A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations

Journal of Molecular Diagnostics

Volumn 15, Issue 6, 2013, Pages 796-809

  Bosdet, Ian E ^a,b   Docking, T Roderick ^a   Butterfield, Yaron S ^a   Mungall, Andrew J ^a   Zeng, Thomas ^a   Coope, Robin J ^a   Yorida, Erika ^a   Chow, Katie ^a   Bala, Miruna ^a   Young, Sean S ^a,b   Hirst, Martin ^a,b,c   Birol, Inanc ^a,b,c   Moore, Richard A ^a,c   Jones, Steven J ^a,b,c   Marra, Marco A ^a,b,c   Holt, Rob ^a,c   Karsan, Aly ^a,b  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; GENOMIC DNA;

AMPLICON; ARTICLE; BRCA2 GENE; BREAST CANCER; CANCER DIAGNOSIS; CONTROLLED STUDY; DIAGNOSTIC TEST; DIAGNOSTIC TEST ACCURACY STUDY; EXON; FALSE NEGATIVE RESULT; FAMILIAL CANCER; GENE; GENE MUTATION; GENE SEQUENCE; GENETIC PROCEDURES; HIGH THROUGHPUT SEQUENCING; HUMAN; INTRON; MAJOR CLINICAL STUDY; POLYMERASE CHAIN REACTION; PREDICTION; SECOND GENERATION SEQUENCING; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TUMOR SUPPRESSOR GENE;

BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; GENE FREQUENCY; GENE LIBRARY; GENES, BRCA1; GENES, BRCA2; HEREDITARY BREAST AND OVARIAN CANCER SYNDROME; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PROSPECTIVE STUDIES; SENSITIVITY AND SPECIFICITY;

EID: 84886085839     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2013.07.004     Document Type: Article

References (45)

