised with the tightly linked DNA probes, pJ3.11 and met. Risk calculations show that the expected false-negative and false-positive rates are approximately 2% and 6%, respectively, for typical nuclear families with one affected living child. Existing probes are sufficiently informative to allow full diagnosis in about two-thirds of couples presenting with at least one affected child. In half of the remainder, the inheritance of one parental mutant chromosome can be deduced.

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Feener CA, Koenig M, Kunkel LM. Division of Genetics, Children's Hospital Harvard Medical School, Boston, Massachusetts 02115.
Alternative splicing of human dystrophin mRNA generates isoforms at the carboxy terminus.
Nature. 1989 Apr 6: 338(6215): 509-11.

Dystrophin is the protein product of the Duchenne/Becker muscular dystrophy locus. It has a relative molecular mass of 427,000 and is encoded by a large RNA transcript processed from more than 65 exons spread over two million base pairs of the human X chromosome. We have used the polymerase chain reaction to see whether any of these exons are used alternatively in the different tissues that express dystrophin. As reported for rat dystrophin, we find that the first exons of the human dystrophin transcript is different in brain and muscle, indicating that dystrophin expression could be differentially regulated in these tissues by usage of distinct promoters. The 3' end of the dystrophin transcript can be alternatively spliced to create numerous isoforms differing at their carboxyl domains; this is the only domain of dystrophin that does not share any similarity with the related cytoskeletal alpha-actinins. These alternative transcripts yield dystrophin molecules which may interact with different proteins of the tissues expressing dystrophin.

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Prenatal diagnosis of cystic fibrosis by DNA amplification for detection of KM-19 polymorphism.

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Ferns GA, Galton DJ.
Haplotypes of the human apoprotein AI-CIII-AIV gene cluster in coronary atherosclerosis.

Restriction fragment length polymorphisms of the apoprotein AI-CIII-AIV gene cluster (on the long arm of chromosome 11) were investigated in a group of Caucasian survivors of myocardial infarction, using genomic hybridisation analysis. Four common haplotypes were identified at this locus, M1P1S1, M2P1S1, M1P2S1, and M2P1S2; where M1 and M2 are the common and uncommon alleles defined using the restriction enzyme MspI, P1 and P2 are the common and uncommon alleles defined by the enzyme PstI, and S1 and S2 are the common and uncommon alleles defined by the enzyme SstI. Seven genotype combinations were observed of approximate frequencies; a/a 0.70 (33/47), a/d 0.15 (7/47), a/b 0.04 (2/47), d/d 0.04 (2/47), a/c 0.02 (1/47), b/c 0.02 (1/47), and c/d 0.02 (1/47). In contrast the corresponding values for normotriglyceridaemic Caucasian controls, without a personal or family history of atherosclerotic heart disease were; 0.83 (40/48), 0.02 (1/48), 0.06 (3/48), 0, 0.04 (2/48), 0.04 (2/48), and 0. The relative incidence of the d haplotype, characterised by the presence of a cleavage site for the enzyme SstI in the fourth exon of the ApoCIII gene, was significantly higher in the patient group (P less than 0.01). However, because of the tight linkage between the polymorphic loci studied, it was not possible to identify haplotypes associated with any greater risk of premature atherosclerosis than when the SstI polymorphism was considered in isolation.

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Fey MF, Wainscoat JS, Mukwala EC, Falusi AG, Vulliamy TJ, Luzzatto L.
Department of Haematology, John Radcliffe Hospital, Oxford, UK.
A PvuII restriction fragment length polymorphism of the glucose-6-phosphate dehydrogenase gene is an African-specific marker.

The site of a PvuII restriction fragment length polymorphism (RFLP) of the human glucose-6-phosphate dehydrogenase (G6PD) gene has been located in intron V, 60 bp upstream of G6PD exon VI. A population survey shows this RFLP to be specific for African populations, with frequencies of the rarer allele (PvuII type 2 site present) of 0.32-0.40 in Kenyans, Nigerians, Zambians, and West Indians. This allele has not been found in the European, Asian and Middle Eastern populations studied. Such population-specific markers may be useful in the study of population affinities and may provide insight into prehistoric migrations of peoples.

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Fojo SS, Beisiegel U, Beil U, Higuchi K, Bojanovski M, Gregg RE, Greten H, Brewer HB Jr. Molecular Disease Branch, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892.
Donor splice site mutation in the apolipoprotein (Apo) C-II gene (Apo C-IIHamburg) of a patient with Apo C-II deficiency.

The DNA, RNA, and protein of apo C-II have been analyzed in a patient with apo C-II deficiency (apo C-IIHamburg). Markedly reduced levels of plasma and intrahepatic C-II apolipoprotein were demonstrated by immunoblotting and immunohistochemical analysis. Northern, slot blot, and in situ hybridization studies revealed low levels of a normal-sized apo C-II mRNA. No major rearrangement of the apo C-II gene was detected by Southern blotting. Sequence analysis of apo C-II genomic clones revealed a G-to-C substitution within the donor splice site of intron II. This base substitution resulted in the formation of a new Dde I and loss of a Hph I restriction enzyme cleavage site. Amplification of the mutant sequence by the polymerase chain reaction and digestion with Dde I and Hph I restriction enzymes established that the patient was homozygous for the G-to-C mutation. This is the initial report of the DNA sequence of an abnormal apo C-II gene from a patient with deficiency of apo C-II. We propose that this donor splice site mutation is the primary genetic defect that leads to defective splicing and ultimately to an apo C-II deficiency in this kindred.

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Forrest D, Onions D, Lees G, Neil JC.
Altered structure and expression of c-myc in feline T-cell tumours.

The c-myc gene is rearranged in a subset of feline T-cell lymphosarcomas. Detailed mapping of c-myc rearrangements showed that some result from feline leukaemia virus (FeLV) proviral integration within or upstream of c-myc, but one case involves a complex 3' alteration and amplification which is apparently not directly virus-induced. S1 nuclease mapping of RNA from normal cells using c-myc probes revealed two presumptive 5' ends, each corresponding to a promoter-like sequence (P1 and P2), and a major 3' discontinuity which mapped to the 3'-most of two possible polyadenylation signals. Analysis of RNA from a series of tumours revealed different modes of c-myc expression. All tumours produced P1 and P2 transcripts with apparently normal structure except for one case where an insertion in intron 1 displaced exon 1 sequences. The abundance ratio of P1/P2 transcripts varied considerably and was high in tumours which carry a rearrangement adjacent to c-myc, but some other T-cell tumours with no apparent myc alteration displayed an equally high ratio. However, a consistent feature was the lack of detectable RNA from normal c-myc alleles in tumours which express a rearranged c-myc allele or a transduced FeLV v-myc gene. We suggest that this may prove to be a useful indicator of the presence of an oncogenically active myc gene, whether this is a rearranged c-myc or transduced v-myc sequence.

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Fournier D, Karch F, Bride JM, Hall LM, Berge JB, Spierer P. INRA, Centre de Recherche d'Antibes, France.
Drosophila melanogaster acetylcholinesterase gene. Structure, evolution and mutations.

Acetylcholinesterase is a key component of cholinergic neurotransmission. In Drosophila melanogaster, acetylcholinesterase is encoded by the Ace locus. We have determined the complete organization of the locus. The transcription unit is 34 kb (1 kb = 10(3) bases) long and encompasses ten exons. We have mapped the 5' end of the transcript, sequenced all the intron/exon boundaries, as well as the 3' end of the transcript. The deduced mature transcript is 4291 nucleotides long without poly(A). Sequencing of the promoter region reveals a potential TATA box and (GA)n motives. The Drosophila coding sequence is more split than its vertebrate counterparts, but the splicing sites of the two last exons are precisely conserved among Drosophila and vertebrate cholinesterases, and intriguingly also with the bovine thyroglobulin gene. Finally, a number of the mutations isolated in earlier genetic work are precisely placed on our molecular map in introns, exons and promoter regions. Among them, for example, a short deletion known to affect acetylcholinesterase level and tissue distribution removes promoter regions and the first non-coding exon.

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Freedenberg DL, Chen SH, Kurachi K, Scott CR.
MspI polymorphic site within the factor IX gene. Localization of the site and an improved method for detection.
Hum Genet. 1987 Jul: 76(3): 262-4.

We have localized the position of the MspI polymorphic site that exists within the factor IX gene. The location of the MspI polymorphic site is within intron D, 1.9 kb upstream from the beginning of exon V and 4 kb downstream from a known polymorphic TaqI site. The use of a specific genomic probe simplifies the interpretation of the MspI polymorphism by reducing the number of non-overlaping DNA fragments to three bands; 2.4, 3.4, and 5.8 kb.

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BanI dimorphic site in the third intron of the human apolipoprotein AI gene (Apo A1).

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Fugger L, Morling N, Ryder LP, Odum N, Georgsen J, Svejgaard A.
Department of Clinical Immunology, State University Hospital (Rigshospitalet), Copenhagen, Denmark.
Typing for HLA-DPB1*03 and HLA-DPB1*06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of "new" DPB1*06 variants.

DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for the HLA-DPB locus. Typing for the individual DPB alleles was exclusively dependent on the hybridizations of the probes but hampered by close sequence homology between different DP alleles yielding complex patterns of reactivity with a panel of probes. We report the combined use of allele-specific DNA in vitro amplification and allele-specific oligonucleotides in typing for DPB1*03 and DPB1*06. Complete concordance with PLT typing was observed for the DPB1*03 alleles, while in the DPB1*06 group, at least three variant DPB1*06 alleles were identified which have not been described previously.

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Fujisaku A, Harley JB, Frank MB, Gruner BA, Frazier B, Holers VM. Arthritis and Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City.

Genomic organization and polymorphisms of the human C3d/Epstein-Barr virus receptor.
J Biol Chem. 1989 Feb 5: 264(4): 2118-25.

The human C3d/Epstein-Barr virus receptor (CR2/CD21) is a 145-kDa protein primarily expressed on mature B lymphocytes. CR2 is a member of the regulators of complement activation (RCA) gene family found on band q32 of chromosome 1. The RCA proteins are characterized by the presence of 60-70 amino acid short consensus repeats (SCR). A full length CR2 cDNA was cloned and used to identify overlapping cosmid genomic clones. Analysis of CR2 exon-intron junctions revealed the presence of three types of exons in the short consensus repeat region of CR2. First, four exons each of which encodes two SCR are present. Five exons encode a single SCR. Six exons encode SCRs which are split in identical positions. The order of these types of exons is in a repeated array of four SCRs, indicating that the contemporary CR2 gene likely evolved from a more primitive gene containing four SCRs. The CR2 full length cDNA clone was used to find restriction fragment length polymorphisms (RFLPs). Restriction enzyme TaqI generated 2.55- and 2.10-kilobase (kb) polymorphic bands. This RFLP was mapped near the exon containing the first two SCRs. HaeIII digestion generated polymorphic bands of 1.45, 1.55, and 1.75 kb. The HaeIII 1.45-kb RFLP band maps near the exon containing the 15th SCR. The TaqI and HaeIII RFLPs will provide tools for the genetic analysis of CR2. The organization of the CR2 gene provides insights into the evolution of human CR2 and the RCA gene family.

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Funke H, Klug J, Frossard P, Kowalski J, Reckwerth A, Assmann G.
Detection of a new Msp I restriction fragment length polymorphism in the apolipoprotein A-I gene.

We report the existence of a Msp I restriction fragment length polymorphism in the first intron of the apolipoprotein A-I gene that is different from the one described by Seilhamer et al. (DNA 3, 309 (1984)). Size comparison of the newly discovered Msp I fragment with a restriction map of the apolipoprotein A-I gene revealed that most likely the cutting site at the 5'-end of the normally seen 673 bp fragment is lost giving rise to the observed 719 bp Msp I fragment. Based on analyses of 136 DNAs of healthy and non-related caucasians the allelic frequency was determined to be 0.06. The observed Msp I genotype frequencies are in Hardy-Weinberg equilibrium.

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Gaitskhoki VS, Voronina OV, Potapova OYu, Kirjukhina LV, Gembitskaya TE, Kapranov NI, Petrova NV, Khafizova ZA, Schwartz EI. Institute for Experimental Medicine, Russian Academy of Medical Sciences, St. Petersburg.
Linkage disequilibrium between cystic fibrosis mutations and polymorphic 4-bp repeat within CFTR gene.

The PCR technique was used in a study of the linkage of cystic fibrosis mutations and a polymorphic (GATT)n repeat in intron 6 of the CFTR gene. Absolute linkage disequilibrium was found between the common delta F-508 mutation and the (GATT)6 allele. This allele was also in linkage disequilibrium with other unidentified mutations in the CFTR gene resulting in the pancreatic insufficient form of disease. The frequency of (GATT)n alleles in the pancreatic sufficient form of CF did not differ significantly from the data obtained in the total population. The significance of the (GATT)n polymorphic repeat for the diagnosis of CF is discussed.

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Gatti RA, Shaked R, Mohandas TK, Salser W. Department of Pathology, University of California at Los Angeles.
Human ferritin genes: chromosomal assignments and polymorphisms.
Am J Hum Genet. 1987 Oct: 41(4): 654-67.

The ferritins are a family of proteins that function intracellularly to sequester iron that otherwise would be toxic to the cell. The molecules are comprised of 24 heavy and light subunits, the heavy:light ratio varying widely in a tissue-specific manner. We cloned DNA sequences for both the heavy (HL217-1) and light (HL227) subunits from a cDNA library derived from messages that are strongly regulated during in vitro-induced differentiation of a promyelocytic leukemia cell line, HL-60, into either neutrophils or macrophages. The heavy-subunit family (FTH) includes 15-20 genes and/or pseudogenes; the light-subunit family (FTL) includes at least three genes. We have confirmed and extended the chromosomal localization of the heavy-subunit "genes" to chromosomes 1-6, 8, 9, 11, 13, 14, 17, and X. We have also identified and characterized two genetic polymorphisms: FTH/BamHI and FTH/TaqI. FTH/BamHI localizes to chromosome 3, is biallelic, and has a heterozygosity frequency of .39, a minor allele frequency of .33, and a polymorphic information content (PIC) of .34. FTH/TaqI is measured by the presence or absence of a single 6-kb fragment that is absent (i.e., "homozygosity" being presumed) in approximately 63% of Caucasians (PIC = .27). We discuss the possibility that gene-family probes that hybridize to many discrete members of dispersed gene families could be used in conjunction with pulsed- or inverted-field gels to screen a large number of specific genomic regions for microdeletions.

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Geisel J, Weisshaar B, Oette K, Doerfler W. Abteilung fur Klinische Chemie, Universitat zu Koln.
A new Apa LI restriction fragment length polymorphism in the low density lipoprotein receptor gene.

The existence of a new Apa LI restriction fragment length polymorphism in the third intron of the low density lipoprotein (LDL) receptor gene was described. As a gene probe we used a newly constructed derivative of pLDLR 3 which did not contain the highly repetitive Alu-sequences in exon 18. This new gene probe detected all exon sequences containing restriction fragments, and enabled us to demonstrate all described polymorphisms, which might be useful for genetic linkage studies. Based on analysis of 72 unrelated normo- and hypercholesterolaemic persons, the frequency of the allele A2, which showed the additional cutting site, was determined to be 0.05. With the simplified gene probe, pLDLR delta, we also studied other polymorphisms. A clear linkage disequilibrium between the Pvu II and Msp I polymorphisms was detected. This, and the previously described linkage disequilibrium of the two Msp I polymorphisms, demonstrate that the LDL receptor gene is apparently less heterogeneous than expected from the number of described polymorphisms.

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Giannelli F, Anson DS, Choo KH, Rees DJ, Winship PR, Ferrari N, Rizza CR, Brownlee GG.
Characterisation and use of an intragenic polymorphic marker for detection of carriers of haemophilia B (factor IX deficiency).

DNA from 33 healthy White subjects was analysed with a 2 X 5 kilobase subgenomic DNA probe derived from the gene for coagulation factor IX, containing the exon "d" region of that gene. Intragenic Taq I restriction-fragment length polymorphism was revealed, with allelic frequencies estimated at 0 X 65 and 0 X 35 (SE = 0 X 06), also detectable by a cDNA probe. The genomic DNA probe is technically superior to the cDNA probe and has been used in three families with haemophilia B (factor IX deficiency). The polymorphic marker segregates with the deleterious mutation, allowing the identification or exclusion of carriers. The allelic frequencies of the Taq I polymorphism are virtually ideal. Therefore, such a polymorphism should be helpful both in genetic counselling of approximately 40% of affected families and in prenatal diagnosis.

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Gibbs RA, Nguyen PN, McBride LJ, Koepf SM, Caskey CT. Baylor College of Medicine, Houston, TX.
Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA.
Proc Natl Acad Sci U S A. 1989 Mar: 86(6): 1919-23.

The Lesch-Nyhan (LN) syndrome is a severe X chromosome-linked disease that results from a deficiency of the purine salvage enzyme hypoxanthine phosphoribosyltransferase (HPRT). The mutations leading to the disease are heterogeneous and frequently arise as de novo events. We have identified nucleotide alterations in 15 independently arising HPRT-deficiency cases by direct DNA sequencing of in vitro amplified HPRT cDNA. We also demonstrate that the direct DNA sequence analysis can be automated, further simplifying the detection of new mutations at this locus. The mutations include DNA base substitutions, small DNA deletions, a single DNA base insertion, and errors in RNA splicing. The application of these procedures allows DNA diagnosis and carrier identification by the direct detection of the mutant alleles within individual families affected by LN.

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Gibson JB, Wilks AV. Research School of Biological Sciences, Australian National University, Canberra.
Molecular structure of a naturally occurring alcohol dehydrogenase null activity allele in Drosophila melanogaster.
Biochem Genet. 1989 Dec: 27(11-12): 679-88. Erratum in: Biochem Genet 1990 Aug: 28(7-8): 443.

An alcohol dehydrogenase null activity allele, AdhnAH52, extracted from a natural population of Drosophila melanogaster has been cloned and sequenced. Compared with the wild-type consensus sequence, the nucleotide sequence of AdhnAH52 contains eight extra bases in intron 2, adjacent to the 5' splice site. It seems likely that the extra bases result from two structural changes, with a 10-base pair insertion at the same site as a 2-base pair deletion. The insertion includes an 8-base pair duplication of an adjoining region. This structural change alters transcription to give rise to an mRNA which is longer than normal and at 10% of the wild-type level.

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Gitschier J, Drayna D, Tuddenham EG, White RL, Lawn RM.
Genetic mapping and diagnosis of haemophilia A achieved through a BclI polymorphism in the factor VIII gene.

Haemophilia A is the most common inherited bleeding disorder in man, affecting approximately 1 male in 10,000. The disease is caused by a deficiency in the gene for factor VIII, a component of the intrinsic coagulation pathway. Due to the broad range of clotting activity in normal and heterozygous females, it is often difficult to confirm the status of women at risk for carrying the disease. A genetic marker in the form of a restriction fragment length polymorphism (RFLP) within or tightly linked to the factor VIII gene would serve as a tag for the haemophilia gene, thus allowing both accurate carrier detection and improved, earlier prenatal diagnosis by chorionic villi sampling. The recent isolation of the factor VIII gene has allowed a search for RFLPs within the gene, and we report here the identification of a common polymorphism within the factor VIII gene, revealed by the restriction enzyme BclI, which can be used diagnostically in about 42% of all families. Although the disease haemophilia A has been mapped to the distal portion of Xq, the BclI RFLP makes possible higher-resolution genetic linkage mapping with respect to other polymorphic markers on this portion of the X chromosome. We have established close linkage of the factor VIII gene to several useful RFLP markers, including the highly informative marker St14. These markers should also be useful for prenatal diagnosis of haemophilia A and for detection of its carriers.

