Replication results for tests of association in the WU validation cohort as compared with the original UC cohort
| Rank . | SNP . | University of Chicago . | Washington University . | Combined . | |||||
|---|---|---|---|---|---|---|---|---|---|
| MAF . | Fisher exact P* . | MAF . | Fisher exact P† . | ||||||
| Controls . | Cases . | Controls . | Cases . | Fisher exact P* . | OR (95% CI) . | ||||
| I. Allele frequency comparisons conducted between all cases and all controls in each cohort (UC: 78 cases, 148 controls; WU: 70 cases, 95 controls) | |||||||||
| 1 | rs953509 | 0.172 | 0.357 | 2.88E−05 | 0.204 | 0.169 | .826 | 8.18E−03 | 1.62 (1.14-2.30) |
| 3 | rs1394384 | 0.250 | 0.089 | 3.79E−05 | 0.228 | 0.162 | .094 | 6.88E−05 | 0.45 (0.29-0.67) |
| 5 | rs556831 | 0.025 | 0.118 | 1.48E−04 | 0.042 | 0.051 | .455 | 2.20E−03 | 2.85 (1.48-5.50) |
| 6 | rs1381392 | 0.128 | 0.282 | 1.54E−04 | 0.142 | 0.193 | .140 | 3.22E−04 | 2.02 (1.38-2.96) |
| 8 | rs1374284 | 0.395 | 0.577 | 2.44E−04 | 0.458 | 0.448 | .615 | 9.15E−03 | 1.48 (1.11-1.98) |
| 9 | rs1335546 | 0.378 | 0.558 | 3.24E−04 | 0.420 | 0.421 | .536 | 7.39E−03 | 1.49 (1.12-2.00) |
| 12 | rs957553 | 0.356 | 0.195 | 4.79E−04 | 0.268 | 0.321 | .875 | .050 | 0.72 (0.52-0.99) |
| 13 | rs1394606 | 0.155 | 0.047 | 5.62E−04 | 0.121 | 0.121 | .574 | .016 | 0.55 (0.33-0.89) |
| 14 | rs1199098 | 0.269 | 0.128 | 6.37E−04 | 0.210 | 0.239 | .775 | .046 | 0.68 (0.47-0.98) |
| 15 | rs666282 | 0.226 | 0.092 | 6.88E−04 | 0.117 | 0.181 | .962 | .102 | 0.70 (0.46-1.07) |
| II. Allele frequency comparisons conducted only between cases with abnormalities of chromosomes 5 or 7 or both and all controls in each cohort (UC: 51 cases, 148 controls; WU: 25 cases; 95 controls) | |||||||||
| 1 | rs953509 | 0.172 | 0.296 | .015 | 0.204 | 0.130 | .917 | .176 | 1.38 (0.87-2.19) |
| 3 | rs1394384 | 0.250 | 0.083 | 7.54E−04 | 0.228 | 0.087 | .022 | 4.55E−05‡ | 0.29 (0.15-0.56) |
| 5 | rs556831 | 0.025 | 0.140 | 1.80E−04 | 0.042 | 0.060 | .411 | 1.02E−03 | 3.74 (1.78-7.87) |
| 6 | rs1381392 | 0.128 | 0.256 | 8.81E−03 | 0.142 | 0.220 | .131 | 4.19E−03‡ | 2.08 (1.29-3.35) |
| 8 | rs1374284 | 0.395 | 0.589 | 1.55E−03 | 0.458 | 0.435 | .672 | .019 | 1.60 (1.09-2.35) |
| 9 | rs1335546 | 0.378 | 0.544 | 7.05E−03 | 0.420 | 0.280 | .977 | .243 | 1.26 (0.86-1.84) |
| 12 | rs957553 | 0.356 | 0.182 | 1.71E−03 | 0.268 | 0.348 | .894 | .071 | 0.66 (0.43-1.03) |
| 13 | rs1394606 | 0.155 | 0.068 | .034 | 0.121 | 0.140 | .733 | .156 | 0.63 (0.34-1.18) |
| 14 | rs1199098 | 0.269 | 0.122 | 4.06E−03 | 0.210 | 0.146 | .218 | 3.43E−03‡ | 0.46 (0.27-0.79) |
| 15 | rs666282 | 0.226 | 0.105 | .023 | 0.117 | 0.200 | .956 | .353 | 0.75 (0.43-1.30) |
| Rank . | SNP . | University of Chicago . | Washington University . | Combined . | |||||
|---|---|---|---|---|---|---|---|---|---|