1. W.D. Foulkes Inherited susceptibility to common cancers N Engl J Med 359 2008 2143 2153
2. A. Antoniou, P.D.P. Pharoah, S. Narod, H.A. Risch, J.E. Eyfjord, J.L. Hopper, N. Loman, H. Olsson, O. Johannsson, Å. Borg, B. Pasini, P. Radice, S. Manoukian, D.M. Eccles, N. Tang, E. Olah, H. Anton-Culver, E. Warner, J. Lubinski, J. Gronwald, B. Gorski, H. Tulinius, S. Thorlacius, H. Eerola, H. Nevanlinna, K. Syrjäkoski, O.P. Kallioniemi, D. Thompson, C. Evans, J. Peto, F. Lalloo, D.G. Evans, and D.F. Easton Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies Am J Hum Genet 72 2003 1117 1130
3. S. Chen, and G. Parmigiani Meta-analysis of BRCA1 and BRCA2 penetrance J Clin Oncol 25 2007 1329 1333
4. M.B. Daly, J.E. Axilbund, S. Buys, B. Crawford, C.D. Farrell, S. Friedman, J.E. Garber, S. Goorha, S.B. Gruber, H. Hampel, V. Kaklamani, W. Kohlmann, A. Kurian, J. Litton, P.K. Marcom, R. Nussbaum, K. Offit, T. Pal, B. Pasche, R. Pilarski, G. Reiser, K.M. Shannon, J.R. Smith, E. Swisher, J.N. Weitzel National Comprehensive Cancer Network Genetic/familial high-risk assessment: breast and ovarian J Natl Compr Canc Netw 8 2010 562 594
5. J.L. Berliner, A.M. Fay Practice Issues Subcommittee of the National Society of Genetic Counselors' Familial Cancer Risk Counseling Special Interest Group Risk assessment and genetic counseling for hereditary breast and ovarian cancer: recommendations of the National Society of Genetic Counselors J Genet Couns 16 2007 241 260
6. M.L. Murray, F. Cerrato, R.L. Bennett, and G.P. Jarvik Follow-up of carriers of BRCA1 and BRCA2 variants of unknown significance: variant reclassification and surgical decisions Genet Med 13 2011 998 1005
7. M. Epplein, K.P. Koon, S.D. Ramsey, and J.D. Potter Genetic services for familial cancer patients: a follow-up survey of National Cancer Institute Cancer Centers J Clin Oncol 23 2005 4713 4718
8. F. Sanger, S. Nicklen, and A.R. Coulson DNA sequencing with chain-terminating inhibitors Proc Natl Acad Sci USA 74 1977 5463 5467
9. B.E. Slatko, J. Kieleczawa, J. Ju, A.F. Gardner, C.L. Hendrickson, and F.M. Ausubel "First Generation" automated DNA sequencing technology Curr Protoc Mol Biol 2011 Oct Chapter 7:Unit 7.2
10. J.P. Schouten, C.J. McElgunn, R. Waaijer, D. Zwijnenburg, F. Diepvens, and G. Pals Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification Nucleic Acids Res 30 2002 e57
11. J. Tol, J.R. Dijkstra, M.E. Vink-Börger, I.D. Nagtegaal, C.J.A. Punt, J.H.J.M. Van Krieken, and M.J.L. Ligtenberg High sensitivity of both sequencing and real-time PCR analysis of KRAS mutations in colorectal cancer tissue J Cell Mol Med 14 2010 2122 2131
12. A.C. Tsiatis, A. Norris-Kirby, R.G. Rich, M.J. Hafez, C.D. Gocke, J.R. Eshleman, and K.M. Murphy Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations J Mol Diagn 12 2010 425 432
13. A. Rohlin, J. Wernersson, Y. Engwall, L. Wiklund, J. Björk, and M. Nordling Parallel sequencing used in detection of mosaic mutations: comparison with four diagnostic DNA screening techniques Hum Mutat 30 2009 1012 1020
14. M.L. Metzker Sequencing technologies-the next generation Nat Rev Genet 11 2009 31 46
15. E.R. Mardis A decade's perspective on DNA sequencing technology Nature 470 2011 198 203
16. L. Mamanova, A.J. Coffey, C.E. Scott, I. Kozarewa, E.H. Turner, A. Kumar, E. Howard, J. Shendure, and D.J. Turner Target-enrichment strategies for next-generation sequencing Nat Methods 7 2010 111 118
17. College of American Pathologists Next generation sequencing checklist questions. Molecular Pathology Checklist 2012 College of American Pathologists Northfield, IL 34 39
18. C.J. Mattocks, M.A. Morris, G. Matthijs, E. Swinnen, A. Corveleyn, E. Dequeker, C.R. Müller, V. Pratt, A. Wallace EuroGentest Validation Group A standardized framework for the validation and verification of clinical molecular genetic tests Eur J Hum Genet 18 2010 1276 1288
19. C.S. Richards, S. Bale, D.B. Bellissimo, S. Das, W.W. Grody, M.R. Hegde, E. Lyon, B.E. Ward Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007 Genet Med 10 2008 294 300
20. O. Anczuków, M. Buisson, M. Léoné, C. Coutanson, C. Lasset, A. Calender, O.M. Sinilnikova, and S. Mazoyer BRCA2 deep intronic mutation causing activation of a cryptic exon: opening toward a new preventive therapeutic strategy Clin Cancer Res 18 2012 4903 4909
21. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
22. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
23. P.J. Turnbaugh, R.E. Ley, M. Hamady, C.M. Fraser-Liggett, R. Knight, and J.I. Gordon The Human Microbiome Project Nature 449 2007 804 810
24. S. Ogino, M.L. Gulley, J.T. den Dunnen, R.B. Wilson Association for Molecular Pathology Training and Education Committee Standard mutation nomenclature in molecular diagnostics [Erratum appeared in J Mol Diagn 2009, 11:494] J Mol Diagn 9 2007 1 6
25. J.T. den Dunnen, and S.E. Antonarakis Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion [Erratum appeared in Hum Mutat 2002, 20:403] Hum Mutat 15 2000 7 12
26. J.T. Robinson, H. Thorvaldsdóttir, W. Winckler, M. Guttman, E.S. Lander, G. Getz, and J.P. Mesirov Integrative Genomics Viewer Nat Biotechnol 29 2011 24 26
27. E.B. Wilson Probable inference, the law of succession, and statistical inference J Am Stat Assoc 22 1927 209 212
28. R Core Team R: A Language and Environment for Statistical Computing: Reference Index. Version 3.0.1 2013 R Foundation for Statistical Computing Vienna
29. B. Andersson, J. Lu, Y. Shen, M.A. Wentland, and R.A. Gibbs Simultaneous shotgun sequencing of multiple cDNA clones DNA Seq 7 1997 63 70
30. P.H. Gunaratne, J.Q. Wu, A.M. Garcia, S. Hulyk, K.C. Worley, J.F. Margolin, and R.A. Gibbs Concatenation cDNA sequencing for transcriptome analysis C R Biol 326 2003 971 977
31. M.N. Bainbridge, M. Wang, D.L. Burgess, C. Kovar, M.J. Rodesch, M. D'Ascenzo, J. Kitzman, Y.Q. Wu, I. Newsham, T.A. Richmond, J.A. Jeddeloh, D. Muzny, T.J. Albert, and R.A. Gibbs Whole exome capture in solution with 3 Gbp of data Genome Biol 11 2010 R62
32. V. Heinrich, J. Stange, T. Dickhaus, P. Imkeller, U. Krüger, S. Bauer, S. Mundlos, P.N. Robinson, J. Hecht, and P.M. Krawitz The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process Nucleic Acids Res 40 2012 2426 2431
33. N.J. Loman, R.V. Misra, T.J. Dallman, C. Constantinidou, S.E. Gharbia, J. Wain, and M.J. Pallen Performance comparison of benchtop high-throughput sequencing platforms [Erratum appeared in Nat Biotechnol 2012, 30:562] Nat Biotechnol 30 2012 434 439
34. J.T. Simpson, K. Wong, S.D. Jackman, J.E. Schein, S.J.M. Jones, and I. Birol ABySS: A parallel assembler for short read sequence data Genome Res 19 2009 1117 1123
35. S. Yoon, Z. Xuan, V. Makarov, K. Ye, and J. Sebat Sensitive and accurate detection of copy number variants using read depth of coverage Genome Res 19 2009 1586 1592
36. W. Wang, Z. Wei, T.W. Lam, and J. Wang Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions Sci Rep 1 2011 55
37. R. Goya, M.G.F. Sun, R.D. Morin, G. Leung, G. Ha, K.C. Wiegand, J. Senz, A. Crisan, M.A. Marra, M. Hirst, D. Huntsman, K.P. Murphy, S. Aparicio, and S.P. Shah SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors Bioinformatics 26 2010 730 736
38. A. McKenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis, A. Kernytsky, K. Garimella, D. Altshuler, S. Gabriel, M. Daly, and M.A. DePristo The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data Genome Res 20 2010 1297 1303
39. M.C. King, J.H. Marks, J.B. Mandell New York Breast Cancer Study Group Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2 Science 302 2003 643 646
40. P.M. Campeau, W.D. Foulkes, and M.D. Tischkowitz Hereditary breast cancer: new genetic developments, new therapeutic avenues Hum Genet 124 2008 31 42
41. J.P. Evans, and J.S. Berg Next-generation DNA sequencing, regulation, and the limits of paternalism JAMA 306 2011 2376 2377
42. A.L. McGuire, T. Caulfield, and M.K. Cho Research ethics and the challenge of whole-genome sequencing Nat Rev Genet 9 2008 152 156
43. I.S. Kohane, D.R. Masys, and R.B. Altman The incidentalome [Erratum appeared in JAMA 2006, 296:1466] JAMA 296 2006 212 215
44. C.J. Bell, D.L. Dinwiddie, N.A. Miller, S.L. Hateley, E.E. Ganusova, J. Mudge, R.J. Langley, L. Zhang, C.C. Lee, F.D. Schilkey, V. Sheth, J.E. Woodward, H.E. Peckham, G.P. Schroth, R.W. Kim, and S.F. Kingsmore Carrier testing for severe childhood recessive diseases by next-generation sequencing Sci Transl Med 3 2011 65ra4
45. D.G. MacArthur, S. Balasubramanian, A. Frankish, N. Huang, J. Morris, and K. Walter A systematic survey of loss-of-function variants in human protein-coding genes [Erratum appeared in Science 2012, 336:296] Science 335 2012 823 828