Next-generation sequencing for the diagnosis of hereditary breast and ovarian cancer using genomic capture targeting multiple candidate genes

European Journal of Human Genetics

Volumn 22, Issue 11, 2014, Pages 1305-1313

  Castéra, Laurent ^a,b   Krieger, Sophie ^a,b,c   Rousselin, Antoine ^a   Legros, Angélina ^a   Baumann, Jean Jacques ^a   Bruet, Olivia ^a   Brault, Baptiste ^a   Fouillet, Robin ^a   Goardon, Nicolas ^a   Letac, Olivier ^a   Baert Desurmont, Stéphanie ^b,d   Tinat, Julie ^b,d   Bera, Odile ^e   Dugast, Catherine ^f   Berthet, Pascaline ^a   Polycarpe, Florence ^a   Layet, Valérie ^g   Hardouin, Agnes ^a,b   Frébourg, Thierry ^b,d,h   Vaur, Dominique ^a,b  

^a Francois Baclesse Anticancer Center   (France)

^b INSERM   (France)

^c UNIVERSITÉ DE CAEN   (France)

^d ROUEN UNIVERSITY HOSPITAL   (France)

^e University Hospital   (France)

^f RENNES UNIVERSITY HOSPITAL   (France)

^g LE HAVRE HOSPITAL   (France)

^h UNIVERSITY OF ROUEN   (France)

Author keywords

BRCA1; BRCA2; breast; cancer; NGS; ovary

Indexed keywords

ATM PROTEIN; BRCA1 ASSOCIATED RING DOMAIN PROTEIN 1; BRCA1 PROTEIN; BRCA2 PROTEIN; CHECKPOINT KINASE 2; GENOMIC DNA; MISMATCH REPAIR PROTEIN PMS2; MLH3 PROTEIN; MRE11 PROTEIN; MRE11A PROTEIN; NIBRIN; NUCLEIC ACID BINDING PROTEIN; PROTEIN MSH2; PROTEIN P53; RAD50 PROTEIN; RAD51 PROTEIN; RAD51C PROTEIN; UNCLASSIFIED DRUG; UVOMORULIN; BRCA1 PROTEIN, HUMAN; BRCA2 PROTEIN, HUMAN; TP53 PROTEIN, HUMAN;

ADULT; AGED; ARTICLE; BIOINFORMATICS; CANCER PATIENT; CANCER SCREENING; CONTROLLED CLINICAL TRIAL; CONTROLLED STUDY; DIAGNOSTIC TEST ACCURACY STUDY; FEMALE; GENE SEQUENCE; GENE TARGETING; GENETIC ANALYZER; GENOME ANALYSIS; GERMLINE MUTATION; HEREDITARY BREAST AND OVARIAN CANCER SYNDROME; HUMAN; INDEL MUTATION; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; MOLECULAR DIAGNOSIS; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; MUTATIONAL ANALYSIS; NEXT GENERATION SEQUENCING; SINGLE BLIND PROCEDURE; TUMOR SUPPRESSOR GENE; BIOLOGY; BREAST NEOPLASMS; BREAST NEOPLASMS, MALE; CASE CONTROL STUDY; GENE REARRANGEMENT; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; MALE; METABOLISM; MIDDLE AGED; MUTATION; OVARIAN NEOPLASMS; PROCEDURES; REPRODUCIBILITY;

ADULT; AGED; BRCA1 PROTEIN; BRCA2 PROTEIN; BREAST NEOPLASMS; BREAST NEOPLASMS, MALE; CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; FEMALE; GENE REARRANGEMENT; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MUTATION; OVARIAN NEOPLASMS; REPRODUCIBILITY OF RESULTS; TUMOR SUPPRESSOR PROTEIN P53;

EID: 84908502657     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2014.16     Document Type: Article

References (40)