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Gitschier J, Kogan S, Levinson B, Tuddenham EG. Howard Hughes Medical Institute, University of California, San Francisco 94143.
Mutations of factor VIII cleavage sites in hemophilia A.

Hemophilia A is caused by a defect in coagulation factor VIII, a protein that undergoes extensive proteolysis during its activation and inactivation. To determine whether some cases of hemophilia are caused by mutations in important cleavage sites, we screened patient DNA samples for mutations in these sites by a two-step process. Regions of interest were amplified from genomic DNA by repeated rounds of primer-directed DNA synthesis. The amplified DNAs were then screened for mutations by discriminant hybridization using oligonucleotide probes. Two cleavage site mutations were found in a survey of 215 patients. A nonsense mutation in the activated protein C cleavage site at amino acid 336 was discovered in a patient with severe hemophilia. In another severely affected patient, a mis-sense mutation results in a substitution of cysteine for arginine in the thrombin activation site at amino acid 1689. This defect is associated with no detectable factor VIII activity, but with normal levels of factor VIII antigen. The severe hemophilia in this patient was sporadic; analysis of the mother suggested that the mutation originated in her gametes or during her embryogenesis. The results demonstrate that this approach can be used to identify factor VIII gene mutations in regions of the molecule known to be important for function.

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Gotoda T, Senda M, Murase T, Yamada N, Takaku F, Furuichi Y. Third Department of Internal Medicine, Faculty of Medicine, University of Tokyo, Japan.

Gene polymorphism identified by PvuII in familial lipoprotein lipase deficiency.
Biochem Biophys Res Commun. 1989 Nov 15: 164(3): 1391-6.

We previously demonstrated that the PvuII polymorphism is a useful marker to analyze the genetic defects in familial lipoprotein lipase (LPL) deficiency. In this study, we have mapped this polymorphic site and cloned the gene fragments containing this site from a patient and a normal subject. Comparative sequence analysis revealed that a C-T transition occurred in the gene of the patient at the PvuII site in the intron 6. Interestingly, the sequence near the PvuII site showed a significant homology to the consensus sequence of the 3' splice site. In addition, the insertional event into the human LPL gene, which was recently reported for a population of Caucasian patients, was not observed for eight unrelated Japanese patients, suggesting that genetic defects underlying familial LPL deficiency should be heterogeneous among races.

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Graham JB, Kunkel GR, Tennyson GS, Lord ST, Fowlkes DM. Department of Pathology, School of Medicine, University of North Carolina, Chapel Hill 27599.
The Malmo polymorphism of factor IX: establishing the genotypes by rapid analysis of DNA.

A DNA polymorphism in the coding region of coagulation factor IX--potentially valuable for carrier detection, prenatal diagnosis, and population studies--was described in 1985. It had been discovered with monoclonal antibodies that distinguish between threonine and alanine as the 148th residue of the peptide. Its use as a diagnostic tool has been limited because threonine-containing factor IX (Malmo A) is dominant to alanine-containing factor IX (Malmo B) in immunoassays of plasma; therefore, detection of Malmo heterozygotes is not possible in all instances. A DNA method for recognizing all heterozygotes has been developed, but it also has limitations. We report the development of another DNA procedure based on amplification of the relevant DNA with the polymerase chain reaction (PCR). This method is quick, avoids the use of isotopes and x-ray film, and specifically identifies all the Malmo genotypes: hemizygotes, homozygotes, and heterozygotes. The procedure can be performed satisfactorily on small samples of blood (less than 1 mL) as suggested by Kogan et al (N Engl J Med 317:985, 1987). The method described is applicable to any genetic polymorphism that overlaps a restriction enzyme recognition site.

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Grandchamp B, Picat C, Mignotte V, Wilson JH, Te Velde K, Sandkuyl L, Romeo PH, Goossens M, Nordmann Y. Laboratoire de Genetique Moleculaire, Faculte de Medecine X, Paris, France.
Tissue-specific splicing mutation in acute intermittent porphyria.

An inherited deficiency of porphobilinogen deaminase [porphobilinogen ammonia-lyase (polymerizing), EC 4.3.1.8] in humans is responsible for the autosomal dominant disease acute intermittent porphyria. Different classes of mutations have been described at the protein level suggesting that this is a heterogeneous disease. It was previously demonstrated that porphobilinogen deaminase is encoded by two distinct mRNA species expressed in a tissue-specific manner. Analysis of the genomic sequences indicated that these two mRNAs are transcribed from two promoters and only differ in their first exon. The first mutation identified in the human porphobilinogen deaminase gene is a single-base substitution (G----A) in the canonical 5' splice donor site of intron 1. This mutation leads to a particular subtype of acute intermittent porphyria characterized by the restriction of the enzymatic defect to nonerythropoietic tissues. Hybridization analysis using oligonucleotide probes after in vitro amplification of genomic DNA offers another possibility of detecting asymptomatic carriers of the mutation in affected families.

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Greenberg A, Hijazzi M, Sharir H, Cohen L, Bergman Y, Ber R, Laskov R. Hubert H. Humphrey Center for Experimental Medicine and Cancer Research, Hadassah Medical School, Jerusalem, Israel.

Extinction of expression of the translocated myc gene in somatic cell hybrids between mouse myeloma and L-cells.

Int J Cancer. 1989 Jan 15: 43(1): 87-92.

Most murine plasma-cell tumors show a t(12;15) reciprocal chromosomal translocation which truncates the first exon of one of the myc gene alleles and fuses it to one of the switch regions of the immunoglobulin (Ig) heavy-chain locus. This results in constitutive activation of the translocated myc gene and the production of smaller-sized mRNA molecules, which are initiated at new sites in the first myc intron. The normal myc allele is not expressed in these myeloma cells. We have studied the expression of the translocated myc gene in somatic cell hybrids between mouse myeloma and L-cells. Our previous findings show that Ig gene expression is extinguished in such hybrids. In the present work we found that the hybrids contain the normal and translocated myc genes. In contrast to the myeloma parental cells which express the translocated myc gene, the hybrids are similar to the L-cells in expressing only the normal myc allele. Our results suggest that the L-cell, fibroblast-like phenotype, is dominant in these hybrids, and show that the translocated myc gene is expressed in a tissue-specific manner in the context of the myeloma cell, and is not expressed when subjected to a fibroblast-like cellular environment.

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Griffiths LR, Zwi MB, McLeod JG, Nicholson GA. Department of Medicine, University of Sydney, Australia.
Chromosome I linkage studies in Charcot-Marie-Tooth neuropathy type I.

Charcot-Marie-Tooth neuropathy type 1 (CMT1) is an autosomal dominant disorder of peripheral nerve. The gene for CMT1 was originally localized to chromosome 1 by linkage to the Duffy blood group, but it has since been shown that not all CMT1 pedigrees show this linkage. We report here the results of linkage studies using five chromosome 1 markers--Duffy (Fy), antithrombin III (AT3), renin (REN), beta-nerve growth factor (NGFB), and salivary amylase (AMY1)--in 16 CMT1 pedigrees. The total lod scores exclude close linkage of CMT1 to any of these markers. However, individual families show probable linkage of CMT1 to Duffy, AT3, and/or AMY1. No linkage was indicated with REN or NGFB. These results indicate the possible location of a CMT1 gene between the AMY1 and AT3 loci at p21 and q23, respectively, on chromosome 1 and support the theory that there is at least one other CMT1 gene.

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Gusella JF, Jones C, Kao FT, Housman D, Puck TT.
Genetic fine-structure mapping in human chromosome 11 by use of repetitive DNA sequences.

A method is described for mapping of the DNA fragments of a human chromosome produced by restriction enzyme treatment of the total DNA from a hybrid cell containing a single human chromosome. The method involves production and selection of somatic cell mutants containing deletions of the human chromosome and application of a hybridization probe consisting of an individual member copy of a repetitive human DNA family. A linear map has been constructed of 19 marker DNA fragments and 5 immunological and biochemical markers on human chromosome 11, selected as a model chromosome for these studies. This approach appears to be widely applicable, is independent of cytogenetic analysis, promises to be capable of revealing the existence of rearrangements as well as deletions, appears to be amenable to further increase in resolving power, and offers potential application in various human genetic problems.

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Gusella JF, Wexler NS, Conneally PM, Naylor SL, Anderson MA, Tanzi RE, Watkins PC, Ottina K, Wallace MR, Sakaguchi AY, et al.
A polymorphic DNA marker genetically linked to Huntington's disease.

Family studies show that the Huntington's disease gene is linked to a polymorphic DNA marker that maps to human chromosome 4. The chromosomal localization of the Huntington's disease gene is the first step in using recombinant DNA technology to identify the primary genetic defect in this disorder.

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Gyllensten UB, Erlich HA. Department of Human Genetics, Cetus Corporation, Emeryville, CA 94608.
Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus.

Single-copy sequences can be enzymatically amplified from genomic DNA by the polymerase chain reaction. By using unequal molar amounts of the two amplification primers, it is possible in a single step to amplify a single-copy gene and produce an excess of single-stranded DNA of a chosen strand for direct sequencing or for use as a hybridization probe. Further, individual alleles in a heterozygote can be sequenced directly by using allele-specific oligonucleotides either in the amplification reaction or as sequencing primers. By using these methods, we have studied the allelic diversity at the HLA-DQA locus and its association with the serologically defined HLA-DR and -DQ types. This analysis has revealed a total of eight alleles and three additional haplotypes. This procedure has wide applications in screening for mutations in human genes and facilitates the linking of enzymatic amplification of genes to automated sequencing.

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Gyllensten UB, Erlich HA. Department of Human Genetics, Cetus Corporation, Emeryville, CA 94608.
Ancient roots for polymorphism at the HLA-DQ alpha locus in primates.

The genes encoding the human histocompatibility antigens (HLA) exhibit a remarkable degree of polymorphism as revealed by immunologic and molecular analyses. This extensive sequence polymorphism either may have been generated during the lifetime of the human species or could have arisen before speciation and been maintained in the contemporary human population by selection or, possibly, by genetic drift. These two hypotheses were examined using the polymerase chain reaction method to amplify polymorphic sequences from the DQ alpha locus, as well as the DX alpha locus, an homologous but nonexpressed locus, in a series of primates that diverged at known times. In general, the amino acid sequence of a specific human DQ alpha allelic type is more closely related to its chimpanzee or gorilla counterpart than to other human DQ alpha alleles. Phylogenetic analysis of the silent nucleotide position changes shows that the similarity of allelic types between species is due to common ancestry rather than convergent evolution. Thus, most of the polymorphism at the DQ alpha locus in the human species was already present at least 5 million years ago in the ancestral species that gave rise to the chimpanzee, gorilla, and human lineages. However, one of the DQ alpha alleles may have arisen after speciation by recombination between two ancestral alleles.

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Haber DA, Buckler AJ, Glaser T, Call KM, Pelletier J, Sohn RL, Douglass EC, Housman DE. Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139.
An internal deletion within an 11p13 zinc finger gene contributes to the development of Wilms' tumor.

We have recently described the isolation of a candidate for the Wilms' tumor susceptibility gene mapping to band p13 of human chromosome 11. This gene, primarily expressed in fetal kidney, appears to encode a DNA binding protein. We now describe a sporadic, unilateral Wilms' tumor in which one allele of this gene contains a 25 bp deletion spanning an exon-intron junction and leading to aberrant mRNA splicing and loss of one of the four zinc finger consensus domains in the protein. The mutation is absent in the affected individual's germline, consistent with the somatic inactivation of a tumor suppressor gene. In addition to this intragenic deletion affecting one allele, loss of heterozygosity at loci along the entire chromosome 11 points to an earlier chromosomal nondisjunction and reduplication. We conclude that inactivation of this gene, which we call WT1, is part of a series of events leading to the development of Wilms' tumor.

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Hamada H, Petrino MG, Kakunaga T.
Molecular structure and evolutionary origin of human cardiac muscle actin gene.
Proc Natl Acad Sci U S A. 1982 Oct: 79(19): 5901-5.

Two recombinant phages that contain cardiac muscle actin gene were isolated from a human DNA library and their structures were determined. Restriction analysis indicates that both clones carry the same EcoRI 13-kilobase fragment where the coding sequence is mapped. The cloned DNA hybridized with polyadenylylated RNA from human fibroblasts, which directs the synthesis of cytoplasmic beta- and gamma-actin in vitro. However, sequence determination of the cloned DNA showed that the entire coding sequence perfectly matched the amino acid sequence of cardiac muscle actin. The initiation codon is followed by a cysteine codon that is not found at the amino-terminal site of any actin isoform, suggesting the necessity of post-translational processing for in vivo actin synthesis. There are five introns interrupting exons at codons 41/42, 150, 204, 267, and 327/328. Surprisingly, these intron locations are exactly the same as those of the rat skeletal muscle actin gene but different from those of nonmuscle beta-actin gene. Nucleotide sequences of all exon/intron boundaries agree with the G-T/A-G rule (G-T at the 5' and A-G at the 3' termini of each intron). The 3'-untranslated sequence has no homology to that of nonmuscle beta- or gamma-actin gene, but Southern blot hybridization has shown that this region has considerable homology to that of one of the other actin genes. These results indicate that the recombinant phages, which we have isolated, contain cardiac muscle actin gene and that cardiac muscle actin gene and skeletal muscle actin genes are derived from their ancestor gene at a relatively recent time in evolutionary development.

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Harper JF, Mages W. Department of Biology, Washington University, St. Louis, MO 63130.
Organization and structure of Volvox beta-tubulin genes.
Mol Gen Genet. 1988 Aug: 213(2-3): 315-24.

Genomic clones encoding two Volvox beta-tubulin genes have been isolated and shown to represent the only two beta-tubulin genes in the genome. Restriction fragment length polymorphism analysis was used to demonstrate that the two genes are genetically linked. One of these genes was sequenced and the mRNA start site(s) determined by primer extension. A comparison of its sequence to those of the two beta-tubulin genes of Chlamydomonas revealed: (1) a high degree of conservation of the coding region, with the predicted amino acid sequence differing only in the C-terminal residue; (2) extensive sequence conservation in the 5' untranslated leader region and a 16 bp (putative regulatory) sequence in the promoter region; (3) the same number and location of introns, with a short region of homology in intron 1, but little significant homology in introns 2 and 3.

------------------------------------------------------------------------------------------------------------------------------------Hastbacka J, de la Chapelle A, Kaitila I, Sistonen P, Weaver A, Lander E. Department of Medical Genetics, University of Helsinki, Finland.
Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland.

Erratum in: Nat Genet 1992 Dec;2(4):343.

Linkage disequilibrium mapping in isolated populations provides a powerful tool for fine structure localization of disease genes. Here, Luria and Delbruck's classical methods for analysing bacterial cultures are adapted to the study of human isolated founder populations in order to estimate (i) the recombination fraction between a disease locus and a marker; (ii) the expected degree of allelic homogeneity in a population; and (iii) the mutation rate of marker loci. Using these methods, we report striking linkage disequilibrium for diastrophic dysplasia (DTD) in Finland indicating that the DTD gene should lie within 0.06 centimorgans (or about 60 kilobases) of the CSF1R gene. Predictions about allelic homogeneity in Finland and mutation rates in simple sequence repeats are confirmed by independent observations.

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Haugen A, Mann D, Murray C, Weston A, Willey JC. Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, Maryland.
Interleukin-1 alpha gene intron containing variable repeat region coding for the SP1 transcription factor recognition sequence is polymorphic.

Mol Carcinog. 1989: 2(2): 68-71.

Interleukin-1 alpha (IL-1 alpha) is a cytokine produced by a number of cell types including macrophages, fibroblasts, keratinocytes, and mesangial cells. We were interested in identifying a DNA restriction fragment length polymorphism (RFLP) for the IL-1 alpha gene for use in studies of genetic alteration in various human cancers. Human genomic DNA from 32 unrelated individuals was digested with various restriction enzymes, alone and in combination, and subjected to Southern blot analysis. Hybridization to 32P-labeled IL-1 alpha cDNA revealed an insertion-deletion-type polymorphic pattern. After digestion with RsaI, insertion-deletion-type polymorphic bands with sizes of 3.4 kb, 3.1 kb, and 2.8 kb and one invariant band of 0.8 kb were observed. These three alleles, designated A1, A2, and A3, had relative frequencies of 0.18, 0.06, and 0.78 with heterozygosity observed in 38% of the unrelated individuals studied. Evaluation of nine related individuals for this RsaI polymorphism was consistent with a Mendelian inheritance. Comparison of restriction patterns following Southern analysis of DNA digested with several different enzymes showed that the polymorphic region resides within the sixth intron. Furthermore, this RFLP results from a variable length region containing multiple copies of a recognition sequence for SP1, an imperfect copy of viral enhancer elements, and an inverse and complementary sequence of the glucocorticoid receptor binding site. The identified polymorphism may be of value in analyses of chromosome 2 and may help to elucidate mechanisms by which IL-1 alpha transcription is regulated.

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Hay CW, Robertson KA, Yong SL, Thompson AR, Growe GH, MacGillivray RT.
Use of a BamHI polymorphism in the factor IX gene for the determination of hemophilia B carrier status.

Blood. 1986 May: 67(5): 1508-11.

A BamHI polymorphism has been identified in the human factor IX gene. This polymorphism, which occurs in approximately 6% of X chromosomes, has been used to determine the carrier status of a female in a family with a history of hemophilia B. This family was uninformative for the previously reported TaqI and Xmnl polymorphisms in the factor IX gene.

Hejtmancik JF, Holcomb JD, Howard J, Vanderford M. Institute for Molecular Genetics, Baylor College of Medicine, Houston, Texas.
In vitro amplification of the alpha 1-antitrypsin gene: application to prenatal diagnosis.

Prenat Diagn. 1989 Mar: 9(3): 177-86. Erratum in: Prenat Diagn 1989 Jul: 9(7): 534.

Discrimination of the M, Z, and S alleles of alpha 1-antritrypsin (AAT) has been carried out using in vitro gene amplification with the polymerase chain reaction (PCR). Amplification of 90 nucleotides surrounding the Z mutation site and 120 nucleotides surrounding the S mutation site dramatically improves the sensitivity and reliability of allele-specific oligonucleotide (ASO) hybridization for direct detection of these alleles. Analysis is performed using Southern blots or dot blots hybridized with 19 base oligonucleotides and differentially washed for allele specificity. Amplification of the Z and S mutation sites can be combined in one PCR to allow detection of both mutations when analysed by gel electrophoresis and Southern transfer. This technique can be performed reliably using less than 0.1 micrograms of genomic DNA or less than 100 amniocytes or white blood cells. This technique has been used to perform prenatal diagnosis on a chorionic villus sample (CVS) in a fetus at risk for the ZZ Pi type form of AAT deficiency.

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Helentjaris T, Gesteland R.
Evaluation of random cDNA clones as probes for human restriction fragment polymorphisms.

The purpose of this study was to evaluate the usefulness of randomly isolated human cDNA clones as probes for human restriction fragment polymorphisms. Clones were chosen from two human cDNA libraries and tested by hybridization against Southern blots of genomic DNA prepared from nine individuals. Three types of hybridization patterns were seen with the individual clones tested, those representative of single copy genes, others representative of gene families, and one characteristic of a mitochondrial gene. Only two of these cDNA clones revealed any polymorphisms among the individuals tested: pDK-08 and RW12, both representative of gene families. Both revealed independent polymorphisms with several of the restriction enzymes tested, and inheritance of these polymorphisms as Mendelian alleles was verified by human pedigree analysis. The results are discussed with regard to the usefulness of such cDNA clones in revealing polymorphisms in human genetic analysis.

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Helmuth R, Fildes N, Blake E, Luce MC, Chimera J, Madej R, Gorodezky C, Stoneking M, Schmill N, Klitz W, et al. Department of Human Genetics, Cetus Corporation, Emeryville, CA 94608.
HLA-DQ alpha allele and genotype frequencies in various human populations, determined by using enzymatic amplification and oligonucleotide probes.

