Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model

European Journal of Human Genetics

Volumn 22, Issue 4, 2014, Pages 535-541

  Tarabeux, Julien ^a,b   Zeitouni, Bruno ^c   Moncoutier, Virginie ^a   Tenreiro, Henrique ^a   Abidallah, Khadija ^a   Lair, Séverine ^c   Legoix Né, Patricia ^a   Leroy, Quentin ^a   Rouleau, Etienne ^a   Golmard, Lisa ^a,b   Barillot, Emmanuel ^c   Stern, Marc Henri ^a,b   Rio Frio, Thomas ^a   Stoppa Lyonnet, Dominique ^a,b,d   Houdayer, Claude ^a,b,d  

^a INSTITUT CURIE   (France)

^b INSTITUT CURIE   (France)

^c INSERM U900   (France)

^d UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

BRCA1; BRCA2; Diagnostics; ION Torrent; PGM

Indexed keywords

ION; PHOSPHOGLUCOMUTASE;

ARTICLE; BIOINFORMATICS; BLOOD SAMPLING; BRCA2 GENE; CONTROLLED STUDY; DIAGNOSTIC PROCEDURE; ELECTROPHORESIS; FRAGMENTATION REACTION; GENE; GENE DELETION; GENE INSERTION; GENE MUTATION; HUMAN; MAJOR CLINICAL STUDY; PRIORITY JOURNAL; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR SUPPRESSOR GENE; TURNAROUND TIME;

BRCA1 PROTEIN; BRCA2 PROTEIN; BREAST NEOPLASMS; COMPUTATIONAL BIOLOGY; FEMALE; GENE REARRANGEMENT; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; OVARIAN NEOPLASMS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SOFTWARE;

EID: 84896548016     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2013.181     Document Type: Article

References (20)

1. Shanks ME, Downes SM, Copley RR et al: Next-generation sequencing (NGS) as a diagnostic tool for retinal degeneration reveals a much higher detection rate in early-onset disease. Eur J Hum Genet 2013; 21: 274-280
2. Artuso R, Fallerini C, Dosa L et al: Advances in Alport syndrome diagnosis using next-generation sequencing. Eur J Hum Genet 2012; 20: 50-57
3. Ozcelik H, Shi X, Chang MC et al: Long-range PCR and next-generation sequencing of BRCA1 and BRCA2 in breast cancer. J Mol Diagn 2012; 14: 467-475
4. Pern F, Bogdanova N, Schurmann P et al: Mutation analysis of BRCA1, BRCA2, PALB2 and BRD7 in a hospital-based series of German patients with triple-negative breast cancer. PLoS One 2012; 7: E47993
5. Feliubadalo L, Lopez-Doriga A, Castellsague 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; 864-870
6. Stoppa-Lyonnet D, Laurent-Puig P, Essioux L et al: BRCA1 sequence variations in 160 individuals referred to a breast/ovarian family cancer clinic. Institut Curie Breast Cancer Group. Am J Hum Genet 1997; 60: 1021-1030
7. Caux-Moncoutier V, Castera L, Tirapo C et al: EMMA, a cost- And time-effective diagnostic method for simultaneous detection of point mutations and large-scale genomic rearrangements: Application to BRCA1 and BRCA2 in 1,525 patients. Hum Mutat 2011; 32: 325-334
8. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens F, Pals G: Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res 2002; 30: E57
9. Rothberg JM, Hinz W, Rearick TM et al: An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011; 475: 348-352
10. Houdayer C, Caux-Moncoutier V, Krieger S et al: Guidelines for splicing analysis in molecular diagnosis derived from a set of 327 combined in silico/in vitro studies on BRCA1 and BRCA2 variants. Hum Mutat 2012; 33: 1228-1238
11. San Lucas FA, Wang G, Scheet P, Peng B: Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. Bioinformatics 2011; 28: 421-422
12. McKenna A, Hanna M, Banks E et al: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303
13. Anders S, Huber W: Differential expression analysis for sequence count data. Genome Biol 2010; 11: R106
14. Wang K, Li M, Hakonarson H: ANNOVAR: Functional annotation of genetic variants from high-Throughput sequencing data. Nucleic Acids Res 2010; 38: E164
15. Hochberg Y, Benjamini Y: More powerful procedures for multiple significance testing. Stat Med 1990; 9: 811-818
16. Goecks J, Nekrutenko A, Taylor J: Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010; 11: R86
17. Michils G, Hollants S, Dehaspe L et al: Molecular analysis of the breast cancer genes BRCA1 and BRCA2 using amplicon-based massive parallel pyrosequencing. J Mol Diagn 2012; 14: 623-630
18. Machado PM, Brandao RD, Cavaco BM et al: Screening for a BRCA2 rearrangement in high-risk breast/ovarian cancer families: Evidence for a founder effect and analysis of the associated phenotypes. J Clin Oncol 2007; 25: 2027-2034
19. Bell CJ, Dinwiddie DL, Miller NA et al: Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med 2011; 3: 65ra64
20. De Leeneer K, De Schrijver J, Clement L et al: Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics. PLoS One 2011; 6: E25531