Table 2:
HR for risk-associated top-10 genes from VCF and MAF files derived using MuTect2, MuSE, Varscan2 and SomaticSniper technique
| MuTect2 |
MuSE |
Varscan2 |
SomaticSniper |
||||
|---|---|---|---|---|---|---|---|
| Gene | HR | Gene | HR | Gene | HR | Gene | HR |
| (P-value) | (P-value) | (P-value) | (P-value) | ||||
| VCF files | |||||||
| SNHG10 | 5.49 (3.94E-06) | CLMP | 3.01 (1.67E-05) | FAM160A2 | 6.81 (4.01E-05) | CLDN20 | 7.06 (6.62E-07) |
| WIZ | 2.69 (9.71E-07) | BIRC6 | 2.80 (4.46E-04) | LOC100420587 | 5.45 (1.31E-07) | NR2C2AP | 5.17 (3.16E-05) |
| MGAT4EP | 2.49 (4.46E-04) | LINC02210-CRHR1 | 2.03 (6.42E-03) | SPDYA | 3.08 (7.70E-04) | ATG9B | 3.34 (2.59E-04) |
| LINC00304 | 2.39 (7.40E-05) | DHX8 | 2.00 (2.90E-02) | BRSK2 | 2.55 (1.01E-03) | HAUS5 | 2.79 (2.22E-05) |
| CACNG7 | 1.93 (5.72E-04) | LINC00972 | 1.91 (9.31E-03) | ADGRF4 | 2.21 (1.23E-02) | LOC100287329 | 2.58 (8.23E-04) |
| OR52B6 | 1.83 (1.12E-03) | PAX7 | 1.90 (8.29E-04) | LINC00972 | 2.11 (2.18E-03) | P4HTM | 2.18 (2.43E-02) |
| TYK2 | 1.80 (2.21E-03) | TAS1R2 | 1.61 (2.63E-02) | TM4SF18 | 2.07 (1.40E-02) | OR6C76 | 2.12 (1.18E-03) |
| PIGO | 1.79 (1.66E-02) | SNTG1 | 1.53 (3.37E-02) | OR5AS1 | 1.86 (1.43E-02) | CLK2 | 1.94 (3.58E-02) |
| S100A12 | 1.71 (1.10E-02) | CNTN5 | 1.34 (2.25E-01) | PDE11A | 1.72 (2.74E-03) | FAM187B | 1.64 (1.51E-02) |
| DNAJC9-AS1 | 1.08 (6.51E-01) | ZNF521 | 1.26 (2.63E-01) | LOC101929073 | 1.29 (2.98E-01) | NOMO3 | 1.34 (1.45E-01) |
| MAF files | |||||||
| LAMC3 | 9.25 (1.78E-06) | ITGB8 | 8.37 (5.69E-07) | SYDE1 | 8.46 (3.71E-05) | CAD | 5.56 (8.10E-04) |
| EVC2 | 4.30 (8.66E-05) | TBX3 | 8.10 (6.06E-05) | ALPP | 4.33 (1.44E-03) | TOP2A | 4.63 (2.73E-03) |
| NYNRIN | 3.94 (1.22E-03) | SIPA1L3 | 4.90 (5.54E-05) | KIAA2026 | 3.85 (1.49E-03) | KIAA2026 | 4.01 (2.62E-03) |
| KIAA2026 | 3.85 (1.49E-03) | CAD | 4.45 (3.58E-03) | CAD | 3.32 (1.91E-02) | EVC2 | 4.00 (1.04E-03) |
| SUPT20H | 3.41 (7.53E-03) | EVC2 | 4.16 (2.97E-04) | BRINP2 | 2.83 (2.43E-02) | KTN1 | 2.56 (1.09E-01) |
| BRINP2 | 2.83 (2.43E-02) | ARHGEF11 | 3.17 (2.37E-02) | TP53 | 1.60 (9.85E-03) | EPHA3 | 2.25 (1.67E-01) |
| LRP1B | 1.93 (7.81E-03) | BRINP2 | 2.80 (2.56E-02) | PCDH15 | 1.48 (2.81E-01) | KIF26B | 2.03 (1.66E-01) |
| TP53 | 1.48 (3.60E-02) | PCDH15 | 1.72 (1.20E-01) | TG | 1.46 (4.53E-01) | PCDH15 | 1.76 (1.78E-01) |
| TG | 1.46 (4.53E-01) | TG | 1.46 (4.55E-01) | PLCB1 | 1.25 (7.00E-01) | TP53 | 1.63 (1.20E-02) |
| PCDH15 | 1.43 (3.30E-01) | CSMD3 | 1.24 (4.54E-01) | XIRP2 | 1.11 (7.55E-01) | TG | 1.18 (8.17E-01) |