Allele and genotype frequencies at the HLA-DQ alpha locus have been determined by the use of polymerase chain reaction (PCR) amplification and nonradioactive oligonucleotide probes. The probes define six alleles and 21 genotypes in a dot-blot format. A total of over 1,400 individuals from 11 populations has been typed by two different laboratories using this method. In contrast to some variable-number-of-tandem-repeat markers that have been used for identity determination, DQ alpha genotype frequencies do not deviate significantly from Hardy-Weinberg equilibrium in all populations studied. The distribution of alleles varies significantly between most of these populations. In Caucasians, the allele frequencies range from 4.3% to 28.5%. In this population, the power of discrimination is .94, and, for paternity determination, the power of exclusion is .642. These population data will allow the use of the HLA-DQ alpha marker in paternity determination, the analysis of individual identity in forensic samples, and anthropological studies.

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Herbert CJ, Dujardin G, Labouesse M, Slonimski PP. Centre de Genetique Moleculaire du CNRS, Laboratoire propre associe a l'Universite Pierre et Marie Curie, Gif-sur-Yvette, France.
Divergence of the mitochondrial leucyl tRNA synthetase genes in two closely related yeasts Saccharomyces cerevisiae and Saccharomyces douglasii: a paradigm of incipient evolution.

We studied the NAM2 genes of Saccharomyces douglasii and Saccharomyces cerevisiae, and showed that they are interchangeable for all the known functions of these genes, both mitochondrial protein synthesis and mitochondrial mRNA splicing. This confirms the prediction that the S. douglasii NAM2D gene encodes the mitochondrial leucyl tRNA synthetase (EC 6.1.1.4.). The observation that these enzymes are interchangeable for their mRNA splicing functions, even though there are significant differences in the intron/exon structure of their mitochondrial genome, suggests that they may have a general role in yeast mitochondrial RNA splicing. A short open reading frame (ORF) precedes the synthetase-encoding ORF, and we showed that at least in S. cerevisiae this is not essential for the expression of the gene; however, it may be involved in a more subtle type of regulation. Sequence comparisons of S. douglasii and S. cerevisiae revealed a particularly interesting situation from the evolutionary point of view. It appears that the two yeasts have diverged relatively recently: there is remarkable nucleotide sequence conservation, with no deletions or insertions, but numerous (albeit non-saturating) silent substitutions resulting from transitions. This applies not only to the NAM2 coding regions, but also to two other ORFs flanking the NAM2 ORF. The regions between the ORFs (believed to be intergenic regions) are much less conserved, with several deletions and insertions. Thus S. douglasii and S. cerevisiae provide an ideal system for the study of molecular evolution, being two yeasts "caught in the act" of speciation.

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Higuchi R, von Beroldingen CH, Sensabaugh GF, Erlich HA. Department of Human Genetics, Cetus Corporation, Emeryville, California 94608.
DNA typing from single hairs.

The characterization of genetic variation at the DNA level has generated significant advances in gene and disease mapping, and in the forensic identification of individuals. The most common method of DNA analysis, that of restriction fragment length polymorphism (RFLP), requires microgram amounts of relatively undegraded DNA for multi-locus typing, and hundreds of nanograms for single-locus comparisons. Such DNA frequently cannot be obtained from forensic samples such as single hairs and blood stains, or from anthropological, genetic or zoological samples collected in the field. To detect polymorphic DNA sequences from single human hairs, we have used the polymerase chain reaction (PCR), in which specific short regions of a gene can be greatly amplified in vitro from as little as a single molecule of DNA. We have detected genetically variable mitochondrial and nuclear DNA sequences from the root region of shed, as well as freshly-plucked, single hairs; mitochondrial DNA (mtDNA) sequences have been detected in a sample from a single hair shaft. We have used three different means of DNA typing on these samples: the determination of amplified DNA fragment length differences, hybridization with allele-specific oligonucleotide probes, and direct DNA sequencing.

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Hill AV, Bowden DK, O'Shaughnessy DF, Weatherall DJ, Clegg JB. Nuffield Department of Clinical Medicine, University of Oxford, England.
Beta thalassemia in Melanesia: association with malaria and characterization of a common variant (IVS-1 nt 5 G----C).
Blood. 1988 Jul: 72(1): 9-14.

Data on the distribution of beta thalassemia among over 6,000 Melanesians reveals a major difference in the carrier rates between populations in the malarious coastal regions of New Guinea and those living in the historically malaria-free Highlands. The island of Maewo in Vanuatu has a particularly high incidence of beta + thalassemia associated with a single restriction enzyme haplotype. Direct cloning into a plasmid vector and sequence analysis demonstrate that the mutation is a G to C transversion at position 5 of intron 1 of the beta-globin gene. Oligonucleotide probe surveys indicate that this variant accounted for all cases of beta thalassemia studied from Maewo. It is also common in coastal Papua New Guinea where haplotype and oligonucleotide probe data suggest that the molecular basis of beta thalassmia is more heterogeneous.

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Hixson JE, Cox LA, Borenstein S. Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas 78284.
The baboon apolipoprotein E gene: structure, expression, and linkage with the gene for apolipoprotein C-1.

To develop the baboon model for molecular genetic studies of atherosclerosis, we have cloned and sequenced the baboon apolipoprotein E (apo E) gene. The baboon apo E gene encodes the E4 isoform with respect to specific amino acid positions, suggesting that the common epsilon 3 allele is not the primal human allele. Rather than accumulating predominantly synonymous nucleotide changes, 50% of substitutions in human and baboon apo E gene coding regions cause amino acid substitutions. However, comparisons of these apo E proteins show conservation of amphipathic helices required for apo E--lipid interactions. The human and baboon apo E genes have diverged less extensively than those from rat and mouse, providing further evidence for a slowing of molecular evolution in primate species. The baboon and rhesus monkey apo E genes (intron 2) contain two Alu repeats that are absent in the human gene, indicating insertion after the divergence of human and cercopithecine lineages, but before the baboon/rhesus divergence. S1 nuclease studies show that transcription of the baboon apo E gene starts at two different positions, one of which corresponds to the human gene start site. To examine linkage of apolipoprotein genes in the baboon genome, we have used a human cDNA probe to detect apo C-I gene sequences approximately 4 kb from the 3' end of the baboon apo E gene.

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Ho CK, Abelson J. Division of Chemistry, California Institute of Technology, Pasadena, CA 91125.
Testing for intron function in the essential Saccharomyces cerevisiae tRNA(SerUCG) gene.

The gene sup61+, which codes for the essential Saccharomyces cerevisiae tRNA(SerUCG), is the only single-copy tRNA gene in this organism know to contain an intron. To assess the role of this intron in tRNA gene expression, an intron-deleted sup61+ gene was constructed in vitro and introduced into the yeast genome. Isogenic intron- and intron+ strains were found to be indistinguishable by criteria that include growth rates, ability to undergo meiosis, levels of mature tRNA(SerUCG) transcribed in vivo, and the suppressor efficiency of amber- and ochre-specific alleles of this gene.

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Ho CK, Rauhut R, Vijayraghavan U, Abelson J. Division of Biology, California Institute of Technology, Pasadena 91125.
Accumulation of pre-tRNA splicing '2/3' intermediates in a Saccharomyces cerevisiae mutant.

In an effort to identify genes involved in the excision of tRNA introns in Saccharomyces cerevisiae, temperature-sensitive mutants were screened for intracellular accumulation of intron-containing tRNA precursors by RNA hybridization analysis. In one mutant, tRNA splicing intermediates consisting of the 5' exon covalently joined to the intron ('2/3' pre-tRNA molecules) were detected in addition to unspliced precursors. The mutant cleaves pre-tRNA(Phe) in vitro at the 3' exon/intron splice site, generating the 3' half molecule and 2/3 intermediate. The 5' half molecule and intron are not produced, indicating that cleavage at the 5' splice site is suppressed. This partial splicing activity co-purifies with tRNA endonuclease throughout several chromatographic steps. Surprisingly, the splicing defect does not appreciably affect cell growth at normal or elevated temperatures, but does confer a pseudo cold-sensitive phenotype of retarded growth at 15 degrees C. The mutant falls into the complementation group SEN2 previously defined by the isolation of mutants defective for tRNA splicing in vitro [Winey, M. and Culbertson, M.R. (1988) Genetics, 118, 609-617], although its phenotypes are distinct from those of the previous sen2 isolates. The distinguishing genetic and biochemical properties of this new allele, designated sen2-3, suggests the direct participation of the SEN2 gene product in tRNA endonuclease function.

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Hodges PE, Rosenberg LE. Yale University School of Medicine, Department of Human Genetics, New Haven, CT 06510.
The spfash mouse: a missense mutation in the ornithine transcarbamylase gene also causes aberrant mRNA splicing.
Proc Natl Acad Sci U S A. 1989 Jun: 86(11): 4142-6.

Ornithine transcarbamylase (ornithine carbamoyltransferase; carbamoyl-phosphate:L-ornithine carbamoyltransferase, EC 2.1.3.3) is a mitochondrial matrix enzyme of the mammalian urea cycle. The X chromosome-linked spfash mutation in the mouse causes partial ornithine transcarbamylase deficiency and has served as a model for the human disease. We show here that the spfash mutation is a guanine to adenine transition of the last nucleotide of the fourth exon of the ornithine transcarbamylase gene. This nucleotide change produces two remarkably different effects. First, this transition causes ornithine transcarbamylase mRNA deficiency because the involved exon nucleotide plays a part in the recognition of the adjacent splice donor site. As a result of the mutation, ornithine transcarbamylase pre-mRNA is spliced inefficiently both at this site and at a cryptic splice donor site 48 bases into the adjacent intron. Second, two mutant proteins are translated from these mRNAs. From the correctly spliced mRNA, the transition results in a change of amino acid 129 from arginine to histidine. This missense substitution has no discernable effect on mitochondrial import, subunit assembly, or enzyme activity. On the other hand, the elongated mRNA resulting from mis-splicing is translated into a dysfunctional ornithine transcarbamylase subunit elongated by the insertion of 16 amino acid residues.

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Houwen RH, Baharloo S, Blankenship K, Raeymaekers P, Juyn J, Sandkuijl LA, Freimer NB.
Wilhelmina Children's Hospital, Utrecht, The Netherlands.
Genome screening by searching for shared segments: mapping a gene for benign recurrent intrahepatic cholestasis.

It is now feasible to map disease genes by screening the genome for linkage disequilibrium between the disease and marker alleles. This report presents the first application of this approach for a previously unmapped locus. A gene for benign recurrent intrahepatic cholestasis (BRIC) was mapped to chromosome 18 by searching for chromosome segments shared by only three distantly related patients. The screening results were confirmed by identifying an extended haplotype conserved between the patients. Probability calculations indicate that such segment sharing is unlikely to arise by chance. Searching the genome for segments shared by patients is a powerful empirical method for mapping disease genes. Computer simulations suggest that, in appropriate populations, the approach may be used to localize genes for common diseases.

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Hsia YE, Ford CA, Shapiro LJ, Hunt JA, Ching NS. Department of Genetics, John A. Burns School of Medicine, University of Hawaii, Honolulu.
Molecular screening for haemoglobin constant spring.

Haemoglobin H/Constant Spring is an important cause of severe haemoglobin H disease, but the Constant Spring protein is difficult to detect by electrophoresis. A technique for allele specific polymerase chain amplification of the 3'-end of the alpha 2 globin gene improved detection of the alpha cs alpha haemoglobin variant in DNA samples by slot-blot hybridisation. The alpha cs alpha mutation was confirmed in subjects that had been previously diagnosed by haemoglobin electrophoresis, and it was also detected in patients who were negative by protein electrophoresis. 10 of 103 unrelated Laotians with HbE were alpha cs alpha heterozygotes. Of these, 3 were negative to the normal probe because they had -alpha 3.7/alpha cs alpha with a single alpha globin deletion. 5 samples did not amplify or hybridise to either probe because they had deletions of both alpha 2 globin regions. The gene frequency for alpha cs alpha is about 0.05 for Laotians. This technique, which is highly specific and sensitive for rapid detection of the alpha cs alpha mutation, is suitable for clinical diagnoses and population studies. The true incidence of alpha cs alpha may prove to be greater than previously suspected from protein electrophoresis.

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Huang LS, Ripps ME, Korman SH, Deckelbaum RJ, Breslow JL. Laboratory of Biochemical Genetics and Metabolism, Rockefeller University, New York, New York 10021.
Hypobetalipoproteinemia due to an apolipoprotein B gene exon 21 deletion derived by Alu-Alu recombination.

We report the molecular defect in an individual with homozygous hypobetalipoproteinemia. A unique TaqI restriction fragment length polymorphism was found in the midportion of the apolipoprotein B (apoB) gene using the genomic probe, pB51. The probe, which identifies TaqI fragments of 8.4 and 2.8 kilobases (kb) in normal individuals, hybridized to a single 11-kb fragment in the proband. The parents of the proband showed all three TaqI fragments, implying that they are heterozygotes for the mutant apoB allele. In this family, the mutant allele cosegregated with low total cholesterol levels and formal linkage analysis gave a decimal logarithm of the ratio score of 3.3 at a recombination frequency of 0. The polymorphic TaqI site was localized to an EcoRI fragment of 4 kb in normal individuals. The corresponding fragment in the proband was 3.4 kb, suggesting a 0.6-kb deletion in the mutant allele. Both the normal 4-kb EcoRI fragment and the mutant 3.4-kb EcoRI fragment were cloned and sequenced. In the normal allele, the 4-kb EcoRI fragment extends from intron 20 to 23. Exon 21 is flanked by Alu sequences that are in the same orientation. The mutant allele had a 694-bp deletion in this region which included a small part of the Alu sequence in intron 20, the entire exon 21, and most of the Alu sequence in intron 21. The polymorphic TaqI site, which lies within the Alu sequence in intron 21, was absent in the proband as a result of the deletion. The deletion of exon 21 results in a frame shift mutation and the introduction of a stop codon. Translation of the encoded mRNA would yield a prematurely terminated protein. This mutant apoB protein would be 1085 amino acids long with the 73 carboxyl-terminal residues out of frame. We postulate that the deletion of exon 21 is the consequence of a crossover event between the Alu sequences in introns 20 and 21 resulting in nonreciprocal exchange between two chromosomes.

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Huang LS, Ripps ME, Breslow JL. Laboratory of Biochemical Genetics and Metabolism, Rockefeller University, New York, NY 10021.
Molecular basis of five apolipoprotein B gene polymorphisms in noncoding regions.

Restriction fragment length polymorphisms (RFLPs) are useful in linkage and clinical association studies of human diseases. In this report, we characterize the molecular basis and frequencies of two new RFLPs, AvaII and BalI, two previously reported RFLPs, HincII and PvuII, and one new sequence polymorphism in the human apolipoprotein B gene. For the AvaII RFLP, the two alleles yield either a 1 kb fragment or 0.7 and 0.3 kb fragments, and have frequencies of 20% and 80%, respectively. The polymorphic site is about 4 kb upstream of exon 1. For the BalI RFLP, the two alleles yield either a 4.9 or 6.2 kb fragment, and have about equal frequencies. The polymorphic site is within an Alu sequence in intron 20, 146 bp 5' to exon 21. The BalI recognition sequence TGGCCA is replaced by TAGCCA. For the HincII RFLP, the two alleles yield either a 1.7 or 1.3 kb fragment and have frequencies of 80% and 20%, respectively. The polymorphic site is in intron 4, 171 bp 3' to exon 4. The HincII recognition sequence GTTAAC, present in the minor allele, is replaced by GTTACC. HincII fragments of 7.4 and 7.0 kb, previously reported for this polymorphism, are the result of partial digestion at the invariant HincII site in intron 3, 334 bp 3' to exon 3. For the PvuII RFLP, the two alleles yield either a 7.5 or 5.5 kb fragment and have frequencies of 96% and 4%, respectively. The polymorphic site is within an Alu sequence in intron 4, 523 bp 5' to exon 5.

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Janco RL, Phillips JA 3rd, Orlando PJ, Woodard MJ, Wion KL, Lawn RM.
Detection of hemophilia A carriers using intragenic factor VIII:C DNA polymorphisms.

A DNA polymorphism for an Xbal site in intron 22 of the human factor VIII:C gene extends the utility of DNA methods for carrier detection in families segregating for hemophilia A. While the DNA polymorphism detected by a BclI site in intron 18 of the factor VIII:C gene was informative for 41% of females studied, the BglI/intron 25 polymorphism provided no additional information because of apparent linkage disequilibrium. In contrast, the Xbal intron 22 polymorphism was useful in 53% of women who were uninformative (homozygous) for either the BclI or BglI polymorphisms. Using the BclI/intron 18 and Xbal/intron 22 intragenic polymorphisms, we could provide highly accurate information for 68% of women we studied who were at risk for carriership. The carrier status of the remaining 32% could be determined utilizing the closely linked Taql/St14 DNA polymorphism.

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Jeffreys AJ.
DNA sequence variants in the G gamma-, A gamma-, delta- and beta-globin genes of man.

DNA prepared from 60 unrelated individuals was cleaved with one of eight different restriction endonucleases and the resulting DNA fragments were separated by agarose gel electrophoresis. DNA fragments containing G gamma-, A gamma-, delta- or beta-globin genes were detected by Southern blot hybridization, using as probe either a 32P-labeled cloned DNA copy of rabbit beta-globin messenger RNA or labeled human beta- and G gamma- globin cDNA plasmids. Three types of variant restriction enzyme patterns of globin DNA fragments were detected in otherwise normal individuals. One variant pattern, found in only one person, was caused by an additional restriction endonuclease Pst I cleavage site in the center of the delta- globin gene intervening sequence; the subject was heterozygous for the presence of this cleavage site and was shown to have inherited it from her mother. Another variant pattern resulted from the appearance of an endonuclease Hind III cleavage site in the intervening sequence of the A gamma-globin gene; this variant is polymorphic, with a gene frequency for the presence of the intragenic Hind III site of 0.23. This Hind III cleavage site polymorphism is also found in the G gamma-globin gene intervening sequence and thus the polymorphism itself appears to be duplicated over the pair of gamma-globin loci. These variants can be used to derive an approximate estimate of the total number of different DNA sequence variants in man.

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Jeffreys AJ, Wilson V, Thein SL.
Hypervariable 'minisatellite' regions in human DNA.

The human genome contains many dispersed tandem-repetitive 'minisatellite' regions detected via a shared 10-15-base pair 'core' sequence similar to the generalized recombination signal (chi) of Escherichia coli. Many minisatellites are highly polymorphic due to allelic variation in repeat copy number in the minisatellite. A probe based on a tandem-repeat of the core sequence can detect many highly variable loci simultaneously and can provide an individual-specific DNA 'fingerprint' of general use in human genetic analysis.

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Jeffreys AJ, Wilson V, Neumann R, Keyte J. Department of Genetics, University of Leicester, UK.
Amplification of human minisatellites by the polymerase chain reaction: towards DNA fingerprinting of single cells.

Hypervariable minisatellites can be amplified from human DNA by the polymerase chain reaction, using primers from DNA flanking the minisatellite to amplify the entire block of tandem repeat units. Minisatellite alleles up to 5-10 kb long can be faithfully amplified. At least six minisatellite loci can be co-amplified from the same DNA sample and simultaneously detected to provide a reproducible and highly variable DNA fingerprint which can be obtained from nanogram quantities of human DNA. The polymerase chain reaction can also be used to analyse single target minisatellite molecules and single human cells, despite the appearance of spurious PCR products from some hypervariable loci. DNA fingerprinting at the level of one or a few cells therefore appears possible.

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Jenkins RN, Osborne-Lawrence SL, Sinclair AK, Eddy RL Jr, Byers MG, Shows TB, Duby AD.
Harold C. Simmons Arthritis Research Center, Dallas, Texas.
Structure and chromosomal location of the human gene encoding cartilage matrix protein.
J Biol Chem. 1990 Nov 15: 265(32): 19624-31.

