Table 1 High confidence genes associated with cancers (TWAS significant, SMR significant, and PP.H4 > 0.8)
From: Prioritization of therapeutic targets for cancers using integrative multi-omics analysis
Type | Gene | TWAS | SMR | Coloc | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
Model | TWAS.Z | TWAS.P | topSNP | eQTL beta | SMR beta | OR (95% CI) | P val | PP.H4 | ||
Kidney cancer (whole blood) | IRF5 | susie | − 4.65 | 0.00000328 | rs3778754 | 0.4 | − 0.40 | 0.67 (0.57–0.78) | 0.000000412 | 0.99 |
Lung (tissue) | AMT | susie | − 4.6 | 0.00000413 | rs113741748 | − 0.45 | − 0.24 | 0.79 (0.71–0.87) | 6.14E−06 | 0.87 |
Breast Mammary Tissue (tissue) | MRPS30 | enet | 7.61 | 2.84E−14 | rs7716571 | 0.23 | 0.47 | 1.59 (1.32–1.93) | 1.68E−06 | 0.99 |
Breast Mammary Tissue (tissue) | RCCD1 | top1 | − 5.18 | 0.000000221 | rs113343095 | 0.55 | − 0.17 | 0.85 (0.79–0.91) | 3.01E−06 | 0.98 |
Malignant melanoma of skin (whole blood) | HERC2P9 | lasso | − 6.66 | 2.82E−11 | rs2003233 | − 0.4 | − 0.78 | 0.46 (0.35–0.6) | 1.63E−08 | 0.87 |
Skin Not Sun Exposed (tissue) | CLPTM1L | enet | − 8.11 | 5.12E−16 | rs31490 | − 0.14 | − 1.62 | 0.2 (0.11–0.35) | 1.45E−08 | 0.97 |
Skin Not Sun Exposed (tissue) | SPATA2L | lasso | 6.92 | 4.63E−12 | rs34404057 | − 0.15 | 1.51 | 4.54 (2.66–7.75) | 2.84E−08 | 0.92 |
Skin Not Sun Exposed (tissue) | GAS8 | enet | 7.06 | 1.63E−12 | rs12930631 | − 0.29 | 0.73 | 2.07 (1.51–2.84) | 6.22E−06 | 0.82 |
Skin Sun Exposed (tissue) | CLPTM1L | susie | − 8.76 | 2.00E−18 | rs401681 | − 0.12 | − 1.81 | 0.16 (0.08–0.34) | 1.44E−06 | 0.98 |
Prostate cancer (whole blood) | EEFSEC | top1 | − 7.57 | 3.85E−14 | rs4857836 | 0.13 | − 0.91 | 0.4 (0.29–0.56) | 9.07E−08 | 0.94 |
Prostate (tissue) | IRX4 | top1 | − 8.49 | 1.99E−17 | rs530543670 | − 0.53 | − 0.26 | 0.77 (0.72–0.83) | 2.05E−12 | 0.99 |
Prostate (tissue) | TPCN2 | enet | 7.79 | 6.47E−15 | rs72932523 | 0.47 | 0.26 | 1.3 (1.16–1.46) | 6.08E−06 | 1 |
Prostate (tissue) | PPP1R14A | top1 | 9.99 | 1.65E−23 | rs12610267 | − 0.2 | 0.70 | 2.02 (1.56–2.61) | 7.96E−08 | 0.99 |
Gastric cancer | THBS3 | enet | 5.08 | 0.000000371 | rs760077 | − 0.41 | 0.56 | 1.75 (1.42–2.14) | 0.000000113 | 0.99 |
Gastric (tissue) | PSCA | top1 | 6.47 | 9.71E−11 | rs2976388 | 0.7 | 0.37 | 1.44 (1.28–1.62) | 1.05E−09 | 0.96 |
Gastric (tissue) | LY6K | susie | 6.88 | 6.10E−12 | rs2976388 | 0.43 | 0.60 | 1.82 (1.4–2.38) | 1.04E−05 | 0.97 |
Gastric (tissue) | THEM6 | enet | 5.23 | 0.000000169 | rs2717600 | 0.26 | 0.93 | 2.54 (1.75–3.68) | 9.01E−07 | 0.89 |
Thyroid (tissue) | SMAD3 | susie | − 6.89 | 5.58E−12 | rs56375023 | − 0.48 | − 0.50 | 0.61 (0.51–0.72) | 1.23E−08 | 0.98 |