Exome Sequencing of Germline DNA from Non-BRCA1/2 Familial Breast Cancer Cases Selected on the Basis of aCGH Tumor Profiling

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Hilbers, Florentine S ^a   Meijers, Caro M ^a   Laros, Jeroen F J ^a   van Galen, Michiel ^a   Hoogerbrugge, Nicoline ^b   Vasen, Hans F A ^c   Nederlof, Petra M ^d   Wijnen, Juul T ^a   van Asperen, Christi J ^a   Devilee, Peter ^a  

^a LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c Netherlands Foundation for the Detection of Hereditary Tumors   (Netherlands)

^d NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BREAST CANCER; CANCER RISK; CASC5 GENE; CHROMOSOME 22; CHROMOSOME 4; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; CUL9 GENE; DNA DAMAGE; DNA REPAIR; DNA SEQUENCE; EXOME; FAMILIAL CANCER; FAMILY ASSESSMENT; FANCD2 GENE; FEMALE; FRAMESHIFT MUTATION; GENE; GENE DELETION; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCATION; GENE MUTATION; GENETIC RISK; GENETIC VARIABILITY; HAUS3 GENE; HUMAN; LIMIT OF DETECTION; LINKAGE ANALYSIS; LNX1 GENE; MAJOR CLINICAL STUDY; MISSENSE MUTATION; MUTYH GENE; NON BRCA1 2 FAMILIAL BREAST CANCER; RNA SPLICING; SMC6 GENE; SPLICE SITE MUTATION; TTK GENE; XRCC2 GENE;

BREAST NEOPLASMS; CHROMOSOMES, HUMAN, PAIR 4; COMPARATIVE GENOMIC HYBRIDIZATION; EXOME; FAMILY; FEMALE; GENES, BRCA1; GENES, BRCA2; GENETIC LINKAGE; GERM-LINE MUTATION; HUMANS; LOD SCORE; OPEN READING FRAMES; PEDIGREE; SEQUENCE ANALYSIS, DNA;

EID: 84873160825     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055734     Document Type: Article

References (38)