Cartilage matrix protein (CMP) is a major component of the extracellular matrix of nonarticular cartilage. The structure and chromosomal location of the human gene encoding CMP was determined by molecular cloning analysis. We used a partial chicken CMP cDNA probe to isolate three overlapping human genomic clones. From one of these clones, a probe containing 2 human CMP exons was isolated and used to map the gene to chromosome 1p35 and to screen a human retina cDNA library. Two overlapping cDNA clones were isolated. The predicted protein sequence of 496 amino acids includes a 22-residue signal peptide and a 474-residue mature protein of Mr 51,344. The human CMP gene and polypeptide are strikingly similar to the chicken CMP gene and polypeptide. Human CMP is 79% identical to chicken CMP and contains two homologous domains separated by an epidermal growth factor-like domain. One potential N-glycosylation site is conserved between the two species. The human CMP gene spans 12 kilobase pairs with 8 exons and 7 introns which are similar in size to those of the chicken CMP gene. Both RNA splice junctions of intron G in the human and chicken CMP genes are nonconforming to the consensus splice sequences. This suggests that the CMP gene utilizes a new RNA splicing mechanism.

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Jinks DC, Minter M, Tarver DA, Vanderford M, Hejtmancik JF, McCabe ER. Department of Microbiology, State University of New York, Buffalo 14214.
Molecular genetic diagnosis of sickle cell disease using dried blood specimens on blotters used for newborn screening.
Hum Genet. 1989 Mar: 81(4): 363-6.

The protein-based technologies used to screen newborns for sickle cell disease require confirmation with a liquid blood specimen. We have developed a strategy for rapid and specific genotypic diagnosis using DNA extracted from a dried blood spot on the filter paper blotter used to screen newborns. DNA could be microextracted from a specimen as small as a 1/8 inch diameter punched disc representing the dried equivalent of approximately 3 microliters of whole blood. We utilized the DNA from a 1/4 inch diameter specimen (12 microliters equivalent) for polymerase chain reaction amplification of the beta-globin region spanning the sickle cell mutation with detection by allele-specific oligonucleotide probes. Molecular confirmation of genotype from the original blotter would reduce the personnel costs associated with obtaining follow-up liquid blood specimens and would provide information to the family in a more timely and less equivocal manner.

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Kagnoff MF, Harwood JI, Bugawan TL, Erlich HA. Department of Medicine, University of California at San Diego, La Jolla 92093.
Structural analysis of the HLA-DR, -DQ, and -DP alleles on the celiac disease-associated HLA-DR3 (DRw17) haplotype.

Celiac disease is strongly associated with the HLA class II D-region serologic markers DR3 (DRw17) and DQw2. Moreover, by restriction fragment length polymorphism analysis, greater than 90% of DR3 (DRw17), DQw2 celiac disease patients have a polymorphic 4.0-kilobase Rsa I DP B gene DNA fragment. The present study sought to determine if there is a unique HLA class II D-region A or B gene structural variant on the DR3 (DRw17) haplotype found in celiac disease. The polymorphic second exons of the coding DRB, DQA and DQB, and DPA and DPB genes in celiac disease patients with the DR3 (DRw17) haplotype were sequenced after amplification by the polymerase chain reaction. To define the DP B genes associated with celiac disease, the second exons of the coding DP B genes from 27 celiac disease patients were amplified similarly and probed by using a panel of sequence specific oligonucleotides. The HLA-DR, -DQ, and -DP A and B gene second exon sequences of celiac disease patients were noted to be identical to sequences that can be found also, although at a significantly lower frequency, in unaffected individuals. This is compatible with a disease model wherein the HLA class II genes on the DR3 (DRw17) haplotype are necessary, but not sufficient, for the phenotypic expression of celiac disease. Analysis of the DP B genes revealed a significant increase in the frequency of the alleles DPB1 and DPB3 in celiac disease. Furthermore, the increased frequency of the 4.0-kilobase Rsa I DP B gene restriction fragment length polymorphism in celiac disease can be accounted for by the overrepresentation in disease of the alleles DPB1 and DPB3. The HLA-associated susceptibility to celiac disease appears to be multigenic, with specific, but structurally normal, allelic variants in the DP and DQ/DR subregions contributing to disease susceptibility.

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Kan YW, Dozy AM.
Antenatal diagnosis of sickle-cell anaemia by D.N.A. analysis of amniotic-fluid cells.

The polymorphism of a restriction endonuclease site has been used for antenatal diagnosis of sickle-cell disease. In a normal person, the beta-globin gene was contained in a Hpa I-digested D.N.A. fragment 7.6 kilobases (kb) in length. In a family where the sickle gene was contained in a variant 13.0 kb fragment, restriction endonuclease mapping was used for antenatal diagnosis. The D.N.A. from amniotic-fluid cells produced both the 7.6 and the 13.0 bk beta-globin gene fragments, indicating the diagnosis of sickle-cell trait. This confirmed the diagnosis reached after investigation of a 100% sample of fetal blood. The method is sensitive and can be performed with cells obtained from 15 ml of uncultured amniotic fluid. This approach may prove useful in antenatal diagnosis of other genetic disorders.

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Kan YW, Dozy AM.
Polymorphism of DNA sequence adjacent to human beta-globin structural gene: relationship to sickle mutation.

Restriction endonuclease mapping of the human globin genes revealed a genetic variation in a Hpa I recognition site about 5000 nucleotides from the 3' end of the beta-globin structural gene. Instead of a normal 7.6-kilobase (kb) fragment which contains the beta-globin structural gene, 7.0-kb and 13.0-kb variants were detected. Both variants were found in people of African origin and were not detected in Asians or Caucasians. The 13.0-kb variant is frequently associated with the sickle hemoglobin mutation and may be useful for the prediction of the sickle cell gene in prenatal diagnosis. Polymorphism in a restriction enzyme site could be considered as a new class of genetic marker and may offer a new approach to linkage analysis and anthropological studies.

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Kan YW, Lee KY, Furbetta M, Angius A, Cao A.
Polymorphism of DNA sequence in the beta-globin gene region. Application to prenatal diagnosis of beta 0 thalassemia in Sardinia.
N Engl J Med. 1980 Jan 24: 302(4): 185-8.

We used a restriction endonuclease to analyze the beta-thalassemia gene in Sardinia. When we digested human DNA with the restriction enzyme Bam HI, the beta-globin gene split into a 5' portion contained in a fragment of DNA 1.8 kb in length and a 3' portion in a fragment 9.3 kb in length. In some subjects, a variation in the nucleotide sequence affecting the site recognized by this enzyme on the 3' side of the beta-globin gene resulted in a different fragment, 22 kb in length, which contained the 3' portion of the beta-globin gene. In Sardinians without beta-thalassemia, the frequency of the 9.3-kb fragment was 0.67, and that of the 22-kb fragment was 0.33. In contrast, all the beta 0-thalassemia genes were associated exclusively with the 9.3-kb fragment. Thus, the beta 0-thalassemia lesion in Sardinians apparently arose on a chromosome that had the 9.3-kb Bam HI fragment. This observation can be used in prenatal diagnosis of beta 0-thalassemia in Sardina, since demonstration of the 22.0-kb fragment would indicate the normal beta-globin genotype and exclude the beta 0-thalassemia lesion on that chromosome. (N Engl J Med 302:185-188, 1980).

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Keim P, Diers BW, Olson TC, Shoemaker RC. Department of Agronomy, Iowa State University, Ames 50011.
RFLP mapping in soybean: association between marker loci and variation in quantitative traits.

We have constructed a genetic map for soybean and identified associations between genetic markers and quantitative trait loci. One-hundred-fifty restriction fragment length polymorphisms (RFLPs) were used to identify genetic linkages in an F2 segregating population from an interspecific cross (Glycine max x Glycine soja). Twenty-six genetic linkage groups containing ca. 1200 recombination units are reported. Progeny-testing of F2-derived families allowed quantitative traits to be evaluated in replicated field trials. Genomic regions, which accounted for a portion of the genetic variation (R2 = 16 to 24%) in several reproductive and morphological traits, were linked to RFLP markers. Significant associations between RFLP markers and quantitative trait loci were detected for eight of nine traits evaluated. The ability to identify genes within a continuously varying trait has important consequences for plant breeding and for understanding evolutionary processes.

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Kelly DP, Whelan AJ, Ogden ML, Alpers R, Zhang ZF, Bellus G, Gregersen N, Dorland L, Strauss AW. Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO 63110.
Molecular characterization of inherited medium-chain acyl-CoA dehydrogenase deficiency.

Deficiency of medium-chain acyl-CoA dehydrogenase (MCAD) is a common inherited defect in energy metabolism. Characterization of the mRNA encoding MCAD in a Dutch MCAD-deficient patient revealed an A----G change at nucleotide position 985 of the MCAD mRNA coding region. This point mutation results in the substitution of a glutamic acid for a lysine at amino acid position 304 of the mature protein. The single base change was not found in any wild-type MCAD mRNAs. A mutant allele-specific oligonucleotide probe was used in a hybridization analysis of amplified genomic DNA of MCAD-deficient family members, a carrier, and normal individuals. The hybridization analysis specifically identified individuals who were heterozygotes or homozygotes. In addition to the point mutation, a significant proportion of the index patient's MCAD mRNA contained a variety of deletions and insertions as a result of exon skipping and intron retention. The missplicing occurred in multiple regions throughout the MCAD mRNA. Analysis of the patient's MCAD gene in the regions where the missplicing occurred most frequently did not reveal a mutation in the splicing acceptor or donor sites. Therefore, the molecular characterization of this family revealed a crucial point mutation in the MCAD gene and an unusual abnormality in MCAD pre-mRNA splicing.

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Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui LC. Department of Genetics, Hospital for Sick Children, Toronto, Ontario, Canada.
Identification of the cystic fibrosis gene: genetic analysis.

Approximately 70 percent of the mutations in cystic fibrosis patients correspond to a specific deletion of three base pairs, which results in the loss of a phenylalanine residue at amino acid position 508 of the putative product of the cystic fibrosis gene. Extended haplotype data based on DNA markers closely linked to the putative disease gene locus suggest that the remainder of the cystic fibrosis mutant gene pool consists of multiple, different mutations. A small set of these latter mutant alleles (about 8 percent) may confer residual pancreatic exocrine function in a subgroup of patients who are pancreatic sufficient. The ability to detect mutations in the cystic fibrosis gene at the DNA level has important implications for genetic diagnosis.

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Knoll BJ, Rothblum KN, Longley M. Department of Pathology and Laboratory Medicine, University of Texas Medical School, Houston 77025.
Nucleotide sequence of the human placental alkaline phosphatase gene. Evolution of the 5' flanking region by deletion/substitution.
J Biol Chem. 1988 Aug 25: 263(24): 12020-7. Erratum in: J Biol Chem 1989 Feb 5;264(4):2391.

Three closely related alkaline phosphatase (ALP) genes reside on the long arm of chromosome 2 in man. One of these genes (the placental ALP-1) encodes the classic heat-stable placental alkaline phosphatase. Another gene (the placental ALP-2) is closely related to the placental ALP-1 and may encode the so-called placental ALP-like enzyme of the testis and thymus. The third member of this gene family (the intestinal ALP gene) encodes the intestinal alkaline phosphatase. The expression of the placental ALP-1 and intestinal ALP genes is highly tissue-specific in spite of nearly 90% sequence similarity within their exons. To help determine the basis for this tissue specificity, the nucleotide sequence of the placental ALP-1 gene and some of its 5' flanking region has been determined and analyzed by comparison with placental ALP-2 and intestinal ALP gene sequences. The placental ALP-1 gene transcription unit has 4087 bases between the major cap site and the most distal of several reported 3' ends. The protein coding region is divided by 10 short introns varying in size from 74 to 241 nucleotides. Three of these introns bisect regions of the gene that encode residues conserved between the active site of the Escherichia coli enzyme and the human placental ALP. This result suggests that the human alkaline phosphatase genes have evolved in an intron-independent fashion. A comparison of the placental ALP-1 5' flanking sequence (up to -540) with the analogous sequence of the intestinal ALP gene revealed several deletion/substitutions which could be important in determining the tissue-specific expression of these genes.

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Kogan SC, Doherty M, Gitschier J. Howard Hughes Medical Institute, University of California, San Francisco, CA 94143.
An improved method for prenatal diagnosis of genetic diseases by analysis of amplified DNA sequences. Application to hemophilia A.
N Engl J Med. 1987 Oct 15: 317(16): 985-90.

We report the development of a rapid nonradioactive technique for the genetic prediction of human disease and its diagnostic application to hemophilia A. This method is based on enzymatic amplification of short segments of human genes associated with inherited disorders. A novel feature of the procedure is the use of a heat-stable DNA polymerase, which allows the repeated rounds of DNA synthesis to proceed at 63 degrees C. The high sequence specificity of the amplification reaction at this elevated temperature permits restriction-site polymorphisms, contained in the amplified samples, to be analyzed by visual inspection of their digestion products on polyacrylamide gels. By means of this method, we have performed carrier detection and prenatal diagnosis of hemophilia in two families with use of the factor VIII intragenic polymorphisms identified by the restriction enzymes BclI and XbaI. Predictions can be made directly from chorionic villi, without previous DNA extraction, and fetal sex can be determined by amplification of sequences specific for the Y chromosome. Specific amplification of genomic sequences with heat-stable DNA polymerase is applicable to the diagnosis of a wide variety of inherited disorders. These include diseases diagnosed by restriction-site variation, such as Duchenne's muscular dystrophy and sickle cell anemia, those due to a collection of known mutations, such as beta-thalassemia, and those due to gene deletion, such as alpha-thalassemia.

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Kogan S, Gitschier J. Department of Medicine, University of California, San Francisco 94143-0724.
Mutations and a polymorphism in the factor VIII gene discovered by denaturing gradient gel electrophoresis.

Hemophilia A results from mutations in the gene coding for coagulation factor VIII. We used denaturing gradient gel electrophoresis to screen for mutations in the region of the factor VIII gene coding for the first acidic domain. Amplification primers were designed employing the MELTMAP computer program to optimize the ability to detect mutations. Screening of amplified DNA from 228 unselected hemophilia A patients revealed two mutations and one polymorphism. Rescreening the same population by making heteroduplexes between amplified patient and control samples prior to electrophoresis revealed one additional mutation. The mutations include two missense and one 4-base-pair deletion, and each mutation was found in patients with severe hemophilia. The polymorphism, located adjacent to the adenine branch site in intron 7, is useful for genetic prediction in some cases where the Bcl I and Xba I polymorphisms are uninformative. These results suggest that DNA amplification and denaturing gradient gel electrophoresis should be an excellent strategy for identifying mutations and polymorphisms in defined regions of the factor VIII gene and other large genes.

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Krawczak M, Konecki DS, Schmidtke J, Duck M, Engel W, Nutzenadel W, Trefz FK. Institut fur Humangenetik der Universitat, Gottingen, Federal Republic of Germany.

Allelic association of the cystic fibrosis locus and two DNA markers, XV2c and KM19, in 55 German families.
Hum Genet. 1988 Sep: 80(1): 78-80.

Allelic association between cystic fibrosis and two linked markers is demonstrated in a sample of 55 German families. It is shown by example how these observations can be used for genetic risk calculation.

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Krawczak M. Institut fur Humangenetik der Universitat, Gottingen, West Germany.
Algorithms for the restriction-site mapping of DNA molecules.

Two algorithms are described that rapidly construct restriction maps of DNA molecules from single- and double-digest data. The implementation of these algorithms into the Pascal programs AMAPK and AMARD allows such mapping to be done on microcomputers.

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Kulozik AE, Lyons J, Kohne E, Bartram CR, Kleihauer E. Department of Paediatrics II, University of Ulm, F.R.G.
Rapid and non-radioactive prenatal diagnosis of beta thalassaemia and sickle cell disease: application of the polymerase chain reaction (PCR).

The standard method for the prenatal diagnosis of the haemoglobinopathies is by restriction enzyme mapping of chorionic villus DNA using Southern blotting and radioactively labelled gene probes. An improvement of the procedure which involves the selective amplification of DNA fragments by the polymerase chain reaction allows one to visualize restriction fragments directly without the use of radioactivity and within 2 d after obtaining the sample. We report here the prenatal diagnosis of two pregnancies at risk for homozygous beta thalassaemia and homozygous sickle cell disease using this novel approach.

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Labouesse M, Herbert CJ, Dujardin G, Slonimski PP.
Three suppressor mutations which cure a mitochondrial RNA maturase deficiency occur at the same codon in the open reading frame of the nuclear NAM2 gene.

Dominant mutations of the nuclear NAM2 gene are able to compensate for a deficiency of the maturase encoded by the fourth intron of the mitochondrial cytochrome b gene. We have determined the complete nucleotide sequence of the NAM2-1 suppressor allele. The results of S1 nuclease protection experiments show that two overlapping poly(A)+ RNAs are transcribed from the gene using different promoters. The longer transcript contains two open reading frames (ORFs), a long ORF which could encode a protein of 894 amino acids, mol. wt 102,000 daltons, and a short ORF of 51 codons which is omitted from the shorter transcript. The wild-type nam2+ and two other suppressor alleles, NAM2-6 and NAM2-7, have been cloned. A comparison of the sequence of the wild-type and the three suppressor alleles shows that on three separate occasions the same codon specifying glycine was mutated (once to serine and twice to cysteine). Finally sequence comparisons identified two regions in the long ORF, distinct from the position of the suppressor mutations, that could correspond to binding domains for a nucleotide and a nucleic acid.

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Lander ES, Botstein D.
Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children.

An efficient strategy for mapping human genes that cause recessive traits has been devised that uses mapped restriction fragment length polymorphisms (RFLPs) and the DNA of affected children from consanguineous marriages. The method involves detection of the disease locus by virtue of the fact that the adjacent region will preferentially be homozygous by descent in such inbred children. A single affected child of a first-cousin marriage is shown to contain the same total information about linkage as a nuclear family with three affected children. Calculations show that it should be practical to map a recessive disease gene by studying DNA from fewer than a dozen unrelated, affected inbred children, given a complete RFLP linkage map. The method should make it possible to map many recessive diseases for which it is impractical or impossible to collect adequate numbers of families with multiple affected offspring.

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Landsman D, McBride OW, Bustin M. Laboratory of Molecular Carcinogenesis, National Cancer Institute, Bethesda, MD 20892.
Human non-histone chromosomal protein HMG-17: identification, characterization, chromosome localization and RFLPs of a functional gene from the large multigene family.

The multigene family of chromosomal protein HMG-17 is the largest known human retropseudogene family. A functional gene was identified and isolated by screening cDNA-selected genomic clones with a set of 5 oligonucleotides whose sequence corresponded to regions in which the sequence of the retropseudogenes differed from that of the cDNA and which did not span previously identified exon/intron junctions. A 7195 bp genomic fragment containing 6 exons, ranging in size from 30 to 817 bp, two of which encode the entire DNA binding domain of the protein, was sequenced. The gene has features which are typical to "housekeeping" genes and is characterized by a very high content of G + C residues in a 1.4 kb fragment starting 500 bp from the cap site and by an "HTF" island in the 5' region. Transcriptional regulatory signals, exon/intraon boundaries and features characteristic of "housekeeping" genes are evolutionary conserved between the human and chicken genes. The HMG-17 gene was localized to human chromosome 1p12-34. RFLP's useful for further mapping were detected. The experimental evidence presented leads to the assumption that the gene characterized is the only functional human HMG-17 gene.

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Lazzeroni LC. Biostatistics Division, Department of Health Research and Policy, Stanford University, Stanford, California 94305, USA. Lazzeroni@stanford.edu
A chronology of fine-scale gene mapping by linkage disequilibrium.

