Summary
In order to facilitate the screening for the less common mutations in the cystic fibrosis (CF) gene viz., the CF transmembrane conductance regulator gene (CFTR), marker haplotypes were determined for German nonCF (N) and CF chromosomes by polymerase chain reaction analysis of four polymorphisms upstream of the CF gene (XV-2c, KM.19, MP6-D9, J44) and six intragenic polymorphisms (GATT, TUB9, M470V, T854T, TUB18, TUB20) that span the CFTR gene from exon 6 through exon 21. Novel informative sequence variants of CFTR were detected in front of exons 10 (1525-61 A or G), 19 (3601-65 C or A), and 21 (4006-200 A or G). The CF locus exhibits strong long-range marker-marker linkage disequilibrium with breakpoints of recombination between XV-2c and KM.19, and between exons 10 and 19 of CFTR. Marker alleles of GATT-TUB9 and TUB18-TUB20 were found to be in absolute linkage disequilibrium. Four major haplotypes encompass more than 90% of German N and CF chromosomes. Fifteen CFTR mutations detected on 421 out of 500 CF chromosomes were each identified on one of these four predominant 7-marker haplotypes. Whereas all analysed ΔF508 chromosomes carried the same KM.19-D9-J44-GATT-TUB9-M470V-T854T haplotype, another frequent mutation in Germany, R553X, was identified on two different major haplotypes. Hence, a priori haplotyping cannot exclude a particular CF mutation, but in combination with population genetic data, enables mutations to be ranked by decreasing probability.
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Chehab EF, Johnson J, Louie E, Goossens M, Kawasaki E, Erlich H (1991) A dimorphic 4-bp repeat in the cystic fibrosis gene is in absolute linkage disequilibrium with the ΔF508 mutation: implications for prenatal diagnosis and mutation origin. Am J Hum Genet 48:223–226
Cooper DN, Krawczak M (1990) The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions. Hum Genet 85:55–74
Cutting GR, Kasch LM, Rosenstein BJ, Zielenski J, Tsui L-C, Antonarakis SE, Kazazian HH Jr (1990) A cluster of cystic fibrosis mutations in the first nucleotide-binding fold of the cystic fibrosis conductance regulator protein. Nature 346:366–368
Dean M, Drumm ML, Stewart C, Gerrard B, Perry A, Hidaka N, Cole JL, Collins FS, Iannuzzi MC (1990a) Approaches to localizing disease genes as applied to cystic fibrosis. Nucleic Acids Res 18:345–350
Dean M, White M, Amos J, Gerrard B, Stewart C, Khaw K-T, Leppert M (1990b) Multiple mutations in highly conserved residues are found in mildly affected cystic fibrosis patients. Cell 61:863–870
Devoto M, Ronchetto P, Fanen P, Orriols JJT, Romeo G, Goossens M, Ferrari M, Magnani C, Seia M, Cremonesi L (1991) Screening for non-delta F508 mutations in five exons of the cystic fibrosis conductance regulator (CFTR) gene in Italy. Am J Hum Genet 48:1127–1132
Dörk T, Wulbrand U, Tümmler B (1991) A Hinf1 polymorphism in the cystic fibrosis gene CFTR. Nucleic Acids Res 19:2517
European Working Group on CF Genetics (EWGCFG) (1990) Gradient of distribution in Europe of the major CF mutation and of its associated haplotype. Hum Genet 85:436–445
Gait MT (1986) Oligonucleotide synthesis: a practical approach. IRL Press, Oxford, UK
Gasparini P, Dognini M, Bonizzato A, Pignatti PF, Morral N, Estivill X (1991a) A tetranucleotide repeat polymorphism in the cystic fibrosis gene. Hum Genet 86:625
Gasparini P, Nunes V, Savoia A, Dognini M, Morral N, Gaona A, Bonizzato A, Chillon M, Sangiuolo F, Novelli G, Dallapiccola B, Pignatti PF, Estivill X (1991b) The search for South European cystic fibrosis mutations: identification of two new mutations, four variants, and intronic sequences. Genomics 10:193–200
Giannelli F, Green PM, High KA, Lozier JN, Lillicrap DP, Ludwig M, Olek K, Reitsma PH, Goossens M, Yoshioka A, Sommer S, Brownlee GG (1990) Haemophilia B: database of point mutations and short additions and deletions. Nucleic Acids Res 18:4053–4059
Gross-Bellard M, Dudet P, Chambon P (1973) Isolation of high-molecular-weight DNA from mammalian cells. Eur J Biochem 36:32–38
Guillermit H, Fanen P, Ferec C (1990) A 3′ splice site consensus sequence mutation in the cystic fibrosis gene. Hum Genet 85:450–453
Gyllenstein UB, Erlich HA (1988) Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc Natl Acad Sci USA 85:7652–7656
Haliassos A, Chomel JC, Tesson L, Baudis M, Kruh J, Kaplan JC, Kitzis A (1989) Modification of enzymatically amplified DNA for the detection of point mutations. Nucleic Acids Res 17:3606
