Long-range (17.7 kb) allele-specific polymerase chain reaction method for direct haplotyping of R117H and IVS-8 mutations of the cystic fibrosis transmembrane regulator gene

Journal of Molecular Diagnostics

Volumn 6, Issue 3, 2004, Pages 264-270

  Pont Kingdon, Genevieve ^a   Jama, Mohamed ^a   Miller, Christine ^a   Millson, Alison ^a   Lyon, Elaine ^a,b  

^a ARUP LABORATORIES   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANS ACTING FACTOR; TRANSMEMBRANE CONDUCTANCE REGULATOR;

ALLELE; ARTICLE; CLINICAL LABORATORY; CONTROLLED STUDY; CYSTIC FIBROSIS; DIAGNOSTIC ACCURACY; EXON; FAMILY STUDY; GENE LOCUS; GENE MUTATION; GENETIC POLYMORPHISM; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HUMAN; HUMAN CELL; INTRON; MISSENSE MUTATION; PATHOGENESIS; PHENOTYPE; POLYMERASE CHAIN REACTION; PREDICTION; REPRODUCIBILITY;

EID: 4344652284     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1525-1578(10)60520-X     Document Type: Article

References (36)

1. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D: The structure of haplotype blocks in the human genome. Science 2002, 296:2225-2229
2. Martin ER, Lai EH, Gilbert JR, Rogala AR, Afshari AJ, Riley J, Finch KL, Stevens JF, Livak KJ, Slotterbeck ED, Slifer SH, Warren LL, Conneally PM, Schmechel DE, Purvis I, Pericak-Vance MA, Roses AD, Vance JM: SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. Am J Hum Genet 2000, 67:383-394
3. McCarthy JJ, Hilfiker R: The use of single-nucleotide polymorphism maps in pharmacogenomics. Nature Biotechnol 2000, 18:505-508
4. Lee JH, Choi JH, Namkung W, Hanrahan JW, Chang J, Song SY, Park SW, Kim DS, Yoon JH, Suh Y, Jang IJ, Nam JH, Kim SJ, Cho MO, Lee JE, Kim KH, Lee MG: A haplotype-based molecular analysis of CFTR mutations associated with respiratory and pancreatic diseases. Hum Mol Genet 2003, 12:2321-2332
5. Ding C, Cantor CR: Direct molecular haplotyping of long-range genomic DNA with M1-PCR. Proc Natl Acad Sci USA 2003, 100: 7449-7453
6. Eitan Y, Kashi Y: Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA). Nucleic Acids Res 2002, 30:e62
7. Lucarelli M, Grandoni F, Rossi T, Mazzilli F, Antonelli M, Strom R: Simultaneous cycle sequencing assessment of (TG)m and Tn tract length in CFTR gene. Biotechniques 2002, 32:540-542, 544-547
8. Mullighan CG, Marshall SE, Fanning GC, Briggs DC, Welsh KI: Rapid haplotyping of mutations in the Duffy gene using the polymerase chain reaction and sequence-specific primers. Tissue Antigens 1998, 51:195-199
9. Mullighan CG, Bunce M, Fanning GC, Marshall SE, Welsh KI: A rapid method of haplotyping HFE mutations and linkage disequilibrium in a Caucasoid population. Gut 1998, 42:566-569
10. Pettersson M, Bylund M, Alderborn A: Molecular haplotype determination using allele-specific PCR and pyrosequencing technology. Genomics 2003, 82:390-396
11. Ruano G, Kidd KK, Stephens JC: Haplotype of multiple polymorphisms resolved by enzymatic amplification of single DNA molecules. Proc Natl Acad Sci USA 1990, 87:6296-6300
12. Yan H, Papadopoulos N, Marra G, Perrera C, Jiricny J, Boland CR, Lynch HT, Chadwick RB, de la Chapelle A, Berg K, Eshleman JR, Yuan W, Markowitz S, Laken SJ, Lengauer C, Kinzler KW, Vogelstein B: Conversion of diplody to haploidy. Nature 2000, 403:723-724
13. Tost J, Brandt O, Boussicault F, Derbala D, Caloustian C, Lechner D, Gut IG: Molecular haplotyping at high throughput. Nucleic Acids Res 2002, 30:e96
14. Ruano G, Kidd KK: Direct haplotyping of chromosomal segments from multiple heterozygotes via allele-specific PCR amplification. Nucleic Acids Res 1989, 17:8392
15. McDonald OG, Krynetski EY, Evans WE: Molecular haplotyping of genomic DNA for multiple single-nucleotide polymorphisms located kilobases apart using long-range polymerase chain reaction and intramolecular ligation. Pharmacogenetics 2002, 12:93-99
16. Sheppard DN, Rich DP, Ostedgaard LS, Gregory RJ, Smith AE, Welsh MJ: Mutations in CFTR associated with mild-disease-form CI- channels with altered pore properties. Nature 1993, 362:160-164
17. Chu CS, Trapnell BC, Curristin S, Cutting GR, Crystal RG: Genetic basis of variable exon 9 skipping in cystic fibrosis transmembrane conductance regulator mRNA. Nat Genet 1993, 3:151-156
