Table 2.
Description of the prognostic germline variants identified in this study.
(A) A description of the two prognostic germline variants (FDR<0.10) in the TCGA dataset identified when testing all 196,022 germline variants.
(B) A description of the prognostic germline variant (FDR<0.10) rs34988193 in ANKDD1a identified when the analysis was restricted to only germline variants with a combined annotation dependent depletion (CADD) score greater than 30 in the TCGA and CGGA datasets.
| Table 2A | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chrom | Pos | Ref | Alt | Population Frequency |
Sample Size |
Number of Heterozygotes |
Number of Homozygotes |
Gene Name |
Median Expression (FPKM) |
p-value | Hazard Ratio |
| rs61757955 | 17 | 75318086 | A | G | 5.01% | 291 | 21 | 0 | GRB2 | 42.2 | 7.08E-10 | 20.4 |
| rs28672782 | 11 | 1446622 | C | T | 16.27% | 50 | 15 | 5 | BRSK2 | 7.29 | <1E-16 | 1.15E-10 |
| Table 2B | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chrom | Pos | Ref | Alt | Population Frequency |
CADD Score |
PhyloP Score | Gene Name | Dataset | Sample Size |
Number of Heterozygotes |
Number of Homozygotes |
p-value | Hazard Ratio |
| rs34988193 | 15 | 64943580 | A | G | 30.90% | 32 | 8.42 | ANKDD1a | TCGA | 450 | 199 | 52 | 0.00113 | 1.73 |
| CGGA | 76 | 18 | 2 | 0.0743 | 1.79 |