Whole Exome Sequencing Suggests Much of Non-BRCA1/BRCA2 Familial Breast Cancer Is Due to Moderate and Low Penetrance Susceptibility Alleles

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Gracia Aznarez, Francisco Javier ^a   Fernandez, Victoria ^a   Pita, Guillermo ^a   Peterlongo, Paolo ^b,c   Dominguez, Orlando ^a   de la Hoya, Miguel ^d   Duran, Mercedes ^e   Osorio, Ana ^a   Moreno, Leticia ^a   Gonzalez Neira, Anna ^a   Rosa Rosa, Juan Manuel ^f   Sinilnikova, Olga ^g,h   Mazoyer, Sylvie ^g   Hopper, John ⁱ   Lazaro, Conchi ^j   Southey, Melissa ⁱ   Odefrey, Fabrice ⁱ   Manoukian, Siranoush ^c   Catucci, Irene ^b,c   Caldes, Trinidad ^d   Lynch, Henry T ^k   Hilbers, Florentine S M ^l   van Asperen, Christi J ^l   Vasen, Hans F A ^l,m   Goldgar, David ⁿ   Radice, Paolo ^b,c   Devilee, Peter ^l   Benitez, Javier ^a,o   more..

^a Centro Nacional de Investigaciones Oncológicas   (Spain)

^b FIRC INSTITUTE OF MOLECULAR ONCOLOGY   (Italy)

^c NATIONAL CANCER INSTITUTE   (Italy)

^d HOSPITAL CLÍNICO SAN CARLOS   (Spain)

^e Universidad de Valladolid y Consejo Superior de Investigaciones Científicas   (Spain)

^f Sistemas Genomicos   (Spain)

^g CENTRE DE RECHERCHE EN CANCÉROLOGIE DE LYON   (France)

^h HOSPICES CIVILS DE LYON   (France)

ⁱ UNIVERSITY OF MELBOURNE   (Australia)

^j CATALAN INSTITUTE OF ONCOLOGY   (Spain)

^k CREIGHTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^l LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

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

ⁿ UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^o CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; DNA;

ALLELE; ARTICLE; AUSTRALIA; AXIN1 GENE; BREAST CANCER; CELL CYCLE REGULATION; CELL PROLIFERATION; CELL SURVIVAL; CNTROB GENE; DNA REPAIR; EXOME; FAMILIAL CANCER; FAMILY STUDY; FANCM GENE; FRANCE; GENE; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC HETEROGENEITY; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HAPLOTYPE MAP; HETEROZYGOSITY; HIGH THROUGHPUT SEQUENCING; HUMAN; INDEL MUTATION; ITALY; MAPKAP1 GENE; NETHERLANDS; PENETRANCE; PTPRF GENE; S1PR3 GENE; SEGREGATION ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SLBP GENE; SPAIN; TIMP3 GENE; TNFSF8 GENE; TUMOR SUPPRESSOR GENE; UBA3 GENE; WNTA GENE;

ALLELES; BREAST NEOPLASMS; EXOME; FEMALE; GENES, BRCA1; GENES, BRCA2; HUMANS;

EID: 84873696289     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0055681     Document Type: Article

References (39)

