Development of allele-specificmultiplex PCR to determine the length of poly-T in intron 8 of CFTR

PeerJ

Volumn 2014, Issue 1, 2014, Pages

  Chen, Neng ^a,b   Prada, Anne E ^a  

^a WILLIAM BEAUMONT HOSPITAL   (United States)

^b OAKLAND UNIVERSITY WILLIAM BEAUMONT SCHOOL OF MEDICINE   (United States)

Author keywords

CFTR; Multiplex allele specific PCR; Poly T analysis

Indexed keywords

EID: 84905968192     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.468     Document Type: Article

References (30)

1. Bayliffe AI, Docter E, Kelly SJ, Robertson NH. 2001. Assay for detection of human CFTR allele variants using specific diagnostic primers. WIPO Patent WO/2001/021833A2.
2. Bienvenu T, Beldjord C, Adjiman M, Kaplan JC. 1993. Male infertility as the only presenting sign of cystic fibrosis when homozygous for the mild mutation R117H. Journal of Medical Genetics 30:797.
3. Chen N, Schrijver I. 2011. Allelic discrimination of cis-trans relationships by digital polymerase chain reaction: GJB2 (p.V27I/p.E114G) and CFTR (p.R117H/5T). Genetics in Medicine 13:1025-1031.
4. Chiang HS, Lu JF, Liu CH,Wu YN,Wu CC. 2009. CFTR (TG)m(T)n polymorphism in patients with CBAVD in a population expressing low incidence of cystic fibrosis. Clinical Genetics 76:282-286.
5. Chillon M, Casals T,Mercier B, Bassas L, Lissens W, Silber S, Romey M-C, Ruiz-Romero J, Verlingue C, Claustres M, Nunes V, Férec C, Estivill X. 1995. Mutations in the cystic fibrosis gene in patients with congenital absence of the vas deferens. New England Journal of Medicine 332:1475-1480.
6. Chmiel JF, Drumm ML, Konstan MW, Ferkol TW, Kercsmar CM. 1999. Pitfall in the use of genotype analysis as the sole diagnostic criterion for cystic fibrosis. Pediatrics 103:823-826.
7. Chu CS, Trapnell BC, Curristin S, Cutting GR, Crystal RG. 1993. Genetic basis of variable exon 9 skipping in cystic fibrosis transmembrane conductance regulator mRNA. Nature Genetics 3:151-156.
8. Coriell Institute. 2009a. Catalog ID: GM18799. Available at http://ccr.coriell.org/Sections/Search/SampleDetail.aspx?Ref=GM18799&PgId=166 (accessed 05 February 2014).
9. Coriell Institute. 2009b. Catalog ID: GM18800. Available at http://ccr.coriell.org/Sections/Search/ Sample Detail.aspx?Ref=GM18800&PgId=166 (accessed 05 February 2014).
10. Costa C, Costa JM,Martin J, Boissier B, Goossens M, Girodon E. 2008. Multiplex allele-specific fluorescent PCR for haplotyping the IVS8 (TG)m(T)n locus in the CFTR gene. Clinical Chemistry 54:1564-1567.
11. Dean M, White MB, Amos J, Gerrard B, Stewart C, Khaw KT, Leppert M. 1990. Multiple mutations in highly conserved residues are found in mildly affected cystic fibrosis patients. Cell 61:863-870.
12. Elucigene Diagnostics. 2004. Product Insert for CF Poly T (Catalogue Code: PT003B2). Available at http://www.elucigene.com/docs/cf/lit/PolyT.pdf (accessed 3 June 2014).
13. Friedman KJ, Heim RA, Knowles MR, Silverman LM. 1997. 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. Human Mutation 10:108-115.
14. Grody WW, Cutting GR, Klinger KW, Richards CS,Watson MS, Desnick RJ, Subcommittee on Cystic Fibrosis Screening, Accreditation of Genetic Services Committee, ACMG. 2001. Laboratory standards and guidelines for population-based cystic fibrosis carrier screening. Genetics in Medicine 3:149-154.
15. Iain BA, Eelco D, James KS, Hastings RN. 2001. Assay for detection of human cftr allele variants using specific diagnostic primers. Publication number WO2001021833 A3.
16. Johnson MA, Yoshitomi MJ, Richards CS. 2007. A comparative study of five technologically diverse CFTR testing platforms. The Journal of Molecular Diagnostics 9:401-407.