The past decade produced several proposals for fine-scale gene mapping using linkage disequilibrium data. The suggested methods fall into two main groups, those that rely on pairwise statistics and those that rely on haplotypes. This paper reviews each strategy's development from a chronological perspective.

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Leitersdorf E, Chakravarti A, Hobbs HH. Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas 75235.

Am J Hum Genet. 1989 Mar: 44(3): 409-21.

Mutations in the low-density lipoprotein (LDL) receptor gene result in the autosomal dominant disorder familial hypercholesterolemia (FH). Many different LDL receptor mutations have been identified and characterized, demonstrating a high degree of allelic heterogeneity at this locus. The ability to identify mutant LDL receptor genes for prenatal diagnosis of homozygous FH or to study the role of the LDL receptor gene in polygenic hypercholesterolemia requires the use of closely linked RFLPs. In the present study we used 10 different RFLPs, including three newly described polymorphisms, to construct 123 independent haplotypes from 20 Caucasian American pedigrees. Our sample contained 31 different haplotypes varying in frequency from 0.8% to 29.3%; the five most common haplotypes account for 67.5% of the sample. The heterozygosity and PIC of each site were determined, and these values disclosed that eight of the RFLPs were substantially polymorphic. Linkage-disequilibrium analysis of the haplotype data revealed strong nonrandom associations among all 10 RFLPs, especially among those sites clustered in the 3' region of the gene. Evolutionary analysis suggests the occurrence of both mutational and recombinational events in the generation of the observed haplotypes. A strategy for haplotype analysis of the LDL receptor gene in individuals of Caucasian American descent is presented.

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Lemaire HG, Salbaum JM, Multhaup G, Kang J, Bayney RM, Unterbeck A, Beyreuther K, Muller-Hill B. Institute fur Genetik, Universitat Koln, FRG.
The PreA4(695) precursor protein of Alzheimer's disease A4 amyloid is encoded by 16 exons.

Alzheimer's disease (AD) is characterized by the cerebral deposition of fibrillar aggregates of the amyloid A4 protein. Complementary DNA's coding for the precursor of the amyloid A4 protein have been described. In order to identify the structure of the precursor gene relevant clones from several human genomic libraries were isolated. Sequence analysis of the various clones revealed 16 exons to encode the 695 residue precursor protein (PreA4(695] of Alzheimer's disease amyloid A4 protein. The DNA sequence coding for the amyloid A4 protein is interrupted by an intron. This finding supports the idea that amyloid A4 protein arises by incomplete proteolysis of a larger precursor, and not by aberrant splicing.

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Lewis RA, Otterud B, Stauffer D, Lalouel JM, Leppert M. Cullen Eye Institute, Department of Ophthalmology, Houston, Texas.
Mapping recessive ophthalmic diseases: linkage of the locus for Usher syndrome type II to a DNA marker on chromosome 1q.

Usher syndrome is a heterogeneous group of autosomal recessive disorders that combines variably severe congenital neurosensory hearing impairment with progressive night-blindness and visual loss similar to that in retinitis pigmentosa. Usher syndrome type I is distinguished by profound congenital (preverbal) deafness and retinal disease with onset in the first decade of life. Usher syndrome type II is characterized by partial hearing impairment and retinal dystrophy that occurs in late adolescence or early adulthood. The chromosomal assignment and the regional localization of the genetic mutation(s) causing the Usher syndromes are unknown. We analyzed a panel of polymorphic genomic markers for linkage to the disease gene among six families with Usher syndrome type I and 22 families with Usher syndrome type II. Significant linkage was established between Usher syndrome type II and the DNA marker locus THH33 (D1S81), which maps to chromosome 1q. The most likely location of the disease gene is at a map distance of 9 cM from THH33 (lod score 6.5). The same marker failed to show linkage in families segregating an allele for Usher syndrome type I. These data confirm the provisional assignment of the locus for Usher syndrome type II to the distal end of chromosome 1q and demonstrate that the clinical heterogeneity between Usher types I and II is caused by mutational events at different genetic loci. Regional localization has the potential to improve carrier detection and to provide antenatal diagnosis in families at risk for the disease.

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Li HH, Gyllensten UB, Cui XF, Saiki RK, Erlich HA, Arnheim N. Department of Biological Sciences, University of Southern California, Los Angeles 90089-0371.
Amplification and analysis of DNA sequences in single human sperm and diploid cells.

The use of the polymerase chain reaction for analysing DNA sequences in individual diploid cells and human sperm shows that two genetic loci can be co-amplified from a single sperm, which may allow the analysis of previously inaccessible genetic phenomena.

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Lifton RP, Sardet C, Pouyssegur J, Lalouel JM. Endocrine-Hypertension Division, Brigham and Women's Hospital, Boston, Massachusetts.
Cloning of the human genomic amiloride-sensitive Na+/H+ antiporter gene, identification of genetic polymorphisms, and localization on the genetic map of chromosome 1p.

We have cloned and mapped a 90-kb region spanning the human genomic amiloride-sensitive Na+/H+ antiporter gene on overlapping cosmid clones. This cloned region extends 27 kb upstream of the 5' end of the longest antiporter cDNA and reveals a primary transcription unit of at least 60 kb. Using these genomic clones we have identified polymorphisms in the antiporter gene in human genomic DNA cleaved with enzymes TaqI and MspI; both are two-allele systems. We have localized both polymorphisms to the same segment within an intron of the antiporter transcription unit. Observed heterozygosity for both markers is 47% in 175 unrelated individuals, with the two polymorphic systems showing complete linkage disequilibrium. We have determined genotypes at the antiporter locus in 667 individuals in 59 reference families. Linkage analysis using 28 other markers on human chromosome 1 precisely locates the antiporter gene (locus APNH) on the genetic map of 1 p. The antiporter gene is closely flanked by two highly informative loci, lying 3 cM proximal to the rhesus blood group locus (Rh) and 4 cM distal to the anonymous DNA marker CMM8 (locus D1S79). These antiporter polymorphisms and informative flanking markers will prove useful in genetic linkage studies employing the antiporter gene.

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Limm TM, Ashdown ML, Naughton MJ, McGinnis MD, Simons MJ. GeneType Pty Ltd., Fitzroy, Australia.
HLA-DQA1 allele and suballele typing using noncoding sequence polymorphisms. Application to 4AOHW cell panel typing.
Hum Immunol. 1993 Sep: 38(1): 57-68.

HLA-DQA1 typing of the 4AOHW cell panel is presented using a novel strategy that exploits both intron and exon polymorphisms. Intron sequences adjacent to the variable HLA-DQA1 second exon exhibit stable polymorphisms that are specific for locus alleles and certain suballelic DR/DQ haplotypes. A PCR-RFLP method has been developed that is based on amplification of a 780-bp segment extending from intron 1 through exon 2 to intron 2. Stable sequence polymorphisms provide restriction enzyme sites and confer mobility variations detected on polyacrylamide minigel electrophoresis. Direct band comparison of amplified products and restriction fragments with known standards facilitates pattern comparison, obviating the requirement for accurate molecular weight determination. This method, using only two enzymes, identifies a total of 11 allelic and suballelic groups, including all eight DQA1 alleles encoded at the second exon.

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Litt M, Luty JA. Department of Biochemistry, Oregon Health Sciences University, Portland 97201.
A hypervariable microsatellite revealed by in vitro amplification of a dinucleotide repeat within the cardiac muscle actin gene.

The human genome contains approximately 50,000 copies of an interspersed repeat with the sequence (dT-dG)n, where n = approximately 10-60. In humans, (TG)n repeats have been found in several sequenced regions. Since minisatellite regions with larger repeat elements often display extensive length polymorphisms, we suspected that (TG)n repeats ("microsatellites") might also be polymorphic. Using the polymerase chain reaction to amplify a (TG)n microsatellite in the human cardiac actin gene, we detected 12 different allelic fragments in 37 unrelated individuals, 32 of whom were heterozygous. Codominant Mendelian inheritance of fragments was observed in three families with a total of 24 children. Because of the widespread distribution of (TG)n microsatellites, polymorphisms of this type may be generally abundant and present in regions where minisatellites are rare, making such microsatellite loci very useful for linkage studies in humans.

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Little PF, Annison G, Darling S, Williamson R, Camba L, Modell B.
Model for antenatal diagnosis of beta-thalassaemia and other monogenic disorders by molecular analysis of linked DNA polymorphisms.

Polymorphisms of DNA restriction sites within the human fetal globin genes have been used to identify chromosomes that carry beta-thalassaemia genes in individuals heterozygous for this disease. This has allowed an antenatal diagnosis for beta-thalassaemia to be carried out by observation of the pattern of the inherited polymorphism of a linked DNA sequence not involved in the genetic pathogenesis of the disease. In the populations we have investigated there is no constant pattern of polymorphism that segregates with the beta-thalassaemia gene. The use of linked polymorphisms should, therefore, be applicable to antenatal diagnosis both of beta-thalassaemia and of any other single-gene defect for which there is a DNA probe specific for a sequence linked to the affected locus.

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Love JM, Knight AM, McAleer MA, Todd JA (Nuffield Department of Surgery, John Radcliffe Hospital, Headington, Oxford, UK.)

Towards construction of a high resolution map of the mouse genome using PCR-analysed microsatellites.
Nucleic Acids Res. 1990 Jul 25:18(14): 4123-30.

Fifty sequences from the mouse genome database containing simple sequence repeats or microsatellites have been analysed for size variation using the polymerase chain reaction and gel electrophoresis. 88% of the sequences, most of which contain the dinucleotide repeat, CA/GT, showed size variations between different inbred strains of mice and the wild mouse, Mus spretus. 62% of sequences had 3 or more alleles. GA/CT and AT/TA-containing sequences were also variable. About half of these size variants were detectable by agarose gel electrophoresis. This simple approach is extremely useful in linkage and genome mapping studies and will facilitate construction of high resolution maps of both the mouse and human genomes.

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Lubahn DB, Brown TR, Simental JA, Higgs HN, Migeon CJ, Wilson EM, French FS (Laboratoires for Reproductive Biology, University of North Carolina, Chapel Hill 27599.)

Sequence of the intron/exon junctions of the coding region of the human androgen receptor gene and identification of a point mutation in a family with complete androgen insensitivity.
Proc Natl Acad Sci U S A. 1989 Dec: 86(23): 9534-8. (Erratum in: Proc Natl Acad Sci U S A 1990 Jun: 87(11): 4411.)

Androgens act through a receptor protein (AR) to mediate sex differentiation and development of the male phenotype. We have isolated the eight exons in the amino acid coding region of the AR gene from a human X chromosome library. Nucleotide sequences of the AR gene intron/exon boundaries were determined for use in designing synthetic oligonucleotide primers to bracket coding exons for amplification by the polymerase chain reaction. Genomic DNA was amplified from 46,XY phenotypic female siblings with complete androgen insensitivity syndrome. AR binding affinity for dihydrotestosterone in the affected siblings was lower than in normal males, but the binding capacity was normal. Sequence analysis of amplified exons demonstrated within the AR steroid-binding domain (exon G) a single guanine to adenine mutation, resulting in replacement of valine with methionine at amino acid residue 866. As expected, the carrier mother had both normal and mutant AR genes. Thus, a single point mutation in the steroid-binding domain of the AR gene correlated with the expression of an AR protein ineffective in stimulating male sexual development.

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Luty JA, Guo Z, Willard HF, Ledbetter DH, Ledbetter S, Litt M. Department of Biochemistry, Oregon Health Sciences University, Portland 97201-3098.
Five polymorphic microsatellite VNTRs on the human X chromosome.
Am J Hum Genet. 1990 Apr: 46(4): 776-83.

The human genome contains approximately 50,000 copies of an interspersed repeat with the sequence (dT.dG/dA.dC)n, where n = approximately 10-60. We and others have found that several of these repeats have variable lengths in different individuals, with allelic fragments varying in size by multiples of 2 bp. These "microsatellite" variable number of tandem repeats (VNTRs) may be scored by PCR, using unique flanking primers to amplify the repeat-containing regions and resolving the products on DNA sequencing gels. Since few VNTRs have been found on the X chromosome, we screened a flow-sorted X chromosome-specific genomic library for microsatellites. Approximately 25% of the phage clones hybridized to a poly (dT-dG).poly(dA-dC) probe. Of seven X-linked microsatellites present in positive phages, five are polymorphic and three have both eight or more alleles and heterozygosities exceeding 75%. Using PCR to amplify genomic DNAs from hybrid cell panels, we confirmed the X localization of these VNTRs and regionally mapped four of them. The fifth VNTR was regionally mapped by virtue of its tight linkage to DXS87 in Centre du Polymorphisme Humain families. We conclude that whatever factors limit the occurrence of "classical" VNTRs and RFLPs on the X chromosome do not appear to operate in the case of microsatellite VNTRs.

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Lyonnet S, Caillaud C, Rey F, Berthelon M, Frezal J, Rey J, Munnich A. Clinique et Unite de Recherches de Genetique Medicale, INSERM U-12, Hopital des Enfants Malades, Paris.
Molecular genetics of phenylketonuria in Mediterranean countries: a mutation associated with partial phenylalanine hydroxylase deficiency.

We report the characterization of a mutation in the phenylalanine hydroxylase (PAH) gene associated with partial residual activity of the enzyme. This point mutation (280glu----lys) was found by sequencing a mutant cDNA clone derived from a needle biopsy of the liver in a child with variant form of phenylketonuria. There is a strict concordance between homozygosity for the mutation and this particular phenotype. The (280glu----lys) mutation is linked to an original and rare RFLP haplotype at the PAH locus found in south Europe and North Africa. So far, this genotype-haplotype association is both inclusive and exclusive. Thirty-three PAH-deficient patients were screened for the mutation by using polymerase chain-reaction amplification of their genomic DNA extracted from Guthrie cards. Since a large number of patients can be screened for a particular mutation by using Guthrie cards, the possibility arises of using these samples collected by national newborn screening centers for prospective and retrospective detection of other mutations in the human genome.

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Ma YH, Ladias JA, Butler R, Schumaker VN, Antonarakis SE, Lusis AJ, Heinzman C, Kwiterovich PO. Department of Chemistry and Biochemistry, University of California, Los Angeles 90024.
Apolipoprotein B gene haplotypes. Association between Ag and DNA polymorphisms.

Berg et al. (Clin Genet 1986;30:515-520) have reported that an Xba I DNA polymorphic site in exon 26 of the apolipoprotein (apo) B gene is associated both with the Ag(x/y) immunochemical polymorphism and with elevated serum lipoprotein levels. Ma et al. (Arteriosclerosis 1987;7:301-305) have reported that the same Xba I polymorphism is associated with a different immunochemical polymorphism, Ag(c/g). To extend and clarify these observations, we have determined the Ag and Xba I polymorphism for 106 individuals. We find that the Xba I restriction fragment length polymorphism is in linkage disequilibrium with both Ag(x/y) and Ag(c/g) loci; thus, all 31 Xba I(X1/X1) genotypes observed in this study are also Ag(y/y). All but one of 22 Xba I(X2/X2) genotypes are also Ag(g/g). For individuals homozygous at either two or three of these loci, it was possible to determine the haplotypes for 128 apo B alleles. Of the eight possible apo B haplotypes, only four were represented in this unambiguous subpopulation, although other minor haplotypes were present in the total population from which it was derived. The identification of major apo B haplotypes in human populations may simplify the search for significant correlations between certain apo B alleles and lipid levels and atherosclerosis.

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Macek M, Tomasova H, Boue J, Kleijer WJ, Sedlacek Z, Hronkova J, Vavrova V, Jelinkova E, Kulovany E, Benesova D, et al. Department of Medical Genetics, Faculty of Pediatrics Prague, Czechoslovakia.
The experience with the foetal diagnosis of the cystic fibrosis in the second and first trimester.

The amniotic fluid activity of gamma glutamyl transpeptidase (GGT), leucine aminopeptidase (LAP) and alcaline phosphatase (AP) and disacharidases was examined in 66 pregnancies with the risk of cystic fibrosis (CF) in the 17th-21st weeks of gestation. So far 28 pregnancies continue. The prenatal diagnosis was confirmed in all so far delivered children or aborted foetuses if the GGT activity was higher than 400 U/1 (10th percentile) or lower than 190 U/1 (3rd percentile) in the 17th-18th weeks. The results of other microvillar and ultrasound examinations were consistent with it. From 3 pregnancies with GGT activity in the range of 3-5 percentiles and abnormal activities of other microvillar enzymes, the CF was confirmed only in one aborted foetus with meconium ileus and with abnormal ultrasound examination. In other 2 pregnancies with normal ultrasound, healthy children were delivered. In 3 pregnancies with the GGT in the range of 5-10 percentiles and abnormal other microvillar enzymes, one false negative GGT and ultrasound examination was disclosed. The other 2 aborted foetuses did not exhibit the signs of CF in necropsy examinations. The meconium ileus was found in 2/4 of aborted foetuses with GGT lower than 3 percentiles, abnormal activities of other microvillar enzymes and abnormal ultrasound examination. The ultrasound examination was correct in 2/10 of pregnancies with GGT lower than 3 percentiles or abnormal activities of other microvillar enzymes. The GGT examination in 19th-21st weeks provided similarly reliable diagnostic results. The importance of fetal karyotyping and ultrasound elimination of other severe congenital anomalies is pointed out for critical interpretation of microvillar enzyme activities testing.

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Magdolen V, Oechsner U, Muller G, Bandlow W. Institute for Genetics and Microbiology, Munich, Federal Republic of Germany.
The intron-containing gene for yeast profilin (PFY) encodes a vital function.
Mol Cell Biol. 1988 Dec: 8(12): 5108-15.

The gene coding for profilin (PFY), an actin-binding protein, occurs as a single copy in the haploid genome of Saccharomyces cerevisiae and is required for spore germination and cell viability. Displacement of one gene copy in a diploid cell by a nonfunctional allele is recessively lethal: tetrad analysis yields only two viable spores per ascus. The PFY gene maps on chromosome XV and is linked to the ADE2 marker. The primary transcript of about 1,000 bases contains an intron of 209 bases and is spliced into a messenger of about 750 bases. The intron was identified by comparison with a cDNA clone, which also revealed the 3' end of the transcript. The 5' end of the mRNA was mapped by primer elongation. The gene is transcribed constitutively and has a coding capacity for a protein of 126 amino acids. The deduced molecular weight of

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Mages W, Salbaum JM, Harper JF, Schmitt R. Lehrstuhl fur Genetik, Universitat Regensburg, Federal Republic of Germany.
Organization and structure of Volvox alpha-tubulin genes.

Southern analysis of Volvox genomic DNA revealed two genes homologous to Chlamydomonas reinhardtii alpha-tubulin cDNA. Restriction fragment length polymorphism analysis indicated that the two genes are not genetically linked. Clones representing one of the alpha-tubulin genes have been isolated from a genomic library of Volvox carteri f. nagariensis. A 3153 bp BamHI fragment containing the entire alpha-tubulin gene (1802 bp) plus 707 bp of the 5'- and 644 bp of the 3'-untranslated regions has been sequenced, revealing the following features: (1) the derived alpha-tubulin primary structure of 451 amino acids is highly conserved, differing in two residues from the alpha 1- and in two additional residues from the alpha 2-tubulin of C. reinhardtii; (2) in comparison to the C. reinhardtii genes, the Volvox alpha-tubulin gene contains a third intron; positions of the other two introns are precisely conserved; (3) codon usages are biased towards G or C, and against A, in the third position; 19 codons are absent from the alpha-tubulin coding sequence, and 5 of these are not used in any of 7 compiled Volvox genes; (4) transcription begins with an A, 30 bp downstream of the putative TATA box; upstream of the TATA box is a 14 bp sequence similar to consensus sequences found in all 4 C. reinhardtii tubulin genes and believed to regulate promoter function.

