Risk of misdiagnosis due to allele dropout and false-positive PCR artifacts in molecular diagnostics analysis of 30,769 genotypes

Journal of Molecular Diagnostics

Volumn 17, Issue 5, 2015, Pages 505-514

  Blais, Jonatan ^a   Lavoie, Sébastien B ^a   Giroux, Sylvie ^a   Bussières, Johanne ^a   Lindsay, Carmen ^a   Dionne, Jacqueline ^a   Laroche, Mélissa ^a   Giguère, Yves ^a,b   Rousseau, François ^a,b  

^a LAVAL UNIVERSITY   (Canada)

^b APOGEE Net CanGèneTest Research and Knowledge Network on Genetic Health Services and Policy   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; CFTR PROTEIN, HUMAN; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR;

ARTICLE; ARTIFACT; CLINICAL LABORATORY; CONTROLLED STUDY; DIAGNOSTIC ERROR; DNA STRAND; FALSE POSITIVE RESULT; GENE AMPLIFICATION; GENE MUTATION; GENETIC SCREENING; GENETIC VARIABILITY; GENOTYPE; HUMAN; INCIDENCE; MAJOR CLINICAL STUDY; MOLECULAR DIAGNOSIS; POLYMERASE CHAIN REACTION; RETROSPECTIVE STUDY; ALLELE; EVALUATION STUDY; GENETICS; GENOTYPING TECHNIQUE; HETEROZYGOSITY LOSS; LABORATORY DIAGNOSIS; PROCEDURES; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARDS; STATISTICS AND NUMERICAL DATA;

ALLELES; ARTIFACTS; CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR; DIAGNOSTIC ERRORS; FALSE POSITIVE REACTIONS; GENOTYPE; GENOTYPING TECHNIQUES; HUMANS; LOSS OF HETEROZYGOSITY; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS;

EID: 84946714790     PISSN: 15251578     EISSN: 19437811     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2015.04.004     Document Type: Article

References (29)