Highsmith WE Jr, Strong T, Burch N, Smith T, Silverman LM, Collins FS, Boucher R, Knowles MR (1990) Identification of a splicing error of exon 14b giving rise to a frameshift mutation in a consanguineous family with mild cystic fibrosis. Pediatr Pulmonol [Suppl] 5:11A
Horn GT, Richards B, Merrill JJ, Klinger KW (1990) Characterization and rapid diagnostic analysis of DNA polymorphisms closely linked to the cystic fibrosis locus. Clin Chem 36:1614–1619
Huth A, Estivill X, Grade K, Billwitz H, Speer A, Rosenthal A, Williamson R, Ramsay M, Coutelle C (1989) Polymerase chain reaction for detection of the pMP6d-9/MypI RFLP, a marker closely linked to the cystic fibrosis mutation. Nucleic Acids Res 17:7118
Hyde SC, Emsley P. Hartshorn MJ, Mimmack MM, Gileadi U, Pearce SR, Gallagher MP, Gill DR, Hubbard RE, Higgins CF (1990) Structural model of ATP-binding proteins associated with cystic fibrosis, multidrug resistance and bacterial transport. Nature 346:362–365
Kerem BS, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui L-C (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245:1073–1080
Kerem B, Zielenski J, Markiewicz D, Bozon D, Gazit E, Yahaf J, Kennedy D, Riordan JR, Collins FS, Rommens JM, Tsui L-C (1990) Identification of mutations in regions corresponding to the two putative nucleotide (ATP-)binding folds of the cystic fibrosis gene. Proc Natl Acad Sci USA 87:8447–8451
Klinger KW, Stanislovitis P, Merril J, Horn GT (1991) Molecular and genetic analysis at the CF locus. Adv Exp Med Biol 290:39–43
Kobayashi K, Knowles M, O'Brien WE, Beaudet AL (1990) Benign missense variations in the cystic fibrosis gene. Am J Hum Genet 47:611–615
Krawczak M, Konecki DS, Schmidtke J, Dück M, Engel W, Nützenadel W, Trefz FK (1988) Allelic association of the cystic fibrosis locus and two DNA markers, XV2c and KM19, in 55 German families. Hum Genet 80:78–80
Orita M, Suzuki Y, Sekiya T, Hayashi K (1989) Rapid and sensitive detection of point mutations and DNA polymorphisms using the polymerase chain reaction. Genomics 5:874–879
Osborne L, Knight RA, Santis G, Hodson M (1991) A mutation in the second nucleotide binding fold of the cystic fibrosis gene. Am J Hum Genet 48:608–612
Quere I, Guillermit H, Mercier B, Audrezet MP, Ferec C (1991) A polymorphism in intron 20 of the CFTR gene. Nucleic Acids Res 19:5453
Reis A, Bremer S, Schlösser M, Dueck M, Böhm I, Hundrieser J, Macek M, Stuhrmann M, Wagner M, Dörk T, Schnieders F, Posselt H-G, Wahn U, Reiss J, Trefz FK, Tümmler B, Krawczak M, Schmidtke J (1990) Distribution patterns of the ΔF508 mutation in the CFTR gene on CF-linked marker haplotypes in the German population. Hum Genet 85:421–422
Riordan JR, Rommens JM, Kerem BS, Alon N, Rozmahel R, Grzelczak Z, Zielenski J, Lok S, Plavsic N, Chou J-L, Drumm ML, Iannuzzi ML, Collins FS, Tsui L-C (1989) Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245:1066–1073
Rommens J, Iannuzzi MC, Kerem BS, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N, Zsiga M, Buchwald M, Riordan JR, Tsui L-C, Collins FS (1989) Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245:1059–1065
Rommens J, Kerem BS, Greer W, Chang P, Tsui L-C, Ray P (1990) Rapid nonradioactive detection of the major CF mutation. Am J Hum Genet 46:395–396
Rosenbaum V, Riesner D (1987) Temperature-gradient gel electrophoresis. Thermodynamic analysis of nucleic acids and proteins in purified form and in cellular extracts. Biophys Chem 26:235–246
Rosenbloom CL, Kerem BS, Rommens JM, Tsui L-C, Wainwright B, Williamson R, O'Brien WED, Beaudet AL (1989) DNA amplification for detection of the XV-2c polymorphism linked to cystic fibrosis. Nucleic Acids Res 17:7117
Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Vidaud M, Fanen P, Martin J, Ghanem N, Nicolas S, Goossens M (1990) Three mutations in the CFTR gene in French cystic fibrosis patients: identification by denaturing gradient gel electrophoresis. Hum Genet 85:446–449
Zielenski J, Rozmahel R, Bozon D, Kerem B-S, Grzelczak Z, Riordan JR, Rommens J, Tsui L-C (1991a) Genomic DNA sequences of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics 10:214–228
Zielenski J, Bozon D, Kerem B-S, Markiewicz D, Durie P, Rommens JM, Tsui L-C (1991b) Identification of mutations in exons 1 through 8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics 10:229–235
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Dörk, T., Neumann, T., Wulbrand, U. et al. Intra- and extragenic marker haplotypes of CFTR mutations in cystic fibrosis families. Hum Genet 88, 417–425 (1992). https://doi.org/10.1007/BF00215676
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DOI: https://doi.org/10.1007/BF00215676