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Maggio A, Acuto S, Lo Gioco P, Di Marzo R, Giambona A, Sammarco P, Caronia F.
Beta A and beta thal DNA haplotypes in Sicily.

A close association between specific restriction fragment polymorphism patterns and specific mutations in Mediterranean people with thalassemia has been demonstrated by Kazazian et al. (1984). This finding is useful to characterize the number and types of mutations in each ethnic group for setting up prenatal diagnosis in the first trimester of pregnancy by the oligonucleotide technique. For this reason we studied 99 beta thal and 46 beta A chromosomes in the Sicilian population. We found seven different cleavage patterns, not considering two new haplotypes so far uncharacterized. Many of the patients (68.3%) were genetic compounds for different haplotypes while only 31.7% were haplotype homozygotes. They may still be thalassemia compound heterozygotes. These findings confirm the molecular basis of the heterogeneity of beta thalassemia in Sicily.

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Mardis ER, Roe BA. University of Oklahoma, Norman 73019.
Automated methods for single-stranded DNA isolation and dideoxynucleotide DNA sequencing reactions on a robotic workstation.

Automated procedures have been developed for both the simultaneous isolation of 96 single-stranded M13 chimeric template DNAs in less than two hours, and for simultaneously pipetting 24 dideoxynucleotide sequencing reactions on a commercially available laboratory workstation. The DNA sequencing results obtained by either radiolabeled or fluorescent methods are consistent with the premise that automation of these portions of DNA sequencing projects will improve the reproducibility of the DNA isolation and the procedures for these normally labor-intensive steps provides an approach for rapid acquisition of large amounts of high quality, reproducible DNA sequence data.

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Martiniuk F, Mehler M, Tzall S, Meredith G, Hirschhorn R. New York University Medical Center, Department of Medicine, NY 10016.
Sequence of the cDNA and 5'-flanking region for human acid alpha-glucosidase, detection of an intron in the 5' untranslated leader sequence, definition of 18-bp polymorphisms, and differences with previous cDNA and amino acid sequences.

Acid maltase or acid alpha-glucosidase (GAA) is a lysosomal enzyme that hydrolyzes glycogen to glucose and is deficient in glycogen storage disease type II. Previously, we isolated a partial cDNA (1.9 kb) for human GAA; we have now used this cDNA to isolate and determine sequence in longer cDNAs from four additional independent cDNA libraries. Primer extension studies indicated that the mRNA extended approximately 200 bp 5' of the cDNA sequence obtained. Therefore, we isolated a genomic fragment containing 5' cDNA sequences that overlapped the previous cDNA sequence and extended an additional 24 bp to an initiation codon within a Kozak consensus sequence. The sequence of the genomic clone revealed an intron-exon junction 32 bp 5' to the ATG, indicating that the 5' leader sequence was interrupted by an intron. The remaining 186 bp of 5' untranslated sequence was identified approximately 3 kb upstream. The promoter region upstream from the start site of transcription was GC rich and contained areas of homology to Sp1 binding sites but no identifiable CAAT or TATA box. The combined data gave a nucleotide sequence of 2,856 bp for the coding region from the ATG to a stop codon, predicting a protein of 952 amino acids. The 3' untranslated region contained 555 bp with a polyadenylation signal at 3,385 bp followed by 16 bp prior to a poly(A) tail. This sequence of the GAA coding region differs from that reported by Hoefsloot et al. (1988) in three areas that change a total of 42 amino acids. Direct determination of the amino acid sequence in one of these areas confirmed the nucleotide sequence reported here but also disagreed with the directly determined amino acid sequence reported by Hoefsloot et al. (1988). At two other areas, changes in base pairs predicted new restriction sites that were identified in cDNAs from several independent libraries. The amino acid changes in all three ares increased the homology to rabbit-human isomaltase. Therefore, we believe that our nucleotide sequence for GAA is more precise. We have also identified single base-pair polymorphisms at 18 sites for human GAA, some of which are not silent.

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Masson P, Rutherford G, Banks JA, Fedoroff N. Department of Embryology Carnegie Institution of Washington Baltimore, Maryland 21210.
Essential large transcripts of the maize Spm transposable element are generated by alternative splicing.
Cell. 1989 Aug 25: 58(4): 755-65.

We used in vitro mutagenesis and cDNA cloning to identify new Suppressor-mutator (Spm) transposable element genes. Frameshift mutations in the ORFs of the tnpA gene's first intron markedly reduce Spm activity in transgenic tobacco, indicating that intron sequences encode essential gene products. Evidence is given that Spm encodes large alternatively spliced transcripts, designated tnpB (4.9 kb), tnpC (5.7 kb), and tnpD (5.8 kb), comprising all of the tnpA exons, most of the tnpA intron 1 ORF1 sequence, and either none, part, or all of the intron 1 ORF2 sequence. Two alternative splice donor sites were identified at the end of exon 1, and the structure of the different exon 1 sequences suggests that Spm employs a novel mode of translational regulation.

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Marx J.
Dissecting the complex diseases.
Science. 1990 Mar 30: 247(4950): 1540-2.

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Mathison L, Winey M, Soref C, Culbertson MR, Knapp G. Laboratorie of Genetics, University of Wisconsin, Madison 53706.
Mutations in the anticodon stem affect removal of introns from pre-tRNA in Saccharomyces cerevisiae.

To evaluate the role of exon domains in tRNA splicing, the anti-codon stem of proline pre-tRNAUGG from Saccharomyces cerevisiae was altered by site-directed mutagenesis of the suf8 gene. Sixteen alleles were constructed that encode mutant pre-tRNAs containing all possible base combinations in the last base pair of the anticodon stem adjacent to the anticodon loop (positions 31 and 39). The altered pre-tRNAs were screened by using an in vitro endonucleolytic cleavage assay to determine whether perturbations in secondary structure affect the intron excision reaction. The pre-tRNAs were cleaved efficiently whenever secondary structure in the anticodon stem was maintained through standard base pairing or G.U interactions. However, most of the pre-tRNAs with disrupted secondary structure were poor substrates for intron excision. We also determined the extent to which the suf8 alleles produce functional products in vivo. Each allele was integrated in one to three copies into a yeast chromosome or introduced on a high-copy-number plasmid by transformation. The formation of a functional product was assayed by the ability of each allele to suppress the +1 frameshift mutation his4-713 through four-base codon reading, as shown previously for the SUF8-1 suppressor allele. We found that alleles containing any standard base pair or G.U pair at position 31/39 in the anticodon stem failed to suppress his4-713. We could not assess in vivo splicing with these alleles because the tRNA products, even if they are made, would be expected to read a normal triplet rather than a quadruplet codon. However, all of the alleles that contained a disrupted base pair at position 31/ 39 in the anticodon stem altered the structure of the tRNA in a manner that caused frameshift suppression. Suppression indicated that splicing must have occurred to some extent in vivo even though most of the suppression alleles produced pre-tRNAs that were cleaved with low efficiency or not at all in vitro. These results have important implications for the interpretation of in vitro cleavage assays in general and for the potential use of suppressors to select mutations that affects tRNA splicing.

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Matoskova B, Rorsman F, Svensson V, Betsholtz C. Department of Pathology, University Hospital, Uppsala, Sweden.
Alternative splicing of the platelet-derived growth factor A-chain transcript occurs in normal as well as tumor cells and is conserved among mammalian species.

Using a polymerase chain reaction approach, we have analyzed the alternative usage of the platelet-derived growth factor A-chain exon 6 in mRNA from various cell types. The results show that this sequence is utilized in a small fraction of the mRNA molecules in normal as well as transformed cells and that this phenomenon is conserved among mammalian species.

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Mattick JS. Centre for Molecular and Cellular Biology, University of Queensland, Brisbane, Australia.
Introns: evolution and function.

The debate continues on the issue of whether nuclear introns were present in eukaryotic protein-coding genes from the beginning (introns-early) or invaded them later in evolution (introns-late). Recent studies concerning the location of introns with respect to gene and protein structure have been interpreted as providing strong support for both positions, but the weight of argument is clearly moving in favour of the latter. Consistent with this, there is now good evidence that introns can function as transposable elements, and that nuclear introns derived from self-splicing group II introns, which then evolved in partnership with the spliceosome. This was only made possible by the separation of transcription and translation. If introns did colonize eukaryotic genes after their divergence from prokaryotes, the original question as to the evolutionary forces that have seen these sequences flourish in the higher organisms, and their significance in eukaryotic biology, is again thrown open. I suggest that introns, once established in eukaryotic genomes, might have explored new genetic space and acquired functions which provided a positive pressure for their expansion. I further suggest that there are now two types of information produced by eukaryotic genes--mRNA and iRNA--and that this was a critical step in the development of multicellular organisms.

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McGee TL, Yandell DW, Dryja TP. Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston 02114.
Structure and partial genomic sequence of the human retinoblastoma susceptibility gene.

This report describes the genomic organization of the human retinoblastoma susceptibility locus. This gene spans approximately 200 kb of DNA within human chromosome 13, band q14. The previously determined cDNA sequence comprises 27 exons, ranging in size from 31 bp to 1873 bp, and 26 introns, ranging in size from 80 bp to 70,500 bp. We have mapped the positions of the exons and the positions of the recognition sites for six restriction endonucleases. We also present the sequence of 9.2% of the locus (18,335 bp), including approximately 200 bp of intron sequence immediately flanking each exon. This map of a wild-type allele will form the foundation for future studies of mutant, oncogenic alleles at this locus.

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McIntosh I, Curtis A, Millan FA, Brock DJ. Human Genetics Unit, University of Edinburgh, Western General Hospital, U.K.
Prenatal exclusion testing for Huntington disease using the polymerase chain reaction.

Prenatal exclusion of Huntington disease (HD) may be carried out by analysis of cosegregating DNA markers on a first-trimester chorionic villus sample. The conventional Southern blot method is time-consuming and requires microgram quantities of DNA and milligram quantities of villus tissue. The use of the polymerase chain reaction (PCR) to amplify genomic DNA by a factor of 10(7) or more makes it possible to do analyses on very small samples in a few hours and without recourse to Southern blotting or hybridization with radioactive probes. We report on a fetus at risk of HD; prenatal testing was carried out by using the PCR to amplify a polymorphic DNA sequence adjacent to the HD locus. The risk of the fetus inheriting the HD gene could not be excluded and the pregnancy was terminated. This represents an example of gene tracking by using amplification of a restriction fragment length polymorphism at some distance from the relevant mutation.

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Metherall JE, Collins FS, Pan J, Weissman SM, Forget BG.
Beta zero thalassemia caused by a base substitution that creates an alternative splice acceptor site in an intron.

A thalassemic beta-globin gene cloned from a haplotype I chromosome contains a T to G transversion at position 116 of IVS1 which results in the generation of an abnormal alternative acceptor splice site. Transient expression studies revealed a 4-fold decrease in the amount of RNA produced with greater than 99% of it being abnormally spliced despite preservation of the normal acceptor splice site at position 130. These results suggest that the mutation at IVS1 position 116 results in beta zero thalassemia. A closely related mutation at position 110 of IVS1 also generates a novel acceptor site and results in a similar decrease in total mRNA produced, but approximately 20% of the mRNA produced is normally spliced and thus the phenotype is that of beta + thalassemia. These observations suggest that short range position effects may play a dramatic role in the choice of potential splice acceptor sites. We demonstrate the presence of abnormally spliced mRNA in reticulocytes of affected individuals and show the mutation at IVS1 position 116 segregating from the mutation at IVS1 position 110 in a three generation pedigree. The mutation results in the creation of a MaeI restriction site, as do a number of other thalassemic mutations, and we demonstrate some difficulties that may arise in the differential diagnosis of these mutations.

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Miura O, Sugahara Y, Nakamura Y, Hirosawa S, Aoki N. First Department of Medicine, Tokyo Medical and Dental University, Japan.
Restriction fragment length polymorphism caused by a deletion involving Alu sequences within the human alpha 2-plasmin inhibitor gene.

A restriction fragment length polymorphism within the human alpha 2-plasmin inhibitor gene has been detected by Southern blot hybridization using an alpha 2-plasmin inhibitor cDNA probe. This restriction fragment length polymorphism can be attributed to the presence of two alleles, A and B, that are distributed in Hardy-Weinberg equilibrium with frequencies of 73.5% and 2.65%, respectively, in 66 unrelated Caucasian individuals or with frequencies of 51.0% and 49.0%, respectively, in 50 unrelated Japanese individuals. The minor allele, B, is due to a deletion of about 720 base pairs in intron 8 of the alpha 2-plasmin inhibitor gene. Sequence analysis of the deletion junction in allele B and the corresponding regions of allele A demonstrated the presence of oppositely oriented Alu sequences at the 5' and 3' deletion boundaries. These data suggest that this restriction fragment length polymorphism was caused by intrastrand recombination between Alu sequences.

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Moller DE, Yokota A, Caro JF, Flier JS. Charles A. Dana Research Institute, Boston, Massachusetts.
Tissue-specific expression of two alternatively spliced insulin receptor mRNAs in man.

Two previously reported insulin receptor cDNA sequences differ by 36 base pairs (bp) in the distal alpha-subunit, suggesting that alternative mRNA splicing within the coding region may occur (two insulin receptor isoforms). We developed a quantitative modification of the polymerase chain reaction technique in order to detect and characterize differential mRNA splicing at this site within the distal alpha-subunit. Using RNA derived from a variety of human cell types, we detected two polymerase chain reaction-amplified cDNA species reflecting the presence or absence of the above 36 nucleotides. Identity of the two cDNA species was confirmed by Southern blots, the use of a BANI restriction site present only in the 36 base pair segment and dideoxy sequencing. The relative expression of the two mRNA forms varied markedly in a tissue-specific manner. Buffy coat leukocytes and Epstein-Barr virus-transformed lymphocytes express only the shorter mRNA. Placenta expresses both species equally; muscle, isolated adipocytes and cultured fibroblasts express somewhat more of the longer mRNA (relative ratios of mRNA abundance of 1.51, 3.18, and 2.77, respectively); liver expresses mostly the longer mRNA (relative ratio of 9.8). In RNA derived from cultured and fresh cells from patients with several states of insulin resistance, the relative expression of the two mRNA species was similar to results obtained with comparable normal tissues. Although the functional significance of alternative splicing of the insulin receptor mRNA is unknown, differential expression of these two receptor mRNAs may provide a structural basis for previously observed tissue-specific differences in insulin binding and action.

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Monteiro MJ, Cox RA.
Primary structure of an alpha-tubulin gene of Physarum polycephalum.

An alpha-tubulin gene of Physarum was isolated as a phage-lambda NM1149 recombinant (designated phage-lambda N alpha Tu). Phage-lambda N alpha Tu contained a 4700 base-pair HindIII nuclear DNA fragment of an allele of the altB locus of Physarum (one of four unlinked alpha-tubulin gene loci). Subfragments of the 4700 base-pair insert of phage-lambda N alpha Tu were cloned into phage M13 and the nucleotide sequence was determined by the dideoxy chain termination method. The start point of transcription was identified by primer extension and a putative polyadenylation site was located by S1 nuclease analysis. The 4650 base-pair HindIII insert into phage-lambda N alpha Tu spans the complete gene; sequences upstream from the 5' end contain the RNA transcription promoter elements (the TATA and CCAAT boxes). The nucleotide sequence encoding alpha-tubulin contains seven intervening sequences, ranging from 63 to 222 nucleotides in size. The exons have a sequence that is identical with a Physarum alpha-tubulin cDNA clone, except for three base changes, one leading to a Val codon in place of a Met codon, another leading to a Glu codon in place of an Asp codon, and the third change is silent. The genomic clone provides the nucleotide sequence coding for the last 26 amino acid residues missing from the cDNA clone. The new sequence data indicate that the alpha-tubulin gene has a C-terminal methionine codon and not a tyrosine codon, which has been found in all alpha-tubulin genes sequenced to date.

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Moschonas N, de Boer E, Flavell RA.
The DNA sequence of the 5' flanking region of the human beta-globin gene: evolutionary conservation and polymorphic differences.

We have determined the DNA sequence of a 1464 bp segment immediately flanking the 5' side of the human beta-globin gene. The sequence shows little similarity to the corresponding regions of the epsilon- or gamma-globin genes. There is about 75% homology, however, between the 5' extragenic regions of the beta-globin genes of man, goat and rabbit respectively. The mouse beta minor globin gene, but not the mouse beta major globin gene, also shares this extensive homology. A short segment of simple sequence DNA is found from about 1418 to 1388 bp upstream from the human beta-globin gene which consists of repeats of the sequence (TTTTA). Similar DNA sequences are also found at several sites in the large intron of the beta-globin gene. We have compared the DNA sequence of the 5' extragenic region of the normal beta-globin gene with the same segment of the beta-globin gene of a patient with beta thalassaemia. Of the two nucleotide differences observed, one generates a polymorphic HinfI site present 990 bp upstream from the beta-globin gene in the thalassaemic beta-globin and absent in the normal gene. A second beta thalassemic beta-globin gene which has the same molecular defect as the above mentioned case, however, lacks this HinfI site. It is therefore not yet clear whether this HinfI site will have any value in prenatal diagnosis of beta thalassaemia.

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Murray JC, Buetow KH, Donovan M, Hornung S, Motulsky AG, Disteche C, Dyer K, Swisshelm K, Anderson J, Giblett E, et al.
Linkage disequilibrium of plasminogen polymorphisms and assignment of the gene to human chromosome 6q26-6q27.

Linkage disequilibrium was observed between newly identified DNA polymorphisms and a previously described protein polymorphism for plasminogen. This finding implies that the two types of polymorphisms describe variation at the same locus. The plasminogen gene was mapped to chromosomal bands 6q26-q27 using somatic-cell hybrids and in situ hybridization. Linkage disequilibrium between protein and DNA polymorphisms has utility in substituting for protein typing in instances where only DNA samples are available, such as from deceased individuals or extinct species. The technique may be useful when cross-hybridizing sequences make the interpretation of Southern blot patterns difficult and may obviate the need for extensive DNA sequencing. In some cases, disequilibrium may provide information useful for determining the appropriate direction for chromosome walks from a marker locus to a target locus.

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Nafa K, Meriane F, Reghis A, Benabadji M, Demenais F, Guilloud-Bataille M, Sultan Y, Kaplan JC, Delpech M. Centre de Transfusion Sanguine, CHU Mustapha, Alger, Algeria.
Investigation of factor VIII:C gene restriction fragment length polymorphisms and search for deletions in hemophiliac subjects in Algeria.

The frequency of alleles for intragenic (intron 17 and intron 25) and extragenic (DXS15 and DXS52) F8C RFLPs was investigated in the Algerian population. Altogether 287 X chromosomes (97 males and 95 females) were studied. The allele frequencies found with the two intragenic F8C RFLPs were not substantially different from those reported in a Mediterranean population. At the highly polymorphic extragenic DXS52 locus the distribution in Algeria differed from that found in France. A new allele (14 kb), called 1 DZ, was found in 3.1% of the chromosomes. Fifty-one families with hemophilia A were studied with the same probes (374 subjects). Of the females, 94% were informative for at least one intra- or extragenic RFLP. Two recombinations were found between DXS52 and F8C, of which one occurred between the DXS15, DXS52 block and F8C, indicating that the two anonymous loci are on the same side of the F8C gene. Only two obvious gene deletions were observed in 73 unrelated hemophiliacs: one encompassed exons 14-22 (about 4.3 kb of cDNA and 36 kb of genomic DNA); the other removed the last exon (exon 26, representing 2 kb of cDNA).

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Nakamura Y, Leppert M, O'Connell P, Wolff R, Holm T, Culver M, Martin C, Fujimoto E, Hoff M, Kumlin E, et al.
Variable number of tandem repeat (VNTR) markers for human gene mapping.