1. Miki Y, Swensen J, Shattuck-Eidens D, Futreal PA, Harshman K, et al. (1994) A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1. Science 266: 66-71.
2. Wooster R, Bignell G, Lancaster J, Swift S, Seal S, et al. (1995) Identification of the breast cancer susceptibility gene BRCA2. Nature 378: 789-792.
3. Borresen AL, Andersen TI, Garber J, Barbier-Piraux N, Thorlacius S, et al. (1992) Screening for germ line TP53 mutations in breast cancer patients. Cancer Res 52: 3234-3236.
4. Lynch ED, Ostermeyer EA, Lee MK, Arena JF, Ji H, et al. (1997) Inherited mutations in PTEN that are associated with breast cancer, cowden disease, and juvenile polyposis. Am J Hum Genet 61: 1254-1260.
5. Giardiello FM, Brensinger JD, Tersmette AC, Goodman SN, Petersen GM, et al. (2000) Very high risk of cancer in familial Peutz-Jeghers syndrome. Gastroenterology 119: 1447-1453.
6. Rahman N, Seal S, Thompson D, Kelly P, Renwick A, et al. (2007) PALB2, which encodes a BRCA2-interacting protein, is a breast cancer susceptibility gene. Nat Genet 39: 165-167.
7. Seal S, Thompson D, Renwick A, Elliott A, Kelly P, et al. (2006) Truncating mutations in the Fanconi anemia J gene BRIP1 are low-penetrance breast cancer susceptibility alleles. Nat Genet 38: 1239-1241.
8. Meindl A, Hellebrand H, Wiek C, Erven V, Wappenschmidt B, et al. (2010) Germline mutations in breast and ovarian cancer pedigrees establish RAD51C as a human cancer susceptibility gene. Nat Genet 42: 410-414.
9. Shamseldin HE, Elfaki M, Alkuraya FS, (2012) Exome sequencing reveals a novel Fanconi group defined by XRCC2 mutation. J Med Genet 49: 184-186.
10. Renwick A, Thompson D, Seal S, Kelly P, Chagtai T, et al. (2006) ATM mutations that cause ataxia-telangiectasia are breast cancer susceptibility alleles. Nat Genet 38: 873-875.
11. Meijers-Heijboer H, van den Ouweland A, Klijn J, Wasielewski M, de Snoo A, et al. (2002) Low-penetrance susceptibility to breast cancer due to CHEK2(*)1100delC in noncarriers of BRCA1 or BRCA2 mutations. Nat Genet 31: 55-59.
12. Loveday C, Turnbull C, Ramsay E, Hughes D, Ruark E, et al. (2011) Germline mutations in RAD51D confer susceptibility to ovarian cancer. Nat Genet 43: 879-882.
13. Orr N, Lemnrau A, Cooke R, Fletcher O, Tomczyk K, et al. (2012) Genome-wide association study identifies a common variant in RAD51B associated with male breast cancer risk. Nat Genet 44: 1182-1184.
14. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
15. Turnbull C, Ahmed S, Morrison J, Pernet D, Renwick A, et al. (2010) Genome-wide association study identifies five new breast cancer susceptibility loci. Nat Genet 42: 504-507.
16. Ahmed S, Thomas G, Ghoussaini M, Healey CS, Humphreys MK, et al. (2009) Newly discovered breast cancer susceptibility loci on 3p24 and 17q23.2. Nat Genet 41: 585-590.
17. Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, et al. (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 39: 865-869.
18. Thomas G, Jacobs KB, Kraft P, Yeager M, Wacholder S, et al. (2009) A multistage genome-wide association study in breast cancer identifies two new risk alleles at 1p11.2 and 14q24.1 (RAD51L1). Nat Genet 41: 579-584.
19. Ghoussaini M, Fletcher O, Michailidou K, Turnbull C, Schmidt MK, et al. (2012) Genome-wide association analysis identifies three new breast cancer susceptibility loci. Nat Genet 44: 312-318.
20. Rosa-Rosa JM, Pita G, Urioste M, Llort G, Brunet J, et al. (2009) Genome-wide linkage scan reveals three putative breast-cancer-susceptibility loci. Am J Hum Genet 84: 115-122.
21. Heron SE, Smith KR, Bahlo M, Nobili L, Kahana E, et al. (2012) Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy. Nat Genet 44: 1188-1190.
22. Horani A, Druley TE, Zariwala MA, Patel AC, Levinson BT, et al. (2012) Whole-Exome Capture and Sequencing Identifies HEATR2 Mutation as a Cause of Primary Ciliary Dyskinesia. Am J Hum Genet 91: 685-693.
23. Campeau PM, Lu JT, Sule G, Jiang MM, Bae Y, et al. (2012) Whole-exome sequencing identifies mutations in the nucleoside transporter gene SLC29A3 in dysosteosclerosis, a form of osteopetrosis. Hum Mol Genet 21: 4904-4909.
24. Comino-Mendez I, Gracia-Aznarez FJ, Schiavi F, Landa I, Leandro-Garcia LJ, et al. (2011) Exome sequencing identifies MAX mutations as a cause of hereditary pheochromocytoma. Nat Genet 43: 663-667.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
26. Wang K, Li M, Hakonarson H, (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38: e164.
27. Garcia MJ, Fernandez V, Osorio A, Barroso A, Llort G, et al. (2009) Analysis of FANCB and FANCN/PALB2 fanconi anemia genes in BRCA1/2-negative Spanish breast cancer families. Breast Cancer Res Treat 113: 545-551.
28. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
29. Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081.
30. 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.
31. Yan Z, Delannoy M, Ling C, Daee D, Osman F, et al. (2010) A histone-fold complex and FANCM form a conserved DNA-remodeling complex to maintain genome stability. Mol Cell 37: 865-878.
32. Snape K, Ruark E, Tarpey P, Renwick A, Turnbull C, et al. (2012) Predisposition gene identification in common cancers by exome sequencing: insights from familial breast cancer. Breast Cancer Res Treat.
33. Thompson ER, Doyle MA, Ryland GL, Rowley SM, Choong DY, et al. (2012) Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles. PLoS Genet 8: e1002894.
34. Snape K, Hanks S, Ruark E, Barros-Nunez P, Elliott A, et al. (2011) Mutations in CEP57 cause mosaic variegated aneuploidy syndrome. Nat Genet 43: 527-529.
35. Chahrour MH, Yu TW, Lim ET, Ataman B, Coulter ME, et al. (2012) Whole-exome sequencing and homozygosity analysis implicate depolarization-regulated neuronal genes in autism. PLoS Genet 8: e1002635.
36. Antoniou AC, Easton DF, (2003) Polygenic inheritance of breast cancer: Implications for design of association studies. Genet Epidemiol 25: 190-202.
37. Fletcher O, Houlston RS, (2010) Architecture of inherited susceptibility to common cancer. Nat Rev Cancer 10: 353-361.
38. Rosa-Rosa JM, Gracia-Aznarez FJ, Hodges E, Pita G, Rooks M, et al. (2010) Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting. PLoS One 5: e9976.
39. Sawyer S, Mitchell G, McKinley J, Chenevix-Trench G, Beesley J, et al. (2012) A Role for Common Genomic Variants in the Assessment of Familial Breast Cancer. J Clin Oncol. Oct 29. [Epub ahead of print].