1. B.C. Lim, S. Lee, J.Y. Shin, H. Hwang, K.J. Kim, Y.S. Hwang, J.S. Seo, J.I. Kim, and J.H. Chae Molecular diagnosis of congenital muscular dystrophies with defective glycosylation of alpha-dystroglycan using next-generation sequencing technology Neuromuscul Disord 23 2013 337 344
2. F.M. de Souza Godinho, H. Bock, T.C. Gheno, and M.L. Saraiva-Pereira Molecular Analysis of Spinal Muscular Atrophy: a genotyping protocol based on TaqMan® real-time PCR Genet Mol Biol 35 2012 955 959
3. A. Didelot, D. Le Corre, A. Luscan, A. Cazes, K. Pallier, J.-F. Emile, P. Laurent-Puig, and H. Blons Competitive allele specific TaqMan PCR for KRAS, BRAF and EGFR mutation detection in clinical formalin fixed paraffin embedded samples Exp Mol Pathol 92 2012 275 280
4. J.L. Montgomery, L.N. Sanford, and C.T. Wittwer High-resolution DNA melting analysis in clinical research and diagnostics Expert Rev Mol Diagn 10 2010 219 240
5. E. Schulze, M. Bettendorf, C. Maser-Gluth, M. Decker, and U. Schwabe Allele-dropout using PCR-based diagnosis for the splicing mutation in intron-2 of the CYP21B-gene: successful amplification with a Taq/Pwo-polymerase mixture Endocr Res 24 1998 637 641
6. C.T. Comey, and B. Budowle Validation studies on the analysis of the HLA DQ alpha locus using the polymerase chain reaction J Forensic Sci 36 1991 1633 1648
7. Wayne PA: Quality management for molecular genetic testing; approved guideline. Wayne, PA: Clinical and Laboratory Standards Institute (CLSI), 2012, Publication MM20-A1.
8. P. Taberlet, S. Griffin, B. Goossens, S. Questiau, V. Manceau, N. Escaravage, L.P. Waits, and J. Bouvet Reliable genotyping of samples with very low DNA quantities using PCR Nucleic Acids Res 24 1996 3189 3194
9. C.R. Miller, P. Joyce, and L.P. Waits Assessing allelic dropout and genotype reliability using maximum likelihood Genetics 160 2002 357 366
10. F. Pompanon, A. Bonin, E. Bellemain, and P. Taberlet Genotyping errors: causes, consequences and solutions Nat Rev Genet 6 2005 847 859
11. C.D. Soulsbury, G. Iossa, K.J. Edwards, P.J. Baker, and S. Harris Allelic dropout from a high-quality DNA source Conserv Genet 8 2007 733 738
12. P.S. Walsh, H.A. Erlich, and R. Higuchi Preferential PCR amplification of alleles: mechanisms and solutions PCR Methods Appl 1 1992 241 250
13. M. Heinrich, M. Müller, S. Rand, B. Brinkmann, and C. Hohoff Allelic drop-out in the STR system ACTBP2 (SE33) as a result of mutations in the primer binding region Int J Legal Med 118 2004 361 363
14. C.W. Lam, and C.M. Mak Allele dropout caused by a non-primer-site SNV affecting PCR amplification-a call for next-generation primer design algorithm Clin Chim Acta 421 2013 208 212
15. E.H. Lee, and H. Lee Enzymes used in nucleic acid amplification H. Lee, S. Morse, O. Olsvik, ∅. Olsvik, Nucleic Acid Amplification Technologies: Application to Disease Diagnosis 1997 Eaton Publishing Cambridge, MA 11 28
16. A. Apte, and S. Daniel PCR primer design Cold Spring Harb Protoc 2009 2009 pdb.ip65
17. S. Ye, S. Dhillon, X. Ke, A.R. Collins, and I.N. Day An efficient procedure for genotyping single nucleotide polymorphisms Nucleic Acids Res 29 2001 E88-8
18. F.K. Fujimura, H. Northrup, A.L. Beaudet, and W.E. O'Brien Genotyping errors with the polymerase chain reaction (letter to the editor) N Engl J Med 322 1990 61
19. M.J. Somerville, K.A. Sprysak, M. Hicks, B.G. Elyas, and L. Vicen-Wyhony An HFE intronic variant promotes misdiagnosis of hereditary hemochromatosis Am J Hum Genet 65 1999 924 926
20. J.J. Wenzel, H. Rossmann, C. Fottner, S. Neuwirth, C. Neukirch, P. Lohse, J.K. Bickmann, T. Minnemann, T.J. Musholt, B. Schneider-Ratzke, M.M. Weber, and K.J. Lackner Identification and prevention of genotyping errors caused by G-quadruplex- and i-motif-like sequences Clin Chem 55 2009 1361 1371
21. C.-W. Lam, and C.M. Mak Allele dropout in PCR-based diagnosis of Wilson disease: mechanisms and solutions Clin Chem 52 2006 517 520
22. W. Rychlik, and R.E. Rhoads A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA Nucleic Acids Res 17 1989 8543 8551
23. L. Jennings, V.M. Van Deerlin, M.L. Gulley College of American Pathologist Molecular Pathology Resource Committee Recommended principles and practices for validating clinical molecular pathology tests Arch Pathol Lab Med 133 2009 743 755
24. R.G. Newcombe Two-sided confidence intervals for the single proportion: comparison of seven methods Stat Med 17 1998 857 872
25. M.J. Knol, W.R. Pestman, and D.E. Grobbee The (mis)use of overlap of confidence intervals to assess effect modification Eur J Epidemiol 26 2011 253 254
26. C. Hüebner, I. Petermann, B.L. Browning, A.N. Shelling, and L.R. Ferguson Triallelic single nucleotide polymorphisms and genotyping error in genetic epidemiology studies: MDR1 (ABCB1) G2677/T/A as an example Cancer Epidemiol Biomarkers Prev 16 2007 1185 1192
27. A.R. Quinlan, and G.T. Marth Primer-site SNPs mask mutations (letter to the editor) Nat Methods 4 2007 192
28. S.J. Tebbutt, and J. Ruan Combining multiple PCR primer pairs for each amplicon can improve SNP genotyping accuracy by reducing allelic drop-out Biotechniques 45 2008 637 638 640, 642
29. G.P. Jeffrey, and P.C. Adams Pitfalls in the genetic diagnosis of hereditary hemochromatosis Genet Test 4 2000 143 146