A large collection of good genetic markers is needed to map the genes that cause human genetic diseases. Although nearly 400 polymorphic DNA markers for human chromosomes have been described, the majority have only two alleles and are thus uninformative for analysis of genetic linkage in many families. A few known marker systems, however, detect loci that respond to restriction enzyme cleavage by producing a fragment that can have many different lengths. This polymorphism is due to variation in the number of tandem repeats of a short DNA sequence. Because most individuals will be heterozygous at such loci, these markers will provide linkage information in almost all families. Ten oligomeric sequences derived from the tandem repeat regions of the myoglobin gene, the zeta-globin pseudogene, the insulin gene, and the X-gene region of hepatitis B virus, were used to develop a series of single-copy probes. These probes revealed new, highly polymorphic genetic loci whose allele sizes reflected variation in the number of tandem repeats.

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Nakamura Y, Lathrop M, O'Connell P, Leppert M, Barker D, Wright E, Skolnick M, Kondoleon S, Litt M, Lalouel JM, et al (Howard Hughes Medical Institute, University of Utah Health Sciences Center, Salt Lake City 84132.)

A mapped set of DNA markers for human chromosome 17.
Genomics. 1988 May: 2(4): 302-9.

We have developed and mapped by genetic linkage a primary set of markers for chromosome 17. The map consists of 21 loci derived from 27 probe/enzyme systems, including eight highly informative markers at loci containing a variable number of tandemly repeated DNA sequences (VNTRs). The map is continuous from the telomeric region of the short arm to the telomeric region of the long arm, covering estimated genetic distances of 218 cM in males and 279 cM in females. The average heterozygosity among all 21 loci in the population sample analyzed is 58%; 77% heterozygosity was observed among the eight VNTR markers that were highly informative. This map will make it possible to detect by linkage the location of genetic defects associated with chromosome 17 and will also provide anchor points for a high-resolution map of this chromosome.

------------------------------------------------------------------------------------------------------------------------------------Nakamura Y, Carlson M, Krapcho K, Kanamori M, White R (Howard Hughes Medical Institute, University of Utah Health Sciences Center, Salt Lake City 84132).

New approach for isolation of VNTR markers.
Am J Hum Genet. 1988 Dec: 43(6): 854-9.

Elsewhere we have reported an efficient method for isolating VNTR (Variable Number of Tandem Repeats) markers. Several of the VNTR markers isolated in those experiments were sequenced, and a DNA sequence of 9 bp (GNNGTGGG) emerged as an apparent consensus sequence for VNTR markers. To confirm this result and to develop more VNTR markers, we synthesized nine different 18-base-long oligonucleotides whose sequences each included GNNGTGGG. When 102 cosmid clones selected by these oligonucleotides were tested for polymorphism, 34 (33%) of them showed multiallelic VNTR polymorphisms (average heterozygosity 68%). This procedure represents a new and efficient approach for isolating additional VNTR markers and supports the idea that the GNNGTGGG sequence may play an important role in the generation of the multiallelic systems within the human genome.

Nakamura Y, Miura O, Sugahara Y, Maseki N, Kaneko Y, Aoki N. First Department of Medicine, Tokyo Medical and Dental University, Japan.
DNA rearrangement and restriction fragment length polymorphism within the first BCR intron in Philadelphia-positive acute leukemia.

In some patients with Philadelphia (Ph)-chromosome positive acute lymphoblastic leukemias, breakpoints on chromosome 22 are reported to occur within the first BCR intron. To analyze the breakpoints in chromosome 22 of Ph-positive acute leukemia patients without rearrangement of the 5.8 kb bcr, we cloned the 3' part of the first BCR intron using a synthetic DNA probe. During the course of study, we mapped the region of the deletion/insertion of 1 kb that causes a restriction fragment length polymorphism (RFLP) and found a racial difference in the frequencies of the alleles giving rise to this RFLP. Analyses of the patients' samples indicated that breakpoints were located within the 8.5 kb EcoRl fragment of the first BCR intron in two of five Ph-positive acute leukemia patients. The data, together with the previous reports, indicate that breakpoints within this approximately 50 kb intron are widely scattered, in contrast to those confined within the 5.8 kb bcr in chronic myelogenous leukemias.

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Nakano T, Suzuki K. Department of Neurology, University of North Carolina School of Medicine, Chapel Hill 27599.
Genetic cause of a juvenile form of Sandhoff disease. Abnormal splicing of beta-hexosaminidase beta chain gene transcript due to a point mutation within intron 12.

Abnormal beta-hexosaminidase beta chain cDNA clones were isolated from a library constructed from cultured fibroblasts of a patient with a juvenile form of Sandhoff disease (genetic beta-hexosaminidase A and B deficiency). Sequence analysis of a cDNA clone isolated from these fibroblasts contained an extra 24-base segment between exons 12 and 13. This segment was identified as the 3' terminus of intron 12. The remainder of the coding sequence was completely normal. The same 24-base insertion was found in four additional clones by sequencing. Restriction mapping analysis of seven other clones was consistent with the presence of the same 24-base intron 12 segment. This insertion is inframe and adds 8 amino acids between amino acids 491 and 492 of the primary sequence of the normal enzyme protein. It is located only 5 amino acids away from a possible glycosylation site. The finding is consistent with the slightly larger than normal size of the beta subunit precursor protein observed by immunoprecipitation. No normally spliced mRNA was detected. Gene amplification by the polymerase chain reaction and subsequent sequencing of genomic DNA indicated that the patient was a compound heterozygote. In one allele, there was a single nucleotide transition from normal G to A at 26 bases from the 3' terminus of intron 12. This mutation generates a consensus sequence for the 3' splice site for an intron, CAG/G, and thus explains the abnormal mRNAs that retain 24 bases of the 3' terminus of intron 12. The intron 12 and flanking exons 12 and 13 sequences were normal in the other allele, which is a priori also genetically abnormal. The other mutant allele therefore is likely to be of an mRNA-negative type.

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Nam HG, Giraudat J, Den Boer B, Moonan F, Loos W, Hauge BM, Goodman HM. Department of Genetics, Harvard Medical School and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114.
Restriction Fragment Length Polymorphism Linkage Map of Arabidopsis thaliana.

We have constructed a restriction fragment length polymorphism (RFLP) linkage map of the nuclear genome of the small flowering plant Arabidopsis thaliana. The map is based on the meiotic segregation of both RFLP and morphological genetic markers from five independent crosses. The morphological markers on each of the five chromosomes were included in the crosses to allow alignment of the RFLP map with the established genetic map. The map contains 94 new randomly distributed molecular markers (nine identified cloned Arabidopsis genes and 85 genomic cosmid clones) that detect polymorphisms between the Landsberg erecta and Columbia races. In addition, 17 markers from an independently constructed RFLP map of the Arabidopsis genome [Chang, C., Bowman, J.L., DeJohn, A.W., Lander, E.S., and Meyerowitz, E.M. (1988). Proc. Natl. Acad. Sci. USA 85, 6856-6860] have been included to permit integration of the two RFLP maps.

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Newgard CB, Fletterick RJ, Anderson LA, Lebo RV.
The polymorphic locus for glycogen storage disease VI (liver glycogen phosphorylase) maps to chromosome 14.

Human liver glycogen phosphorylase deficiency, also known as glycogen storage disease type VI (GSD VI) or Hers disease, is characterized by hepatomegaly and reduced or absent glycogenolytic response to the injection of glucagon. The recently isolated cDNA encoding the liver isozyme of glycogen phosphorylase was used to map the gene and identify restriction-fragment polymorphisms in normal Caucasians as a prerequisite for detecting linked GSD VI abnormalities. Results of restriction-enzyme analysis using a downstream fragment of the liver glycogen phosphorylase cDNA indicated the existence of a single gene copy per haploid genome. Hybridization of this downstream liver phosphorylase probe to dual laser-excited, sorted human chromosomes localized the gene to human chromosome 14. When the downstream probe was tested on genomic DNA cut with seven different restriction enzymes, a single MspI restriction-fragment-length polymorphism (RFLP) was observed in a single individual. In contrast, similar Southern blots performed with an upstream portion of the cDNA encoding liver phosphorylase revealed common RFLPs for four of eight enzymes tested, with minor polymorphic allele frequencies ranging from 33% to 44%. One of the four enzymes (TaqI) revealed two independent polymorphisms. If random distribution of these haplotypes among normal and disease loci, is assumed, approximately 92% of fetuses at risk for Hers disease will be informative when tested with the upstream liver phosphorylase probe.

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Newton CR, Heptinstall LE, Summers C, Super M, Schwarz M, Anwar R, Graham A, Smith JC, Markham AF. ICI Diagnostics, Gadbrook Park, Northwich, Cheshire.

Amplification refractory mutation system for prenatal diagnosis and carrier assessment in cystic fibrosis.
Lancet. 1989 Dec 23-30: 2(8678-8679): 1481-3.

The amplification refractory mutation system (ARMS) has been applied to prenatal diagnosis and carrier detection of cystic fibrosis. The nucleotide sequence of both alleles of the PstI restriction fragment length polymorphism at the KM19 locus, which displays linkage disequilibrium with cystic fibrosis, has been determined. ARMS enables direct analysis of alleles of this polymorphism in DNA isolated from chorionic villus biopsy or white blood cells.

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Nottenburg C, St John T, Weissman IL.
Unusual immunoglobulin DNA sequences from the nonexpressed chromosome of mouse normal B lymphocytes: implications for allelic exclusion and the DNA rearrangement process.

Allelic exclusion of immunoglobulin gene products results in the expression of only one of two possible alleles in normal B lineage cells. Attempts to define the role of heavy chain gene rearrangements in this process have revealed the nonexpressed allele to be rarely in its germline context, but rather incompletely rearranged (D/J rearrangements) or completely rearranged (V/D/J rearrangements) and in a context that cannot be expressed as a protein. Nearly all DNA sequences of heavy chain genes from the nonexpressed allele have originated from plasmacytomas, virus-induced pre-B leukemias, and hybridomas--all clonal cell lines perhaps altered by the neoplastic process. In this communication, we present the first examples of isolation and DNA sequence analysis of heavy chain gene rearrangements from the nonexpressed allele of normal B lymphocytes. Splenic B lymphocytes from allotype heterozygous (BALB/c X C57BL/6J)F1 mice expressing the BALB/c IgD allotype were detected with a monoclonal antibody, H10-4.22, to the BALB/c delta chain genetic marker and were isolated with a FACS (fluorescence-activated cell sorter). lambda phage clones containing the JH gene region from the sorted cells were isolated, and those containing sequences derived from the C57BL/6J nonexpressed chromosome were identified by a restriction fragment length polymorphism. DNA sequences of seven rearranged clones from the nonexpressed allele are presented. Five of these rearrangements have unexpected compositions. Four of the five clones contain V/D/J rearrangements with no obvious impediments to expression generated by the rearrangements. The novel variable region gene in one of these V/D/J rearrangements is a member of a newly described VH gene family. The fifth clone has a 3.5 kb deletion removing all of the JH gene segments. The remaining two clones contain D/J rearrangements that are typical of the initial stage of variable region assembly. These findings suggest that the mechanisms that generate nontranslatable heavy chains do not exclusively account for allelic exclusion. Rather, several different mechanisms may contribute to the establishment of allelic exclusion in normal B lymphocytes.

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Nozari G, Rahbar S, Wallace RB. City of Hope National Medical Center, Duarte, California 91010.
Haplotype analysis of the human beta-globin gene complex using multiple locus specific oligonucleotide probes.

Three oligonucleotide probes complementary to specific DNA sequences of the six human globin genes (epsilon, G gamma, A gamma, psi beta, delta, beta) were synthesized. The oligonucleotides were used either singly or in combination as hybridization probes to determine the haplotype of the human beta-globin gene cluster employing the four conventionally used restriction endonucleases HincII, HindIII, AvaII, and BamHI, in addition to HpaI. Polymorphism in the epsilon- and psi beta-genes (HincII) can be simultaneously determined with a single probe mixture. One of the probes complementary to both the psi beta- and gamma-genes is useful for determining both HindIII and HincII polymorphisms. The advantages of these probes relative to conventional cDNA probes are discussed.

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Ochman H, Gerber AS, Hartl DL. Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110.

A method is presented for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. The method uses the polymerase chain reaction (PCR), but it has the primers oriented in the reverse direction of the usual orientation. The template for the reverse primers is a restriction fragment that has been ligated upon itself to form a circle. This procedure of inverse PCR (IPCR) has many applications in molecular genetics, for example, the amplification and identification of sequences flanking transposable elements. In this paper we show the feasibility of IPCR by amplifying the sequences that flank an IS1 element in the genome of a natural isolate of Escherichia coli.

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O'Hara PJ, Grant FJ. ZymoGenetics, Inc., Seattle, WA 98103.
The human factor VII gene is polymorphic due to variation in repeat copy number in a minisatellite.

The gene coding for human factor VII, a vitamin K-dependent coagulation factor, contains five minisatellite imperfect tandem repeats with monomer element lengths ranging from 14 to 37 bp, and copy numbers ranging from 6 to 52. Three of these repeats are entirely within introns, one is entirely in an untranslated portion of an exon, and one spans an exon-intron border and contains coding sequence. A consensus sequence derived from a comparison of the monomers is similar to a core sequence found in other minisatellites. All of the minisatellites display higher-order periodicities. At least one of these minisatellites is polymorphic. A variation in repeat copy number has been observed in a tandem-repeat region in the seventh factor-VII intron.

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Ohno K, Suzuki K. Department of Neurology, University of North Carolina School of Medicine, Chapel Hill 27599.
A splicing defect due to an exon-intron junctional mutation results in abnormal beta-hexosaminidase alpha chain mRNAs in Ashkenazi Jewish patients with Tay-Sachs disease.

Abnormal beta-hexosaminidase alpha chain mRNAs from an Ashkenazi Jewish patient with the classical infantile Tay-Sachs disease contained intact or truncated intron 12 sequences. Sequence analysis showed a single nucleotide transversion at the 5' donor site of intron 12 from the normal G to C. This provides the first evidence that this junctional mutation, also found independently in two other laboratories by analysis of genomic clones, results in functional abnormality. Analysis with normal and mutant oligonucleotides as probes indicated that our patient was a compound heterozygote with only one allele having the transversion. The patient studied in the other two laboratories was also a compound heterozygote. Another Ashkenazi Jewish patient was normal in this region in both alleles. Thus, the splicing defect is the underlying genetic cause in some but not all Ashkenazi Jewish patients with Tay-Sachs disease.

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Old JM, Heath C, Fitches A, Thein SL, Jeffreys AJ, Petrou M, Modell B, Weatherall DJ.
Meiotic recombination between two polymorphic restriction sites within the beta globin gene cluster.

Analysis of beta globin gene haplotypes for prenatal diagnosis of beta thalassaemia has revealed a recombination event within the beta globin gene cluster. Both a change in the AvaII polymorphic site within the beta globin gene and a change in the phenotype of the beta globin gene were observed. Paternity was established by the pedigree analysis of hypervariable 'minisatellite' DNA polymorphisms and the most probable explanation of the recombination event is a crossover between the psi beta globin gene and the beta globin gene. The data provide direct evidence in support of a DNA region 3' to the beta globin gene with a recombination frequency much higher than expected, and have important implications for the prenatal diagnosis of beta thalassaemia by linked restriction fragment length polymorphisms.

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Olson M, Hood L, Cantor C, Botstein D. Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110.

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Orkin SH, Kazazian HH Jr, Antonarakis SE, Goff SC, Boehm CD, Sexton JP, Waber PG, Giardina PJ.

Linkage of beta-thalassaemia mutations and beta-globin gene polymorphisms with DNA polymorphisms in human beta-globin gene cluster.

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Orkin SH, Kazazian HH Jr, Antonarakis SE, Ostrer H, Goff SC, Sexton JP.
Abnormal RNA processing due to the exon mutation of beta E-globin gene.

As is typical of all beta-thalassaemias, the erythroid cells of individuals with the variant haemoglobin E (alpha 2 beta 2(26Glu leads to Lys)) exhibit a quantitative deficiency in their content of beta-globin (in this case beta E-globin) and its messenger RNA2,3. To determine the molecular basis of this phenotype, we have investigated the structure and expression of cloned beta E-globin genes. We report here that the complete nucleotide sequence of a beta E-gene revealed the expected GAG leads to AAG change in codon 26 but no other mutations. Expression of beta E-globin genes introduced into HeLa cells revealed two abnormalities of RNA processing: slow excision of intervening sequence-1 (IVS-1) and alternative splicing into exon-1 at a cryptic donor sequence within which the codon 26 nucleotide substitution resides. These results demonstrate a disturbance in the expression of the beta E-gene attributable solely to the exon mutation-a novel mechanism for gene dysfunction.

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Thalassemia due to a mutation in the cleavage-polyadenylation signal of the human beta-globin gene.

A beta-globin gene cloned from a person with beta-thalassemia contained a T----C substitution within the conserved sequence AATAAA that forms a portion of the recognition signal for endonucleolytic cleavage and polyadenylation of primary mRNA transcripts. By Northern blot analysis a novel beta-globin RNA species, 1500 nucleotides in length, was detected in erythroid RNA. Nuclease protection studies of erythroid RNA, as well as RNA generated upon transient expression of the cloned mutant gene in HeLa cells, located the 3' terminus of this novel, polyadenylated RNA 900 nucleotides downstream of the normal poly(A) addition site, within 15 nucleotides of the first AATAAA in the 3'-flanking region of the beta-globin gene. These findings define the in vivo terminus of an elongated RNA and establish that human beta-globin transcription may extend at least 900 nucleotides 3' of the normal polyadenylation site.

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Palsdottir A, Fossdal R, Arnason A, Edwards JH, Jensson O.
Heterogeneity of human C4 gene size. A large intron (6.5 kb) is present in all C4A genes and some C4B genes.

In this article we present a study showing that the human C4 genes differ in length because of the presence or absence of a 6.5 kb intron near the 5' end of the gene. DNA from individuals of known HLA, factor B, and C4 haplotypes was analyzed for restriction fragment length polymorphism (RFLP) by Southern blot analysis with C4-specific cDNA probes. The RFLP patterns obtained showed that the C4 genes are either 22.5 kb or 16 kb in length. They are referred to as long and short C4 genes, respectively. A population study was carried out to examine the distribution of the gene size according to C4 allotypes and haplotypes. Long C4 genes included all C4A genes studied and also some C4B allotypes, e.g., B1 on most C4 A3B1 haplotypes. Similarly, C4B null genes were found to be of the long form. Other C4B allotypes tested were found to be coded for by short C4 genes, including B2, B1 in C4 A6B1 and C4 AQOB1 (with a single C4B gene haplotype).

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Paolella G, Santamaria R, Buono P, Salvatore F. Istituto di Scienze Biochimiche, II Facolta di Medicina e Chirurgia, Universita degli Studi di Napoli, Italy.
Mapping of a restriction fragment length polymorphism within the human aldolase B gene.

Peripheral blood DNA was hybridized to the full-length cDNA and the cloned structural gene of human aldolase B. With PvuII endonuclease a restriction fragment length polymorphism was detected that was present in the heterozygous state in about 21% of the individuals tested. A map of the human aldolase gene was constructed for the two groups of individuals found to produce different fragments after PvuII digestion. This allowed the localization of the polymorphic site within the gene, which was found to be due to the loss of a PvuII site in the last intron upstream from the 3' end. This polymorphism may be used as a genetic marker to study individuals affected by hereditary fructose intolerance.

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Parker R, Siliciano PG, Guthrie C.
Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA.

