RGD Reference Report - Genome-wide association study identifies novel breast cancer susceptibility loci. - Rat Genome Database

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Genome-wide association study identifies novel breast cancer susceptibility loci.

Authors: Easton, DF  Pooley, KA  Dunning, AM  Pharoah, PD  Thompson, D  Ballinger, DG  Struewing, JP  Morrison, J  Field, H  Luben, R  Wareham, N  Ahmed, S  Healey, CS  Bowman, R  Meyer, KB  Haiman, CA  Kolonel, LK  Henderson, BE  Le Marchand, L  Brennan, P  Sangrajrang, S  Gaborieau, V  Odefrey, F  Shen, CY  Wu, PE  Wang, HC  Eccles, D  Evans, DG  Peto, J  Fletcher, O  Johnson, N  Seal, S  Stratton, MR  Rahman, N  Chenevix-Trench, G  Bojesen, SE  Nordestgaard, BG  Axelsson, CK  Garcia-Closas, M  Brinton, L  Chanock, S  Lissowska, J  Peplonska, B  Nevanlinna, H  Fagerholm, R  Eerola, H  Kang, D  Yoo, KY  Noh, DY  Ahn, SH  Hunter, DJ  Hankinson, SE  Cox, DG  Hall, P  Wedren, S  Liu, J  Low, YL  Bogdanova, N  Schurmann, P  Dork, T  Tollenaar, RA  Jacobi, CE  Devilee, P  Klijn, JG  Sigurdson, AJ  Doody, MM  Alexander, BH  Zhang, J  Cox, A  Brock, IW  MacPherson, G  Reed, MW  Couch, FJ  Goode, EL  Olson, JE  Meijers-Heijboer, H  Van den Ouweland, A  Uitterlinden, A  Rivadeneira, F  Milne, RL  Ribas, G  Gonzalez-Neira, A  Benitez, J  Hopper, JL  McCredie, M  Southey, M  Giles, GG  Schroen, C  Justenhoven, C  Brauch, H  Hamann, U  Ko, YD  Spurdle, AB  Beesley, J  Chen, X  Mannermaa, A  Kosma, VM  Kataja, V  Hartikainen, J  Day, NE  Cox, DR  Ponder, BA  Day, Nicholas E  Cox, David R  Ponder, Bruce A J 
Citation: Easton DF, etal., Nature. 2007 Jun 28;447(7148):1087-93.
RGD ID: 2289657
Pubmed: PMID:17529967   (View Abstract at PubMed)
PMCID: PMC2714974   (View Article at PubMed Central)
DOI: DOI:10.1038/nature05887   (Journal Full-text)

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r2 > 0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10(-7)). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P < 0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.



RGD Manual Disease Annotations    Click to see Annotation Detail View

  
Object SymbolSpeciesTermQualifierEvidenceWithNotesSourceOriginal Reference(s)
FGFR2Humanbreast cancer  IAGP DNA:SNP:intron:dbSNP ID rs2981582 and p=2X10-76RGD 
Fgfr2Ratbreast cancer  ISORGd:736865 RGD 
Fgfr2Mousebreast cancer  ISORGd:736865 RGD 
MAP3K1Humanbreast cancer  IAGP DNA:SNP:linkage disequilibrium block:minor allele of SNP rs889312 and p=7x10e-20RGD 
Map3k1Ratbreast cancer  ISOMAP3K1 (Homo sapiens) RGD 
Map3k1Mousebreast cancer  ISOMAP3K1 (Homo sapiens) RGD 

Objects Annotated

Genes (Rattus norvegicus)
Fgfr2  (fibroblast growth factor receptor 2)
Map3k1  (mitogen-activated protein kinase kinase kinase 1)

Genes (Mus musculus)
Fgfr2  (fibroblast growth factor receptor 2)
Map3k1  (mitogen-activated protein kinase kinase kinase 1)

Genes (Homo sapiens)
FGFR2  (fibroblast growth factor receptor 2)
MAP3K1  (mitogen-activated protein kinase kinase kinase 1)


Additional Information