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Genetics of Breast and Ovarian Cancer (PDQ®)

  • Updated: 03/04/2013

Table 8. High-probability Breast Cancer Susceptibility Loci Identified Through Genome-Wide Association Studies

Putative Gene(s) Chromosome  SNP Study Citationa Odds Ratio (OR) (95% Confidence Interval [CI])b Comments 
Intergenic /NOTCH21p11.2rs11249433[89]1.08 (1.02–1.15) [109]Stronger in ER+, low-grade [109]; also in BRCA2 [119]
ERBB2 2q34rs13393577[120]1.53 (1.37–1.70) [120]Identified in Korean subjects [120]
Intergenic2q35rs13387042[107]1.21 (1.14–1.29) [109]Stronger in bilateral and lobular [116]; also in BRCA1 and BRCA2 [121]
SLC4A7, NEK103p24rs4973768[115]1.16 (1.10–1.24) [109]Also in BRCA2 [121]
MRPS30 5p12rs10941679[114]1.11c (1.04–1.19) [109]Strongest in PR+, low-grade [122]; also in BRCA2 [121]
TERT-/CLPTM15p15rs10069690[117]1.25 (1.16–1.34) [117]Strongest in triple-negative [117]
MAP3K1 5q11.2rs889312[106]1.22 (1.14–1.30) [109]Stronger in ER+ [109]; also in BRCA2 [121]
RNF146 6q22rs2180341[110]1.24 (1.13–1.36) [123]Stronger in Ashkenazi Jews [123]
ESR1 6q25.1rs2046210[111]1.15c (1.08–1.22) [109]Also in BRCA1 [119]
TAB2 6q25.1rs9485372[124]0.90 (0.87–0.92) [124]Identified in Chinese subjects [124]
Intergenic7q32.3rs2048672[125]1.11 (1.05–1.17) [125]Identified in East Asian subjects [125]
Intergenic/MYC8q24.21rs13281615[106]1.14 (1.07–1.21) [109]Stronger in ER+ [109]
CDKN2A, CDKN2B 9p21rs1011970[109]1.09 (1.04–1.14) [109]Stronger in ER+ [109]; also in BRCA2 [126]
Intergenic9q31.2rs865686[127]0.89(0.85–0.92) [127]Also in BRCA2 [126]
ANKRD16, FBXO18 10p15.1rs2380205[109]0.94 (0.91–0.98) [109]
ZNF365 10q21.2rs10995190[109]0.86 (0.82–0.91) [109]Stronger in ER+ in general population [109]; also in BRCA2 [128]
ZMIZ1 10q22.3rs704010[109]1.07 (1.03–1.11) [109]
FGFR2 10q26.13rs2981582[106]1.43 (1.35–1.53) [109]Strongest for ER+, low-grade [116]; also in BRCA2 [121]
LSP1 11p15.5rs3817198[106]1.12 (1.05–1.19) [109]Also in BRCA2 [121]
Intergenic11q13rs614367[109]1.15 (1.10–1.20) [109]Restricted to ER+ tumors; strongest for ER+/PR+[109]
BARX211q24.3rs7107217[124]1.08 (1.05–1.11) [124]Identified in Chinese subjects [124]
PTHLH 12p11rs10771399[129]0.85 (0.83–0.88) [129]Also in BRCA1 [126]
Intergenic12q24rs1292011[129]0.92 (0.91–0.94) [129]Restricted to ER+ [129]; also in BRCA2 [126]
RAD51B 14q24.1rs999737[89]0.89 (0.83–0.95) [109]Associated with all subtypes, including triple-negative [90]; also in BRCA2 [126]
TOX3 16q12.1rs3803662[106]1.30 (1.22–1.39) [109]Stronger in ER+ [116]; also in BRCA1 and BRCA2 [121]
COX11 17q23.2rs6504950[115]0.92c (0.86–0.99) [109]
BABAM1 19p13.1rs8170[118]1.26 (1.17–1.35) [130]Restricted to triple-negative in general population [118]; also in BRCA1 [130]
NRIP1 21q21rs2823093[129]0.94 (0.92–0.96) [129]Restricted to ER+ [129]

ER- = estrogen receptor–negative; ER+ = estrogen receptor–positive; PR- = progesterone receptor–negative; PR+ = progesterone receptor–positive; SNP = single nucleotide polymorphism; triple-negative = ER-/PR-/HER2/neu-.
aInitial study that demonstrated genome-wide significance for each locus.
bAll associations observed in the general population, unless otherwise indicated; when relevant, if association was also observed in BRCA1 or BRCA2 mutation carriers, it is indicated.
cOR for best tagSNP was used [109] as a surrogate for published SNP.

References

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