Table 2. Results of the association between SNPs and OS as a prognostic effect and as a predictive effect. Ten most statistically significant SNPs associated with OS with same direction of effect (either reduced or increased OS), in at least three out of four trials.
Rows in bold are those with p-value<0.05 in at least three out of four trials. Ch chromosome, NA Intergenic SNP, MAF minor allele frequencies in CALGB 80303, 40503, 80405, and ICON7, respectively, HR hazard ratio, CI confidence interval. Direction of effect increasing (−) or decreasing (+) OS in CALGB 80303, 40503, 80405, and ICON7, respectively. “_” SNP not present in the genotyping platform of the trial.
| Prognostic effect | |||||||||||
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| SNP | Ch | Gene | Feature | 5’ flanking | 3’ flanking | Base change | MAF | Direction of effect | Effect size (β) | HR (95% CI) | p-value |
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| rs680949 | 9 | PRUNE2 | intron | LOC392352 | LOC392352 | A>G | 0.07/0.06/0.07/0.06 | ++++ | 0.45 | 1.57 (1.33– 1.86) | 1.02x10 −7 |
| rs218527 | 18 | NA | NA | LOC100129774 | LOC100128360 | G>A | 0.09/0.10/0.10/0.11 | ++++ | 0.39 | 1.48 (1.28–1.71) | 1.83x10 −7 |
| rs2795492 | 9 | CORO2A | intron | TRIM14 | TBC1D2 | G>A | 0.41/0.41/0.42/0.42 | ---- | −0.22 | 0.81 (0.73–0.88) | 5.41x10−6 |
| rs476612 | 9 | LOC100129762 | intron | LOC392352 | PRUNE2 | A>C | _/0.06/0.07/0.06 | _+++ | 0.52 | 1.68 (1.34–2.12) | 8.45x10 −6 |
| rs7615734 | 3 | NA | NA | TPRG1 | TP63 | A>G | 0.16/0.18/0.18/0.21 | ++++ | 0.26 | 1.29 (1.15–1.45) | 9.58x10−6 |
| rs6712389 | 2 | NA | NA | KIAA1604 | LOC729009 | G>A | _/0.31/0.29/0.27 | _--- | −0.28 | 0.76 (0.67–0.86) | 1.16x10−5 |
| rs16852804 | 2 | BARD1 | intron | LOC100128203 | ABCA12 | G>A | 0.06/0.10/0.07/0.06 | ++++ | 0.41 | 1.51 (1.25–1.82) | 1.40x10−5 |
| rs10950639 | 7 | NA | NA | AGR3 | LOC100131425 | A>G | _/0.17/0.21/0.20 | _+++ | 0.29 | 1.33 (1.17–1.52) | 1.40x10−5 |
| rs4807493 | 19 | PIP5K1C | UTR-3’ | C19orf29 | TJP3 | G>A | 0.21/0.17/0.18/0.20 | -+-- | −0.25 | 0.78 (0.70–0.88) | 2.26x10−5 |
| rs2103445 | 8 | NA | NA | CALB1 | TMEM64 | G>A | _/0.30/0.29/0.31 | _+++ | 0.25 | 1.29 (1.15–1.45) | 2.29x10−5 |
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| Predictive effect | |||||||||||
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| SNP | Ch | Gene | Feature | 5’ flanking | 3’ flanking | Base change | MAF | Direction of effect | Effect size (β) | p-value | |
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| rs4969481 | 17 | DCXR | near 3’ | RAC3 | DCXR | G>A | 0.13/0.16/0.14/0.14 | ---- | −0.70 | 1.18x10−7 | |
| rs11895736 | 2 | LTBP1 | intron | TTC27 | RASGRP3 | A>G | 0.12/0.14/0.14/0.14 | ---- | −0.68 | 6.85x10−7 | |
| rs448960 | 20 | LOC100129869 | near 3’ | PMEPA1 | LOC100129869 | A>G | _/0.49/0.46/0.47 | _--- | −0.58 | 7.50x10−6 | |
| rs10763269 | 10 | NA | NA | LOC389970 | ZWINT | G>A | 0.27/0.24/0.22/0.21 | ++++ | 0.48 | 1.09x10−5 | |
| rs13392750 | 2 | NA | NA | ANKRD44 | LOC729342 | A>G | _/0.46/0.46/0.43 | _+++ | 0.58 | 1.23x10−5 | |
| rs3795897 | 2 | AGAP1 | intron | LOC642692 | LOC100130154 | G>A | 0.13/0.11/0.17/0.13 | ++++ | 0.68 | 1.43x10 −5 | |
| rs1150743 | 6 | NA | NA | HLA-J | ETF1P1 | G>A | 0.11/0.11/0.10/0.10 | ++++ | 0.66 | 1.83x10−5 | |
| rs10915428 | 1 | NA | NA | hCG_2036596 | LOC644357 | A>C | 0.46/0.44/0.51/0.48 | ---- | −0.39 | 1.86x10−5 | |
| rs11860804 | 16 | NA | NA | LOC729847 | DYNLRB2 | G>A | _/0.49/0.50/0.49 | _--- | −0.49 | 1.87x10−5 | |
| rs6453031 | 5 | RGNEF | intron | UTP15 | ENC1 | A>C | _/0.15/0.16/0.16 | _--- | −0.63 | 1.88x10−5 | |