1. Miki Y, Swensen J, Shattuck-Eidens D et al: A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 1994; 266: 66-71.
2. Wooster R, Bignell G, Lancaster J et al: Identification of the breast cancer susceptibility gene BRCA2. Nature 1995; 378: 789-792.
3. Antoniou A, Pharoah PD, Narod S 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: 1117-1130.
4. Tutt A, Robson M, Garber JE et al: Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and advanced breast cancer: a proof-of-concept trial. Lancet 2010; 376: 235-244.
5. Audeh MW, Carmichael J, Penson RT et al: Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and recurrent ovarian cancer: a proof-of-concept trial. Lancet 2010; 376: 245-251.
6. Mann GJ, Thorne H, Balleine RL et al: Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource. Breast Cancer Res 2006; 8: R12.
7. Spiegelman JI, Mindrinos MN, Oefner PJ: High-accuracy DNA sequence variation screening by DHPLC. Biotechniques 2000; 29: 1084-1090, 1092.
8. Duponchel C, Di RC, Cicardi M, Tosi M: Rapid detection by fluorescent multiplex PCR of exon deletions and duplications in the C1 inhibitor gene of hereditary angioedema patients. Hum Mutat 2001; 17: 61-70.
9. 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 1525 patients. Hum Mutat 2011; 32: 325-334.
10. Wittwer CT: High-resolution DNA melting analysis: advancements and limitations. Hum Mutat 2009; 30: 857-859.
11. 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.
12. Walsh T, Casadei S, Coats KH et al: Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. JAMA 2006; 295: 1379-1388.
13. Bubien V, Bonnet F, Brouste V et al: High cumulative risks of cancer in patients with PTEN hamartoma tumour syndrome. J Med Genet 2013; 50: 255-263.
14. Giardiello FM, Brensinger JD, Tersmette AC et al: Very high risk of cancer in familial Peutz-Jeghers syndrome. Gastroenterology 2000; 119: 1447-1453.
15. Pharoah PD, Guilford P, Caldas C: Incidence of gastric cancer and breast cancer in CDH1 (E-cadherin) mutation carriers from hereditary diffuse gastric cancer families. Gastroenterology 2001; 121: 1348-1353.
16. Meindl A, Hellebrand H, Wiek C et al: Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nat Genet 2010; 42: 410-414.
17. Byrnes GB, Southey MC, Hopper JL: Are the so-called low penetrance breast cancer genes, ATM, BRIP1, PALB2 and CHEK2, high risk for women with strong family histories? Breast Cancer Res 2008; 10: 208.
18. Rehm HL, Bale SJ, Bayrak-Toydemir P et al: ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15: 733-747.
19. Walsh T, Lee MK, Casadei S et al: Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 2010; 107: 12629-12633.
20. Craig DW, Pearson JV, Szelinger S et al: Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 2008; 5: 887-893.
21. Kenny EM, Cormican P, Gilks WP et al: Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection. DNA Res 2011; 18: 31-38.
22. Xie C, Tammi MT: CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 2009; 10: 80.
23. Li H, Handsaker B, Wysoker A et al: The sequence alignment/map format and SAMtools. Bioinformatics 2009; 25: 2078-2079.
24. Caputo S, Benboudjema L, Sinilnikova O, Rouleau E, Beroud C, Lidereau R: Description and analysis of genetic variants in French hereditary breast and ovarian cancer families recorded in the UMD-BRCA1/BRCA2 databases. Nucleic Acids Res 2012; 40: D992-1002.
25. Petitjean A, Mathe E, Kato S et al: Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database. Hum Mutat 2007; 28: 622-629.
26. Tavtigian SV, Byrnes GB, Goldgar DE, Thomas A: Classification of rare missense substitutions, using risk surfaces, with genetic-and molecular-epidemiology applications. Hum Mutat 2008; 29: 1342-1354.
27. 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.
28. 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.
29. Tinat J, Bougeard G, Baert-Desurmont S et al: 2009 version of the Chompret criteria for Li Fraumeni syndrome. J Clin Oncol 2009; 27: e108-e109.
30. Li J, Lupat R, Amarasinghe KC et al: CONTRA: copy number analysis for targeted resequencing. Bioinformatics 2012; 28: 1307-1313.
31. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z: Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009; 25: 2865-2871.
32. Tarabeux J, Zeitouni B, Moncoutier V et al: Streamlined ion torrent PGM-based diagnostics: BRCA1 and BRCA2 genes as a model. Eur J Hum Genet 2014; 22: 535-541.
33. Masciari S, Dillon DA, Rath M et al: Breast cancer phenotype in women with TP53 germline mutations: a Li-Fraumeni syndrome consortium effort. Breast Cancer Res Tr e a t 2012; 133: 1125-1130.
34. Gonzalez KD, Noltner KA, Buzin CH et al: Beyond Li Fraumeni syndrome: clinical characteristics of families with p53 germline mutations. J Clin Oncol 2009; 27: 1250-1256.
35. Heymann S, Delaloge S, Rahal A et al: Radio-induced malignancies after breast cancer postoperative radiotherapy in patients with Li-Fraumeni syndrome. Radiat Oncol 2010; 5: 104.
36. Limacher JM, Frebourg T, Natarajan-Ame S, Bergerat JP: Two metachronous tumors in the radiotherapy fields of a patient with Li-Fraumeni syndrome. Int J Cancer 2001; 96: 238-242.
37. Ferrarini A, Auteri-Kaczmarek A, Pica A et al: Early occurrence of lung adenocarcinoma and breast cancer after radiotherapy of a chest wall sarcoma in a patient with a de novo germline mutation in TP53. Fam Cancer 2011; 10: 187-192.
38. Bonadona V, Bonaiti B, Olschwang S et al: Cancer risks associated with germline mutations in MLH1, MSH2, and MSH6 genes in Lynch syndrome. JAMA 2011; 305: 2304-2310.
39. Lindor NM, Petersen GM, Hadley DW et al: Recommendations for the care of individuals with an inherited predisposition to Lynch syndrome: a systematic review. JAMA 2006; 296: 1507-1517.
40. Walsh T, Casadei S, Lee MK et al: Mutations in 12 genes for inherited ovarian, fallopian tube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci USA 2011; 108: 18032-18037.