18. Niksic M, Romano M, Buratti E, Pagani F, Baralle FE: Functional analysis of cis-acting elements regulating the alternative splicing of human CFTR exon 9. Hum Mol Genet 1999, 8:2339-2349
19. Chu CS, Trapnell BC, Murtagh Jr JJ, Moss J, Dalemans W, Jallat S, Mercenier A, Pavirani A, Lecocq JP, Cutting GR: Variable deletion of exon 9 coding sequences in cystic fibrosis transmembrane conductance regulator gene mRNA transcripts in normal bronchial epithelium. EMBO J 1991, 10:1355-1363
20. Teng H, Jorissen M, Van Poppel H, Legius E, Cassiman JJ, Cuppens H: Increased proportion of exon 9 alternatively spliced CFTR transcripts in vas deferens compared with nasal epithelial cells. Hum Vol Genet 1997, 6:85-90
21. Manson A, Huxley C: Skipping of exon 9 of human CFTR in YAC-transgenic mice. Genomics 2001, 77:127-134
22. Noone PG, Pue CA, Zhou Z, Friedman KJ, Wakeling EL, Ganeshananthan M, Simon RH, Silverman LM, Knowles MR: Lung disease associated with the IVS8 5T allele of the CFTR gene. Am J Respir Crit Care Med 2000, 162:1919-1924
23. Rosenstein BJ, Cutting GR: The diagnosis of cystic fibrosis: a consensus statement. Cystic Fibrosis Foundation Consensus Panel. J Pediatr 1998, 132:589-595
24. Kiesewetter S, Macek Jr M, Davis C, Curristin SM, Chu CS, Graham C, Shrimpton AE, Cashman SM, Tsui LC, Mickle J, Amos J, Highsmith WE, Shuber A, Witt DR, Crystal RG, Cutting GR: A mutation in CFTR produces different phenotypes depending on chromosomal background. Nat Genet 1993, 5:274-278
25. Costes B, Girodon E, Ghanem N, Flori E, Jardin A, Soufir JC, Goossens M: Frequent occurrence of the CFTR intron 8 (TG)n 5T allele in men with congenital bilateral absence of the vas deferens. Eur J Hum Genet 1995, 3:285-293
26. Gervais R, Dumur V, Rigot JM, Lafitte JJ, Roussel P, Claustres M, Demaille J: High frequency of the R117H cystic fibrosis mutation in patients with congenital absence of the vas deferens. N Engl J Med 1993, 328:446-447
27. Friedman KJ, Heim RA, Knowles MR, Silverman LM: Rapid characterization of the variable length polythymidine tract in the cystic fibrosis (CFTR) gene: association of the 5T allele with selected CFTR mutations and its incidence in atypical sinopulmonary disease. Hum Mutat 1997, 10:108-115
28. Baron H, Fung S, Aydin A, Bahring S, Luft FC, Schuster H: Oligonucleotide ligation assay (OLA) for the diagnosis of familial hypercholesterolemia. Nature Biotechnol 1996, 14:1279-1282
29. Grody WW, Cutting GR, Klinger KW, Richards CS, Watson MS, Desnick RJ: Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genet Med 2001, 3:149-154
30. Cheng S, Fockler C, Barnes WM, Higuchi R: Effective amplification of long targets from cloned inserts and human genomic DNA. Proc Natl Acad Sci USA 1994, 91:5695-5699
31. Shrimpton AE: R117H and IVS8-5T cystic fibrosis mutation detection by restriction enzyme digestion. Mol Diagn 2000, 5:235-238
32. Woolley AT, Guillemette C, Li Cheung C, Housman DE, Lieber CM: Direct haplotyping of kilobase-size DNA using carbon nanotube probes. Nature Biotechnol 2000, 18:760-763
33. Tishkoff SA, Pakstis AJ, Ruano G, Kidd KK: The accuracy of statistical methods for estimation of haplotype frequencies: an example from the CD4 locus. Am J Hum Genet 2000, 67:518-522
34. Michalatos-Beloin S, Tishkoff SA, Bentley KL, Kidd KK, Ruano G: Molecular haplotyping of genetic markers 10 kb apart by allele-specific long-range PCR. Nucleic Acids Res 1996, 24:4841-4843
35. Cuppens H, Lin W, Jaspers M, Costes B, Teng H, Vankeerberghen A, Jorissen M, Droogmans G, Reynaert I, Goossens M, Nilius B, Cassiman JJ: Polyvariant mutant cystic fibrosis transmembrane conductance regulator genes: the polymorphic (Tg)m locus explains the partial penetrance of the T5 polymorphism as a disease mutation. J Clin Invest 1998, 101:487-496
36. Groman JD, Hefferon TW, Casals T, Bassas L, Estivill X, Des Georges M, Guittard C, Koudova M, Fallin MD, Nemeth K, Fekete G, Kadasi L, Friedman K, Schwarz M, Bombieri C, Pignatti PF, Kanavakis E, Tzetis M, Schwartz M, Novelli G, D'Apice MR, Sobczynska-Tomaszewska A, Bal J, Stuhrmann M, Macek Jr M, Claustres M, Cutting GR: Variation in a repeat sequence determines whether a common variant of the cystic fibrosis transmembrane conductance regulator gene is pathogenic or benign. Am J Hum Genet 2004, 74:176-179