Table 2.
Ovarian cancer GWAS SNPs and LOH
| SNPa | Risk Alleleb | Locus | hetc | hom | AA | BB | NC | N | CHI sq | Direction | % LOHd | N LOH | Affy SNP | Rsquared |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs1243180 | NA | 10p12 | ||||||||||||
| rs1243188 | minor/A | 10p12 | 112 | 183 | 22 | 6 | 41 | 364 | 0.0025 | yes | 0.20 | 28 | SNP_A-2024177 | 0.881 |
| rs7098100 | minor/B | 10p12 | 132 | 181 | 1 | 9 | 41 | 364 | 0.0114 | yes | 0.07 | 10 | SNP_A-8636193 | 0.781 |
| rs757210 | NA | 17q12 | ||||||||||||
| rs11658063 | minor/B | 17q12 | 23 | 148 | 44 | 44 | 105 | 364 | 1.0000 | . | 0.79 | 88 | SNP_A-8714923 | 0.704 |
| rs9303542 | NA | 17q21 | ||||||||||||
| rs4451990 | minor/B | 17q21 | 20 | 197 | 49 | 61 | 37 | 364 | 0.2526 | . | 0.85 | 110 | SNP_A-2282117 | 1 |
| rs12944592 | minor/B | 17q21 | 24 | 198 | 54 | 60 | 28 | 364 | 0.5741 | . | 0.83 | 114 | SNP_A-1836563 | 1 |
| rs12452212 | minor/A | 17q21 | 19 | 196 | 74 | 53 | 22 | 364 | 0.0624 | yes | 0.87 | 127 | SNP_A-2128564 | 1 |
| rs9894812 | minor/A | 17q21 | 20 | 198 | 70 | 48 | 28 | 364 | 0.0428 | yes | 0.86 | 118 | SNP_A-2209606 | 1 |
| rs8170 | NA | 19p13 | ||||||||||||
| rs34084277 | minor/B | 19p13 | 80 | 260 | 9 | 8 | 7 | 364 | 0.8084 | . | 0.18 | 17 | SNP_A-1788674 | 1 |
| rs2072590 | NA | 2q31 | ||||||||||||
| rs711830 | minor/B | 2q31 | 77 | 160 | 8 | 14 | 105 | 364 | 0.2008 | . | 0.22 | 22 | SNP_A-8652216 | 0.965 |
| rs7651446 | NA | 3q25 | ||||||||||||
| rs344008 | minor/A | 3q25 | 58 | 297 | 2 | 3 | 4 | 364 | 0.6547 | . | 0.08 | 5 | SNP_A-8543714 | 0.85 |
| rs2292336 | minor/B | 3q25 | 48 | 299 | 2 | 5 | 10 | 364 | 0.2568 | . | 0.13 | 7 | SNP_A-8587822 | 0.85 |
| rs17380639 | minor/A | 3q25 | 28 | 320 | 11 | 3 | 2 | 364 | 0.0325 | yes | 0.33 | 14 | SNP_A-2078455 | 0.85 |
| rs11782652 | minor/B | 8q21 | 38 | 291 | 8 | 7 | 20 | 364 | 0.7963 | . | 0.28 | 15 | SNP_A-8702651 | . |
| rs10088218 | major/A | 8q24 | 47 | 280 | 11 | 11 | 15 | 364 | 1.0000 | . | 0.32 | 22 | SNP_A-1801410 | . |
| rs1516974 | major/A | 8q24 | 45 | 291 | 4 | 15 | 9 | 364 | 0.0116 | no | 0.30 | 19 | SNP_A-2088878 | 1 |
| rs3814113 | NA | 9p22 | ||||||||||||
| rs7032221 | major/B | 9p22 | 123 | 201 | 6 | 11 | 23 | 364 | 0.2253 | yes | 0.12 | 17 | SNP_A-8603886 | 1 |
| rs10738467 | major/B | 9p22 | 111 | 206 | 5 | 11 | 31 | 364 | 0.1336 | yes | 0.13 | 16 | SNP_A-8328297 | 0.892 |
| rs10962668 | major/B | 9p22 | 103 | 177 | 7 | 22 | 55 | 364 | 0.0053 | yes | 0.22 | 29 | SNP_A-4198891 | 0.794 |
a SNPs in bold are those named in the GWAS iCOG publication [29] All others are linked as indicated by the R-squared value of >0.7. If the minor allele is the risk allele named, it is assumed that this will also be the case for the linked SNP
b Minor = risk allele is the less frequent allele in the population. A, B = risk allele corresponds to the “A” or “B” allele respectively in the Affymetrix array nomenclature. NA = not on Affymetrix SNP6 array
c Het = Number of cases where germline and tumour are heterozygous, hom = cases where germline is heterozygous, AA, BB = germline is heterozygous, tumour is homozygous for A or B respectively, NC = no call in either tumour or germline. N = total number
d % LOH is the number of individuals with loss of one allele divided by the total number of heterozygous individuals as measured at that SNP, i.e. not the overall % of LOH that could be determined from all cases using a wider genetic window. This may therefore include regions of extreme allelic imbalance (e.g. likely for 8q24)