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Table 1 Major genome-wide association and candidate gene studies to identify SNPs associated with breast cancer risk in populations of European and Asian ancestry

From: Common breast cancer risk variants in the post-COGS era: a comprehensive review

Reference Study design Populationa SNPs stratified by ER status Number of SNPs Number of cases / controls Novel SNPs identified in study and later confirmed in COGS (with exceptions noted)
BCAC, 2006 [23] Candidate gene European and Asian (BCAC) No 16 Variable per SNP All with borderline statistical significance
Cox and colleagues, 2007 [24] Candidate gene European and Asian (BCAC) No 9 11,391 to 18,290 / 14,753 to 22,670 rs1045485b, rs1982073c
Easton and colleagues, 2007 [25] Multistage GWAS I/II: English, III: European and Asian (BCAC) No I: 227,876, II: 12,711, III: 30 I: 390 / 364, II:3,990 / 3,916, III: 21,860 / 22,578 rs889312, rs13281615, rs2981582d, rs3817198
Hunter and colleagues, 2007 [26] Multistage GWAS I/II: European American (CGEMS) No I: 528,173, II: 8 I: 1,145 / 1,142, II: 1,776 / 2,072 rs1219648d, rs2420946d
Stacey and colleagues, 2007 [27], Stacey and colleagues, 2008 [28] Multistage GWAS - > candidate gene I: Icelandic, II: multi-ethnic American (MEC), Swedish, Dutch, Spanish Yes I: 311,524, IIa: 9, IIb: 10 I: 2,183 / 12,877, IIa: 3,898 / 6,921, IIb: 5,028 / 32,090 rs13387042 (ER+), rs10941679 (ER+), rs3803662e (ER+)
Zheng and colleagues, 2009 [29] Multistage GWAS and replication set (R) I/II/III: Chinese, R: European American Yes I: 607,728, II: 29, III: 4, R: 1 I: 1,505 / 1,522, II: 1,554 / 1,576, III: 3,472 / 900, R: 1,590 / 1,466 rs2046210 (ER+/ER–)
Thomas and colleagues, 2009 [30] Multistage GWAS I/II: European and Asian (BCAC) and European American (CGEMS) Yes I: 528,173, II: 30,278, III: 24 I: 1,145 / 1,142, II: 4,547 / 4,434, III: 4,078 / 5,223 rs999737, rs11249433 (ER+)
Ahmed and colleagues, 2009 [31] Candidate gene in two stages I/II: European and Asian (BCAC) and European American (CGEMS) No I: 814, II: 3 I: 3,878 / 3,928, II: 33,134 / 36,141 rs4973768, rs6504950
Turnbull and colleagues, 2010 [32] Multistage GWAS I: English, II: European No I: 582,886, II: 15 I: 3,659 / 4,897, II: 11,431 / 11,081 rs3757318, rs1011970, rs2380205b, rs10995190, rs704010, rs614367
Fletcher and colleagues, 2011 [33] Multistage GWAS I/II/III: English No I: 296,114, II: 1,223, III:14 I: 1,136 / 1,142, II: 3,080 / 3,936, III: 4,237 / 5,044 rs865686
Ghoussaini and colleagues, 2012 [34] Candidate gene European and Asian (BCAC) No 72 54,588 / 58,098 rs10771399, rs1292011, rs2823093
Michailidou and colleagues, 2013 [35] Large-scale candidate gene study 52 BCAC studies (41 European, nine Asian, two African ancestry) Yes in associated studies 199,961 (iCOGS array) 52,675 / 49,436 41 SNPsf
  1. COGS, Collaborative Oncological Gene–environment Study; ER, estrogen receptor; GWAS, genome-wide association study; SNP, single nucleotide polymorphism. aThe Breast Cancer Association Consortium (BCAC) population includes individuals of the following descent: Australian, European, Asian, American. The multiethnic cohort (MEC) population includes American individuals of the following descent: European, Latin, Hawaiian, Japanese, African. The Cancer Genetic Markers of Susceptibility (CGEMS) population is a nested case–control study within the Nurses' Health study in the United States. bSNPs showing borderline association with breast cancer risk in main COGS breast cancer GWAS. cNot tested in COGS and not considered an established locus by COGS. dThese SNPs are in the FGFR2 genomic region; rs2981579 from this region was tested in COGS. ers3803662 was newly identified by Easton and colleagues as well as by Stacey and colleagues [25, 27]. frs616488, rs11552449, rs4849887, rs2016394, rs1550623, rs16857609, rs6762644, rs12493607, rs9790517, rs6828523, rs10472076, rs1353747, rs1432679, rs11242675, rs204247, rs720475, rs9693444, rs6472903, rs2943559, rs11780156, rs10759243, rs7072776, rs11814448, rs7904519, rs11199914, rs3903072, rs11820646, rs12422552, rs17356907, rs11571833, rs2236007, rs2588809, rs941764, rs17817449, rs13329835, rs527616, rs1436904, rs4808801, rs3760982, rs132390, and rs6001930.