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Table 2 Ovarian cancer GWAS SNPs and LOH

From: Loss of heterozygosity: what is it good for?

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
  1. 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
  2. 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
  3. 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
  4. 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)