| MAF . | Fisher exact P* . | MAF . | Fisher exact P† . | ||||||
| Controls . | Cases . | Controls . | Cases . | Fisher exact P* . | OR (95% CI) . | ||||
| I. Allele frequency comparisons conducted between all cases and all controls in each cohort (UC: 78 cases, 148 controls; WU: 70 cases, 95 controls) | |||||||||
| 1 | rs953509 | 0.172 | 0.357 | 2.88E−05 | 0.204 | 0.169 | .826 | 8.18E−03 | 1.62 (1.14-2.30) |
| 3 | rs1394384 | 0.250 | 0.089 | 3.79E−05 | 0.228 | 0.162 | .094 | 6.88E−05 | 0.45 (0.29-0.67) |
| 5 | rs556831 | 0.025 | 0.118 | 1.48E−04 | 0.042 | 0.051 | .455 | 2.20E−03 | 2.85 (1.48-5.50) |
| 6 | rs1381392 | 0.128 | 0.282 | 1.54E−04 | 0.142 | 0.193 | .140 | 3.22E−04 | 2.02 (1.38-2.96) |
| 8 | rs1374284 | 0.395 | 0.577 | 2.44E−04 | 0.458 | 0.448 | .615 | 9.15E−03 | 1.48 (1.11-1.98) |
| 9 | rs1335546 | 0.378 | 0.558 | 3.24E−04 | 0.420 | 0.421 | .536 | 7.39E−03 | 1.49 (1.12-2.00) |
| 12 | rs957553 | 0.356 | 0.195 | 4.79E−04 | 0.268 | 0.321 | .875 | .050 | 0.72 (0.52-0.99) |
| 13 | rs1394606 | 0.155 | 0.047 | 5.62E−04 | 0.121 | 0.121 | .574 | .016 | 0.55 (0.33-0.89) |
| 14 | rs1199098 | 0.269 | 0.128 | 6.37E−04 | 0.210 | 0.239 | .775 | .046 | 0.68 (0.47-0.98) |
| 15 | rs666282 | 0.226 | 0.092 | 6.88E−04 | 0.117 | 0.181 | .962 | .102 | 0.70 (0.46-1.07) |
| II. Allele frequency comparisons conducted only between cases with abnormalities of chromosomes 5 or 7 or both and all controls in each cohort (UC: 51 cases, 148 controls; WU: 25 cases; 95 controls) | |||||||||
| 1 | rs953509 | 0.172 | 0.296 | .015 | 0.204 | 0.130 | .917 | .176 | 1.38 (0.87-2.19) |
| 3 | rs1394384 | 0.250 | 0.083 | 7.54E−04 | 0.228 | 0.087 | .022 | 4.55E−05‡ | 0.29 (0.15-0.56) |
| 5 | rs556831 | 0.025 | 0.140 | 1.80E−04 | 0.042 | 0.060 | .411 | 1.02E−03 | 3.74 (1.78-7.87) |
| 6 | rs1381392 | 0.128 | 0.256 | 8.81E−03 | 0.142 | 0.220 | .131 | 4.19E−03‡ | 2.08 (1.29-3.35) |
| 8 | rs1374284 | 0.395 | 0.589 | 1.55E−03 | 0.458 | 0.435 | .672 | .019 | 1.60 (1.09-2.35) |
| 9 | rs1335546 | 0.378 | 0.544 | 7.05E−03 | 0.420 | 0.280 | .977 | .243 | 1.26 (0.86-1.84) |
| 12 | rs957553 | 0.356 | 0.182 | 1.71E−03 | 0.268 | 0.348 | .894 | .071 | 0.66 (0.43-1.03) |
| 13 | rs1394606 | 0.155 | 0.068 | .034 | 0.121 | 0.140 | .733 | .156 | 0.63 (0.34-1.18) |
| 14 | rs1199098 | 0.269 | 0.122 | 4.06E−03 | 0.210 | 0.146 | .218 | 3.43E−03‡ | 0.46 (0.27-0.79) |
| 15 | rs666282 | 0.226 | 0.105 | .023 | 0.117 | 0.200 | .956 | .353 | 0.75 (0.43-1.30) |
SNP markers genotyped in the WU cohort are listed by descending order of significance along with their rank in the UC cohort. Site-adjusted odds ratios (ORs) are given for the combined cohort with 95% CIs.
MAF indicates minor allele frequency.
Denotes a 2-sided Fisher exact test.
Denotes a 1-sided Fisher exact test.
SNPs are more significantly associated with t-AML in the combined cohort than in the original UC cohort.