1. Ahmed M, Lalloo F, Evans DG, (2009) Update on genetic predisposition to breast cancer. Expert Rev Anticancer Ther 9: 1103-1113 doi:10.1586/era.09.38.
2. Stratton MR, Rahman N, (2008) The emerging landscape of breast cancer susceptibility. Nat Genet 40: 17-22.
3. Turnbull C, Rahman N, (2008) Genetic predisposition to breast cancer: past, present, and future. Annu Rev Genomics Hum Genet 9: 321-345 10.1146/annurev.genom.9.081307.164339 [doi].
4. Wooster R, Neuhausen SL, Mangion J, Quirk Y, Ford D, et al. (1994) Localization of a breast cancer susceptibility gene, BRCA2, to chromosome 13q12-13. Science 265: 2088-2090.
5. Jonsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, et al. (2005) Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res 65: 7612-7621 65/17/7612 [pii];10.1158/0008-5472.CAN-05-0570 [doi].
6. Joosse SA, van Beers EH, Tielen IH, Horlings H, Peterse JL, et al. (2009) Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat 116: 479-489 10.1007/s10549-008-0117-z [doi].
7. Joosse SA, Brandwijk KI, Devilee P, Wesseling J, Hogervorst FB, et al. (2012) Prediction of BRCA2-association in hereditary breast carcinomas using array-CGH. Breast Cancer Res Treat 132: 379-389 10.1007/s10549-010-1016-7 [doi].
8. Tirkkonen M, Johannsson O, Agnarsson BA, Olsson H, Ingvarsson S, et al. (1997) Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res 57: 1222-1227.
9. van Beers EH, van WT, Wessels LF, Li Y, Oldenburg RA, et al. (2005) Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res 65: 822-827 65/3/822 [pii].
10. Wessels LF, van WT, Hart AA, van't Veer LJ, Reinders MJ, et al. (2002) Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res 62: 7110-7117.
11. Didraga MA, van Beers EH, Joosse SA, Brandwijk KI, Oldenburg RA, et al. (2011) A non-BRCA1/2 hereditary breast cancer sub-group defined by aCGH profiling of genetically related patients. Breast Cancer Res Treat 130: 425-436 10.1007/s10549-011-1357-x [doi].
12. Oldenburg RA, Kroeze-Jansema KH, Houwing-Duistermaat JJ, Bayley JP, Dambrot C, et al. (2008) Genome-wide linkage scan in Dutch hereditary non-BRCA1/2 breast cancer families identifies 9q21-22 as a putative breast cancer susceptibility locus. Genes Chromosomes Cancer 47: 947-956 10.1002/gcc.20597 [doi].
13. Lathrop GM, Lalouel JM, (1984) Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet 36: 460-465.
14. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES, (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 58: 1347-1363.
15. Easton DF, Bishop DT, Ford D, Crockford GP, (1993) Genetic linkage analysis in familial breast and ovarian cancer: results from 214 families. The Breast Cancer Linkage Consortium. Am J Hum Genet 52: 678-701.
16. Gordon A (2010) FASTX-Toolkit. Available: http://hannonlab.cshl.edu/fastx_toolkit/. Accessed 2012 May.
17. Lunter G, Goodson M, (2011) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21: 936-939 gr.111120.110 [pii];10.1101/gr.111120.110 [doi].
18. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760 btp324 [pii];10.1093/bioinformatics/btp324 [doi].
19. Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, et al. (2009) VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25: 2283-2285 btp373 [pii];10.1093/bioinformatics/btp373 [doi].
20. University of Washington (2011) SeattleSeq. Available: http://snp.gs.washington.edu/SeattleSeqAnnotation134/. Accessed 2012 Jun.
21. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789-796 10.1038/nature02168 [doi];nature02168 [pii].
22. 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073 nature09534 [pii];10.1038/nature09534 [doi].
23. NHLBI Exome Sequencing Project (ESP) (2012) Exome Variant Server. Available: http://evs.gs.washington.edu/EVS/ Accessed 2012 Jun.
24. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249 nmeth0410-248 [pii];10.1038/nmeth0410-248 [doi].
25. Park DJ, Lesueur F, Nguyen-Dumont T, Pertesi M, Odefrey F, et al. (2012) Rare mutations in XRCC2 increase the risk of breast cancer. Am J Hum Genet 90: 734-739 S0002-9297(12)00145-0 [pii];10.1016/j.ajhg.2012.02.027 [doi].
26. Hilbers FS, Wijnen JT, Hoogerbrugge N, Oosterwijk JC, Collee MJ, et al. (2012) Rare variants in XRCC2 as breast cancer susceptibility alleles. J Med Genet 49: 618-620 jmedgenet-2012-101191 [pii];10.1136/jmedgenet-2012-101191 [doi].
27. Antoniou AC, Pharoah PD, McMullan G, Day NE, Ponder BA, et al. (2001) Evidence for further breast cancer susceptibility genes in addition to BRCA1 and BRCA2 in a population-based study. Genet Epidemiol 21: 1-18 10.1002/gepi.1014 [pii];10.1002/gepi.1014 [doi].
28. Antoniou AC, Pharoah PD, McMullan G, Day NE, Stratton MR, et al. (2002) A comprehensive model for familial breast cancer incorporating BRCA1, BRCA2 and other genes. Br J Cancer 86: 76-83 10.1038/sj.bjc.6600008 [doi].
29. Cui J, Antoniou AC, Dite GS, Southey MC, Venter DJ, et al. (2001) After BRCA1 and BRCA2-what next? Multifactorial segregation analyses of three-generation, population-based Australian families affected by female breast cancer. Am J Hum Genet 68: 420-431 S0002-9297(07)64094-4 [pii];10.1086/318187 [doi].
30. Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, et al. (2010) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42: 790-793 ng.646 [pii];10.1038/ng.646 [doi].
31. Botstein D, Risch N, (2003) Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat Genet 33 (Suppl) (): 228-237 10.1038/ng1090 [doi];ng1090 [pii].
32. Alvarez S, Diaz-Uriarte R, Osorio A, Barroso A, Melchor L, et al. (2005) A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation. Clin Cancer Res 11: 1146-1153 11/3/1146 [pii].
33. Gronwald J, Jauch A, Cybulski C, Schoell B, Bohm-Steuer B, et al. (2005) Comparison of genomic abnormalities between BRCAX and sporadic breast cancers studied by comparative genomic hybridization. Int J Cancer 114: 230-236 10.1002/ijc.20723 [doi].
34. Mangia A, Chiarappa P, Tommasi S, Chiriatti A, Petroni S, et al. (2008) Genetic heterogeneity by comparative genomic hybridization in BRCAx breast cancers. Cancer Genet Cytogenet 182: 75-83 S0165-4608(08)00024-1 [pii];10.1016/j.cancergencyto.2008.01.002 [doi].
35. Muranen TA, Greco D, Fagerholm R, Kilpivaara O, Kampjarvi K, et al. (2011) Breast tumors from CHEK2 1100delC mutation carriers: genomic landscape and clinical implications. Breast Cancer Res 13: R48 bcr2874 [pii];10.1186/bcr2874 [doi].
36. CHEK2 Breast Cancer Case-Control Consortium (2004) CHEK2*1100delC and susceptibility to breast cancer: a collaborative analysis involving 10,860 breast cancer cases and 9,065 controls from 10 studies. Am J Hum Genet 74: 1175-1182 10.1086/421251 [doi];S0002-9297(07)62704-9 [pii].
37. Keinan A, Clark AG, (2012) Recent explosive human population growth has resulted in an excess of rare genetic variants. Science 336: 740-743 336/6082/740 [pii];10.1126/science.1217283 [doi].
38. Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, et al. (2012) Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature nature11690 [pii];10.1038/nature11690 [doi].