Validation of an NGS Approach for Diagnostic BRCA1/BRCA2 Mutation Testing

Molecular Diagnosis and Therapy

Volumn 19, Issue 2, 2015, Pages 119-130

  Dacheva, Daniela ^a   Dodova, Rumyana ^a   Popov, Ivan ^a   Goranova, Teodora ^a   Mitkova, Atanaska ^a   Mitev, Vanio ^a   Kaneva, Radka ^a  

^a MEDICAL UNIVERSITY OF SOFIA   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; BIOLOGY; BREAST NEOPLASMS; EXON; FEMALE; GENE LIBRARY; GENETIC SCREENING; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; MUTATION; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR SUPPRESSOR GENE; WORKFLOW;

ALLELES; BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; EXONS; FEMALE; GENE LIBRARY; GENES, BRCA1; GENES, BRCA2; GENETIC TESTING; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; WORKFLOW;

EID: 84937758180     PISSN: 11771062     EISSN: 11792000     Source Type: Journal    
DOI: 10.1007/s40291-015-0136-5     Document Type: Article

References (28)

1. National Cancer Institute, NIH. BRCA1 and BRCA2: Cancer Risk and Genetic Testing [Internet]. 2014. Available from: http://www.cancer.gov/cancertopics/causes-prevention/genetics/brca-fact-sheet.
2. National Comprehensive Cancer Network. Genetic/Familial High-Risk Assessment: Breast and Ovarian (2013) [Internet]. Available from: http://www.nccn.org/professionals/physician_gls/f_guidelines.asp#breast_risk.
3. Antoniou A, Pharoah PD, Narod S, Risch HA, Eyfjord JE, Hopper JL, et al. 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. 2003;72:1117–30.
4. Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007;25:1329–33.
5. Kobayashi H, Ohno S, Sasaki Y, Matsuura M. Hereditary breast and ovarian cancer susceptibility genes (review). Oncol Rep. 2013;30:1019–29.
6. Karami F, Mehdipour P. A comprehensive focus on global spectrum of BRCA1 and BRCA2 mutations in breast cancer. Biomed Res Int. 2013;2013:928562.
7. National Human Genome Research Institute. Breast Cancer Information Core [Internet]. 2000. Available from: http://www.genome.gov/10001504.
8. De Leeneer K, Coene I, Poppe B, De Paepe A, Claes K. Rapid and sensitive detection of BRCA1/2 mutations in a diagnostic setting: comparison of two high-resolution melting platforms. Clin Chem. 2008;54:982–9.
9. Marsh DJ, Howell VM. The use of denaturing high performance liquid chromatography (DHPLC) for mutation scanning of hereditary cancer genes. Methods Mol Biol. 2010;653:133–45.
10. Mattocks CJ, Watkins G, Ward D, Janssens T, Bosgoed EA, van der Donk K, et al. Interlaboratory diagnostic validation of conformation-sensitive capillary electrophoresis for mutation scanning. Clin Chem. 2010;56:593–602.
11. Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, et al. Assuring the quality of nextgeneration sequencing in clinical laboratory practice. Nat Biotechnol. 2012;30:1033–6.
12. Rehm HL, Bale SJ, Bayrak-Toydemir P, Berg JS, Brown KK, Deignan JL, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med. 2013;15:733–47.
13. Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30:434–9.
14. Costa JL, Sousa S, Justino A, Kay T, Fernandes S, Cirnes L, et al. Nonoptical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting. Hum Mutat. 2013;34:629–35.
15. Bosdet IE, Docking TR, Butterfield YS, Mungall AJ, Zeng T, Coope RJ, et al. A clinically validated diagnostic second-generation sequencing assay for detection of hereditary BRCA1 and BRCA2 mutations. J Mol Diagn. 2013;15:796–809.
16. Tarabeux J, Zeitouni B, Moncoutier V, Tenreiro H, Abidallah K, Lair S, et al. Streamlined ion torrent PGMbased diagnostics: BRCA1 and BRCA2 genes as a model. Eur J Hum Genet. 2014;22:535–41.
17. Feliubadaló L, Lopez-Doriga A, Castellsagué E, del Valle J, Menéndez M, Tornero E, et al. Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes. Eur J Hum Genet. 2013;21:864–70.
18. Weitzel J, Costa J, Mensenkamp A, Ekici A, Herzog J, Ligtenberg M, et al. BRCA1 and BRCA2 (BRCA) gene analyses on an economic platform: a global consortium to demonstrate the feasibility of a shared, dedicated workflow for non-optical next generation sequencing (NGS) with a custom BRCA AmpliSeq™ kit on the Ion Torrent PGMTM. Meet. Am. Soc. Hum. Genet. Boston; 2013.
19. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol Clifton NJ. 2000;132:365–86.
20. Helmholtz Center Munich, Institute of Human Genetics. ExonPrimer [Internet]. Available from: http://ihg.gsf.de/ihg/ExonPrimer.html.
21. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–9.
22. Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013;Chapter 7:Unit 7.20.
23. Choi Y, Sims GE, Murphy S, Miller JR, Chan AP. Predicting the functional effect of amino acid substitutions and indels. PLoS One. 2012;7:e46688.
24. Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, et al. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 2013;14:193–202.
25. Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW. Shining a light on dark sequencing: characterising errors in ion Torrent PGM data. PLoS Comput Biol. 2013;9:e1003031.
26. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics. 2012;13:341.
27. International HapMap Consortium. The International HapMap Project. Nature. 2003;426:789–96.
28. Meldrum C, Doyle MA, Tothill RW. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev. 2011;32:177–95.