17. Kozlov IA, Dang M, Sikes K, Kotseroglou T, Barker DL, Zhao C. 2005. Significant improvement of quality for long oligonucleotides by using controlled pore glass with large pores. Nucleosides, Nucleotides and Nucleic Acids 24:1037-1041.
18. Little S. 2001. Amplification-refractory mutation system (ARMS) analysis of point mutations. Current Protocols in Human Genetics Chapter 9:Unit 9.8.
19. Macek Jr M, Mackova A, Hamosh A, Hilman BC, Selden RF, Lucotte G, Friedman KJ, Knowles MR, Rosenstein BJ, Cutting GR. 1997. Identification of common cystic fibrosis mutations in African-Americans with cystic fibrosis increases the detection rate to 75%. American Journal of Human Genetics 60:1122-1127.
20. Mak V, Zielenski J, Tsui LC, Durie P, Zini A,Martin S, Longley TB, Jarvi KA. 1999. Proportion of cystic fibrosis gene mutations not detected by routine testing in men with obstructive azoospermia. Journal of the American Medical Association 281:2217-2224.
21. Millson A, Pont-Kingdon G, Page S, Lyon E. 2005. Direct molecular haplotyping of the IVS-8 poly(TG) and polyT repeat tracts in the cystic fibrosis gene by melting curve analysis of hybridization probes. Clinical Chemistry 51:1619-1623.
22. Moskowitz SM, Chmiel JF, Sternen DL, Cheng E, Cutting GR. 2008. CFTR-related disorders. In: Pagon R, Adam M, Bird T, Pagon RA, Adam MP, Ardinger HH, Bird TD, Dolan CR, Fong C-T, Smith RJH, Stephens K, eds. GeneReviewsTM[Internet]. Seattle, WA: University of Washington, Seattle. Available at http://www.ncbi.nlm.nih.gov/books/NBK1250/.
23. Pont-Kingdon G, Jama M,Miller C,Millson A, Lyon E. 2004. 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. The Journal of Molecular Diagnostics 6:264-270.
24. Rohlfs EM, Zhou Z, Heim RA, Nagan N, Rosenblum LS, Flynn K, Scholl T, Akmaev VR, Sirko-Osadsa DA, Allitto BA, Sugarman EA. 2011. Cystic fibrosis carrier testing in an ethnically diverse US population. Clinical Chemistry 57:841-848.
25. Saunders GC, Dukes J, Parkes HC, Cornett JH. 2001. Interlaboratory study on thermal cycler performance in controlled PCR and random amplified polymorphic DNA analyses. Clinical Chemistry 47:47-55.
26. Sebastian S, Spitzer SG, Grosso LE, Amos J, Schaefer FV, Lyon E,Wolff DJ, Hajianpour A, Taylor AK,Millson A, Stenzel TT. 2004. Multicenter characterization and validation of the intron-8 poly(T) tract (IVS8-T) status in 25 Coriell cell repository cystic fibrosis reference cell lines for cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation assays. Clinical Chemistry 50:251-254.
27. Sugarman EA, Rohlfs EM, Silverman LM, Allitto BA. 2004. CFTR mutation distribution among U.S. Hispanic and African American individuals: evaluation in cystic fibrosis patient and carrier screening populations. Genetics in Medicine 6:392-399.
28. Trujillano D, Ramos MD, Gonzalez J, Tornador C, Sotillo F, Escaramis G, Ossowski S, Armengol L, Casals T, Estivill X. 2013. Next generation diagnostics of cystic fibrosis and CFTR-related disorders by targeted multiplex high-coverage resequencing of CFTR. Journal of Medical Genetics 50:455-462.
29. Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S. 2007. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics 8:275.
30. Watson MS, Cutting GR, Desnick RJ, Driscoll DA, Klinger K,Mennuti M, Palomaki GE, Popovich BW, Pratt VM, Rohlfs EM, StromCM, Richards CS,Witt DR, Grody WW. 2004. Cystic fibrosis population carrier screening: 2004 revision of American College of Medical Genetics mutation panel. Genetics in Medicine 6:387-391.