The U2 snRNP binds to the site of branch formation during splicing of mammalian pre-mRNA in vitro. In Saccharomyces cerevisiae the branch site is within the so-called TACTAAC box (UACUAAC box), an absolutely conserved intron sequence required for splicing. Based on the identification and sequence of a U2 analogue in yeast, a specific base pairing interaction between the UACUAAC box and a highly conserved region of this snRNA can be proposed. To test this hypothesis, we have taken advantage of two mutations constructed previously in the UACUAAC box of an actin-HIS4 fusion. These mutant strains were transformed with stable plasmids bearing U2-like snRNAs into which changes predicted to restore base pairing had been introduced. Allele-specific suppression of biological and biochemical phenotypes was observed in both cases. Recognition of the UACUAAC box thus relies, at least in part, on Watson-Crick base pairing with the yeast U2 analogue.

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Patterson M, Gitschier J, Bloomfield J, Bell M, Dorkins H, Froster-Iskenius U, Sommer S, Sobell J, Schaid D, Thibodeau S, et al. Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford, England.

An intronic region within the human factor VIII gene is duplicated within Xq28 and is homologous to the polymorphic locus DXS115 (767).
Am J Hum Genet. 1989 May: 44(5): 679-85.

The genomic sequences recognized by the anonymous probe 767 (DXS115) are localized to two sites within Xq28. One site lies within intron 22 of the factor VIII gene (FBC). Physical mapping suggests that the second site lies within 1.2 megabases of the F8C gene. The RFLPs detected by 767 are located within the second site. Genetic data suggest that F8C and DXS115 are tightly linked (theta max = .04; Zmax = 8.30). Recombination events in meioses informative for DXS52 (St14), DXS115, and F8C suggest that DXS115 and F8C lie distal to DXS52.

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Paul H, Galton D, Stocks J.
DNA polymorphic patterns and haplotype arrangements of the apo A-1, apo C-III, apo A-IV gene cluster in different ethnic groups.
Hum Genet. 1987 Mar: 75(3): 264-8.

The allelic frequency of five different restriction fragment length polymorphisms (RFLPs) in the A-1, C-III, A-IV gene region has been determined in Caucasians, Negroes, Indian Asians, and Japanese. The polymorphic sites are with Taq-1 at the 5' end of the A-1 gene, with Msp-1 in the third intron of the A-1 gene, with Pst-1 in the intergenic sequence between the A-1 and C-III genes, with Sst-1 in the 3' non-coding region of the C-III gene, and with Pvu-II in the third intron of the C-III gene. The alleles identified by three of the RFLPs showed large differences in frequency amongst the races, especially between Caucasians and non-Caucasians. Alleles of the Msp-1 polymorphism and Sst-1 polymorphism, which were rare in Caucasians (frequencies 0.03 and 0.01), were more common in Japanese (frequencies 0.37 and 0.35), Indian Asians (frequencies 0.37 and 0.26), and Negroes (frequencies 0.31 and 0.31). In contrast with a Pvu-II polymorphism one allele was rare in Japanese and in Indian Asians (frequency 0.01) but more common in Caucasians (frequency 0.11). Linkage disequilibrium was evident between some of the alleles and a total of seven haplotypes were identified among the different races.

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Peake IR, Bowen D, Bignell P, Liddell MB, Sadler JE, Standen G, Bloom AL. Department of Haematology, University of Wales College of Medicine, Cardiff, UK.
Family studies and prenatal diagnosis in severe von Willebrand disease by polymerase chain reaction amplification of a variable number tandem repeat region of the von Willebrand factor gene.

We have previously demonstrated within intron 40 of the von Willebrand factor (vWF) gene a region of ATCT repeats that was shown to vary in length between two different DNA clones from unrelated individuals. The polymerase chain reaction (PCR) was used to examine the variability in length of this variable number tandem repeat (VNTR) in 53 normal individuals, using primers to DNA sequence flanking the repeat region. Overall, eight different length allelic bands were seen. These were individually sequenced and shown to contain from 6 to 14 ATCT repeats (a nine-repeat band was not seen). Seventy-five percent of individuals were shown to be heterozygous for this vWF.VNTR, and family studies showed Mendelian inheritance with allelic frequencies from 1% (vWF.VNTR [8] and vWF.VNTR [14]) to 39% (vWF.VNTR [7]). In the family of a patient with type III severe von Willebrand disease (vWD), vWF.VNTR results mirrored the phenotypic data and results with previously reported intragenic vWF restriction fragment length polymorphisms (RFLP). The patient was shown to be a compound heterozygote. In a family with a child with severe type III vWD, prenatal diagnosis by vWF.VNTR analysis on DNA obtained by chorionic villus sampling at 10 weeks gestation during a subsequent pregnancy indicated a severely affected fetus. This diagnosis was confirmed by fetal blood sampling at 18 weeks.

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Petersen MB, Economou EP, Slaugenhaupt SA, Chakravarti A, Antonarakis SE. Center for Medical Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205.
Linkage analysis of the human HMG14 gene on chromosome 21 using a GT dinucleotide repeat as polymorphic marker.

A (GT)n repeat in intron 4 of the functional human HMG14 gene on chromosome 21 was used as polymorphic marker to map this gene relative to the genetic linkage map of human chromosome 21. Variation in the length of the (GT)n repeat was detected by electrophoresis on polyacrylamide gels of DNA amplified by the polymerase chain reaction using primers flanking the repeat. The observed heterozygosity of this polymorphism in 40 CEPH families was 58% with six different alleles. Linkage analysis localized the HMG14 gene close to the ETS2 gene and locus D21S3 in chromosomal band 21q22.3.

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Prenatal diagnosis of sickle cell anemia by restriction and endonuclease analysis: HindIII polymorphisms in gamma-globin genes extend test applicability.
Proc Natl Acad Sci U S A. 1980 May;77(5):2853-6.

Polymorphism for a Hpa I restriction endonuclease site associated with about 60% of beta S genes in American Blacks allows exact prenatal diagnosis of sickle cell anemia by amniocentesis in 36% of couples at risk. In three families in whom exact diagnosis by Hpa I sites was impossible, we found analysis for the presence of polymorphic HindIII sites in the G gamma and A gamma intervening sequences would allow an exact prenatal diagnosis of sickle cell status in all three. In one of these families, the presence of an A gamma HindIII site in amniocyte DNA confirmed the diagnosis (sickle cell trait) made by synthetic studies using fetal erythrocytes obtained at fetoscopy. Studies of other Black families and individuals provide evidence for linkage disequilibrium in the G gamma-A gamma-delta-beta gene complex involving the four sites, G gamma HindIII, A gamma HindIII, beta S, and Hpa I, which span 33 kilobases (kb). Ten of 14 chromosomes bearing a beta S gene in a 7.6-kb Hpa I fragment contained a G gamma but not an A gamma HindIII site, whereas 16 of 16 chromosomes bearing a beta S gene in a 13-kb Hpa I fragment lacked both the G gamma and A gamma HindIII sites. Two-thirds of beta A-bearing chromosomes lacked both G gamma and A gamma sites, whereas one-third contained either the G gamma or both G gamma and A gamma sites. These data demonstrate that combined analysis of both Hpa I and HindIII polymorphisms and verification of their linkage phase should increase the fraction of couples for whom amniocentesis can provide an exact diagnosis of sickle cell status from 36% to greater than 80%.

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Philipsen JN, de Vries JE, Samallo J, van Dijk C, Arnberg AC, AB G. Laboratory of Biochemistry, Groningen, The Netherlands.
Characterization of a polymorphism in the 3' part of the chicken vitellogenin gene.

An allele giving rise to a polymorphism within the 3' part of the chicken vitellogenin gene was cloned, sequenced, and compared to the previously cloned allele. The polymorphism is formed by a perfect copy of 343 bp from intron 32 in tandem array with a perfect copy of 244 bp from intron 33; this 587-bp element is inserted in a head-to-tail arrangement in intron 33. We propose a mechanism in which an unequal crossing-over resulted in a vitellogenin gene with two exons 33, one of which was subsequently deleted. Thus, intron 33 was enlarged by the tandem repeats without affecting the protein-encoding sequence of the gene. At the boundaries of the repeated elements, two short direct repeats are found that resemble the recombination signals of immunoglobulin genes. They may have had a key role in the formation of the new allele.

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Pietu G, Thomas-Maison N, Sie P, Larrieu MJ, Meyer D. INSERM U. 143, Hopital de Bicetre, Le Kremlin-Bicetre, France.
Haemophilia A in a female: study of a family using intragenic and extragenic restriction site polymorphisms.

Restriction fragment length polymorphisms (RFLPs) were studied in a large Algerian family which includes 6 haemophiliacs and a previously described case of female haemophilia A. The female propositus is 66 years old with a normal karyotype. Her parents are first cousins. Her 3 sons are haemophiliacs and her 3 daughters with affected children are obligate carriers. The proband has an excessive bleeding tendency and markedly reduced levels of F.VIII (VIII C 0.03 U/ml, VIII Ag 0.01 U/ml) with elevated vWF Ag (2.30 U/ml), similar to the levels observed in affected males from the family. Four RFLPs can be identified by Southern blotting after digesting genomic DNA with the restriction enzymes Bcl I, Bgl I, Kpn I/Xba I and Taq I and hybridization with a 647 bp Stu I/Sca I F.VIII genomic probe, a 1.8 Kb EcoRI F.VIII cDNA probe, a 1.0 Kb EcoRI/Sst I fragment of intron 22 and the extragenic probe ST 14, respectively. With these four RFLPs, the propositus was found to be homozygous for the alleles segregating in this family with the abnormal X-chromosome. The carrier status was proven in a granddaughter and excluded in another. In conclusion, this RFLP linkage analysis is another argument to suggest that the propositus, a rare case of female haemophilia, is homozygous for the abnormal gene.

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Poncz M, Schwartz E, Ballantine M, Surrey S.
Nucleotide sequence analysis of the delta beta-globin gene region in humans.
J Biol Chem. 1983 Oct 10: 258(19): 11599-609.

The continuous DNA sequence of a 16.5-kilobase pair region encompassing the linked delta beta-globin gene cluster in humans is presented with a detailed restriction endonuclease map. There are 38 differences (0.5%) in comparison with published sequence data, corrected for errors in sequencing, resulting in polymorphic rates of 0.2% in exons and 0.76% in 5'-gene flanking regions. Fifteen changes result in the generation or elimination of restriction sites which may be useful in linkage disequilibrium studies. Two pairs of inverted Alu repeats, a pyrimidine-rich region 5' to delta, and (TG)n, (Pu/Py)n, and (ATTTT)n tracts 5' to beta are described. Dinucleotide frequencies and deviation from expected values approximated those found in total human genomic DNA. Regions of less than 50% A + T content were found associated with Alu sequences, a 150-base pair region immediately 5' to the beta gene, exon regions from both genes, and an area 3' to the beta gene. These regions also contained significantly lower than expected CpG levels compared to other regions, suggesting a possible relationship between DNA organizational patterns and functionally important regions. In addition, strand asymmetries in base composition in this region differ from those associated with the fetal globin genes.

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Potter H, Dressler D.
A 'Southern Cross' method for the analysis of genome organization and the localization of transcription units.

A 'Southern Cross' hybridization method is described which permits the rapid restriction mapping of DNA molecules, up to 40 kb in size, for at least ten enzymes in a single operation. The procedure allows the full set of 32P-end-labelled fragments derived from one restriction enzyme digest to intersect and attempt to hybridize to the gel-separated fragments of as many as ten unlabelled digests immobilized on parallel sheets of filter paper. A two-dimensional array of hybridization spots is revealed on each recipient paper, indicating which radioactive and non-radioactive DNA fragments have sequences in common. A restriction map can then be directly and simply deduced from the matrix of hybridization spots in each cross-blot. The method affords advantages over other procedures for obtaining restriction maps in terms of the time required, the number of restriction enzymes that can be mapped, and the potential for eliminating ambiguity. It is also sufficiently sensitive to detect DNA rearrangements and restriction-site polymorphisms in moderately complex genomes. Furthermore, the procedure is applicable to other aspects of the study of genome organization: for example, the exon and intron areas of a segment of cloned genomic DNA can be identified by cross-hybridizing a set of radioactive restriction fragments from the genomic clone against immobilized RNA from a cell type of interest.

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Quirk SM, Bell-Pedersen D, Belfort M. Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany 12201-0509.
Intron mobility in the T-even phages: high frequency inheritance of group I introns promoted by intron open reading frames.
Cell. 1989 Feb 10: 56(3): 455-65.

Intron mobility in the T-even phages has been demonstrated. Efficient nonreciprocal conversion of intron minus (In-) alleles to intron plus (In+) occurred for the td and sunY genes, but not for nrdB. Conversion to In+ was absolutely dependent on expression of the respective intron open reading frame (ORF). Introns were inserted at their cognate sites in an intronless phage genome via an RNA-independent, DNA-based, duplicative recombination event that was stimulated by exon homology. The td intron ORF product directs the endonucleolytic cleavage of DNA, targeting the site of intron integration. A 21 nucleotide deletion of the integration site abolished high frequency intron inheritance. These experiments provide a novel example of gene conversion in prokaryotes, while suggesting a molecular rationale for the inconsistent distribution of introns within highly conserved exon contexts of the T-even phage genomes.

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Quirk SM, Bell-Pedersen D, Tomaschewski J, Ruger W, Belfort M. New York State Department of Health, Wadsworth Center for Laboratories and Research, Albany 12201.
The inconsistent distribution of introns in the T-even phages indicates recent genetic exchanges.

Group I self-splicing introns are present in the td, nrdB and sunY genes of bacteriophage T4. We previously reported that whereas the td intron is present in T2, T4 and T6, the nrdB intron is present in T4 only. These studies, which argue in favor of introns as mobile genetic elements, have been extended by defining the distribution of all three T4 introns in a more comprehensive collection of T2, T4 and T6 isolates. The three major findings are as follows: First, all three introns are inconsistently distributed throughout the T-even phage family. Second, different T2 isolates have different intron complements, with T2H and T2L having no detectable introns. Third, the intron open reading frames are inherited or lost as a unit with their respective flanking intron core elements. Furthermore, exon sequences flanking sites where introns are inserted in the T4 td, sunY and nrdB genes were determined for all the different T-even isolates studied. Six of eighteen residues surrounding the junction sequences are identical. In contrast, a comprehensive comparison of exon sequences in intron plus and intron minus variants of the sunY gene indicate that sequence changes are concentrated around the site of intron occurrence. This apparent paradox may be resolved by hypothesizing that the recombination events responsible for intron acquisition or loss require a consensus sequence, while these same events result in sequence heterogeneity around the site.

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Ragusa A, Lombardo M, Bouhassira E, Beldjord C, Lombardo T, Nagel RL, Labie D, Krishnamoorthy R. INSERM, Paris.
Nucleotide variations in the 3' A gamma enhancer region are linked to beta-gene cluster haplotypes and are unrelated to fetal hemoglobin expression.

Molecular cloning and sequence analysis of a nondeletion form of Sicilian beta o hereditary persistence of fetal hemoglobinemia (HPFH) (mutation in IVS2 nt1 position) homozygous for haplotype III revealed the presence of four sequence variations: C----T at -158 5' to G gamma, T----C at +2285, C----A at +2476, and A----G at +2676, all 3' to A gamma. The latter three variations in the putative A gamma enhancer are identical to those observed in the case of Seattle HPFH. However, a severe beta o-thalassemia case from Algeria (mutation in IVS1 nt1 position), also homozygous for haplotype III, revealed the same nucleotide variation, albeit an inefficient HbF production. We conclude that the variations in the A gamma enhancer element do not play a role in the regulation of HbF production. To assess both the linkage of these sites with the beta-cluster haplotype and the extent of the polymorphism, we examined several black and Mediterranean chromosomes, by PCR amplification followed by both EspI digestion and oligonucleotide hybridization. Our data indicate that these sequence variations in the enhancer element are absent in Mediterranean haplotypes I, V, and VII but are consistently associated with Mediterranean haplotypes II, III, and IX, as well as with the black beta c-associated haplotype. The common feature of all the latter haplotypes is the presence of a polymorphic PvuII site between A gamma and psi beta, which is thus in linkage disequilibrium with the variations in the A gamma enhancer.

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Rathbun GA, Born W, Kuziel WA, Tucker PW. Department of Microbiology, University of Texas Health Science Center, Dallas 75235.
Diversity of the mouse T cell receptor C gamma 1 gene: structural analysis in C57BL/Ka.

We have isolated an unusual T cell receptor gamma chain cDNA clone (gamma 7.1) from a library made from RNA derived from adult thymus of C57BL/Ka mice. This cDNA clone corresponds to the appropriately processed C gamma 1 constant region exons preceded by 1.5 kb of J-C gamma 1 intron. The gamma 7.1 coding region is extremely homologous to the C gamma 1 gene of BALB/c mice, differing at the protein level by a single deletion (alanine 139) and a single substitution. This latter change eliminates the sole N-linked sugar attachment site, providing a basis for strain-specific glycosylation patterns. The J-C gamma 1 intronic region contains two DNA segments (termed psi J gamma 1 and psi J gamma 2) that are highly reminiscent of joining (J) segments; both have potentially functional recombination and donor splice sequences flanking an open reading frame. Northern analysis suggests that gamma 7.1 may be derived from a large, variable region-containing precursor.

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Raulf F, Robertson SM, Schartl M. Genecenter, Max-Planck-Institute for Biochemistry, Munich-Martinsried, Federal Republic of Germany.
Evolution of the neuron-specific alternative splicing product of the c-src proto-oncogene.
J Neurosci Res. 1989 Sep: 24(1): 81-8.

The observation of a slower migrating form of pp60c-src in neural tissue of chicken and mouse has recently been shown to be due to an alternative transcript form of the c-src gene (Martinez et al.: Science 237:411-415, 1987; Levy et al.: Mol Cell Biol 7:4142-4145, 1987). An insertion of 18 basepairs between exons 3 and 4, presumed to be due to alternative splicing of a mini-exon, gives rise to six amino acid residues not found in the non-neuronal (termed fibroblastic) form of pp60c-src. We have addressed the question of the evolutionary origin of the c-src neuronal insert and its functional significance regarding neural-specific expression of the c-src gene. To this end we have investigated whether the c-src gene of a lower vertebrate (the teleost fish Xiphophorus) gives rise to a neural-specific transcript in an analogous manner. We could show that the fish c-src gene does encode for a "fibroblastic" and a "neuronal" form of transcript and that the neuronal transcript does indeed arise by way of alternative splicing of a mini-exon. The mini-exon is also 18 basepairs long and we could demonstrate directly that this exon lies within the intron separating exons 3 and 4. For comparative purposes we have examined whether the fish c-yes gene, the member of the src gene family most closely related to c-src, also encodes a neural tissue-specific transcript. No evidence for a second transcript form in brain was obtained.

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Rees A, Stocks J, Paul H, Ohuchi Y, Galton D.
Haplotypes identified by DNA polymorphisms at the apolipoprotein A-1 and C-III loci and hypertriglyceridaemia. A study in a Japanese population.

A Japanese group comprising 40 hypertriglyceridaemic and 35 normolipidaemic subjects were genotyped for two intragenic DNA restriction fragment length polymorphisms (RFLPs) at the A-1 and C-III gene loci. An Sst-1 polymorphism is located at the 3' end of the C-III gene and a Msp-1 polymorphism in the third intron of the A-1 gene. The polymorphic restriction sites are 3.8kb apart. The polymorphism with Sst-1 was present at allelic frequencies of 0.67 (S1 allele) and 0.33 (S2 allele), and the polymorphism with Msp-1 was present at allelic frequencies of 0.55 (M1 allele) and 0.45 (M2 allele). The alleles S1, S2, M1, and M2 are in linkage disequilibrium and three haplotypes were identified S1-M1, S1-M2, and S2-M2. Unlike the previously reported association of the S2 allele with hypertriglyceridaemia found in Caucasians there was no difference in the frequency of S2 allele between normolipidaemic and hyperlipidaemic Japanese. However one of the haplotypes S1-M2 was significantly increased in the hypertriglyceridaemic subjects (32% versus 11% P less than 0.025). Thu