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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.