Table 1.
Germline and somatic variants pathway associations. Pathways with permutation P-values <0.05 are shown.
| Pathway | Source | Mutation | pCR (n=26) | RD (n=31) | Mutation Rate in pCR | Mutation Rate in RD | Permutation P value | OR | OR Lower 95% CI |
|---|---|---|---|---|---|---|---|---|---|
| PI3K | Nanostring metabolic |
Germline | 16 | 9 | 0.6154 | 0.2903 | 0.0082 | 3.9111 | 2.2232 |
| DNA Damage Repair | Nanostring metabolic |
Germline | 10 | 5 | 0.3846 | 0.1613 | 0.0307 | 3.2500 | 1.7254 |
| MAPK | Nanostring metabolic |
Germline | 8 | 4 | 0.3077 | 0.1290 | 0.0435 | 3.0000 | 1.5141 |
| WNT_BETA _CATENIN _SIGNALING |
MSigDB Hallmark |
Germline | 16 | 13 | 0.6154 | 0.4194 | 0.0493 | 2.2154 | 1.2870 |
| INTERFERON_ALPHA _RESPONSE |
MSigDB Hallmark |
Somatic | 12 | 5 | 0.4615 | 0.1613 | 0.0048 | 4.4571 | 2.3808 |
| MAPK | Nanostring metabolic |
Somatic | 25 | 23 | 0.9615 | 0.7419 | 0.0076 | 8.6957 | 2.8966 |
| Myc | Nanostring metabolic |
Somatic | 24 | 22 | 0.9231 | 0.7097 | 0.0089 | 4.9091 | 2.1290 |
| DNA Damage Repair | Nanostring metabolic |
Somatic | 25 | 23 | 0.9615 | 0.7419 | 0.0131 | 8.6957 | 2.8966 |
| Transcriptional Regulation | Nanostring metabolic |
Somatic | 25 | 23 | 0.9615 | 0.7419 | 0.0175 | 8.6957 | 2.8966 |
| Wnt_pathway | Nanostring hallmarks |
Somatic | 24 | 23 | 0.9231 | 0.7419 | 0.0184 | 4.1739 | 1.7971 |
| Cell Cycle | Nanostring metabolic | Somatic | 24 | 23 | 0.9231 | 0.7419 | 0.0184 | 4.1739 | 1.7971 |
| Transcriptional_misregulation | Nanostring hallmarks |
Somatic | 24 | 23 | 0.9231 | 0.7419 | 0.0217 | 4.1739 | 1.7971 |
| WNT_BETA _CATENIN _SIGNALING |
MSigDB Hallmark |
Somatic | 24 | 23 | 0.9231 | 0.7419 | 0.0217 | 4.1739 | 1.7971 |
| MYC_ TARGETS_V2 |
MSigDB Hallmark |
Somatic | 7 | 3 | 0.2692 | 0.0968 | 0.0250 | 3.4386 | 1.6221 |
| DNA_REPAIR | MSigDB Hallmark |
Somatic | 25 | 25 | 0.9615 | 0.8065 | 0.0268 | 6.0000 | 1.9645 |
| HYPOXIA | MSigDB Hallmark |
Somatic | 16 | 12 | 0.6154 | 0.3871 | 0.0287 | 2.5333 | 1.4670 |
| INTERFERON_GAMMA _RESPONSE |
MSigDB Hallmark |
Somatic | 15 | 10 | 0.5769 | 0.3226 | 0.0313 | 2.8636 | 1.6481 |
| UV _RESPONSE _UP |
MSigDB Hallmark |
Somatic | 12 | 8 | 0.4615 | 0.2581 | 0.0320 | 2.4643 | 1.3956 |
| APICAL _SURFACE |
MSigDB Hallmark |
Somatic | 8 | 4 | 0.3077 | 0.1290 | 0.0333 | 3.0000 | 1.5141 |
| Cell_cycle_and_apoptosis | Nanostring hallmarks |
Somatic | 25 | 24 | 0.9615 | 0.7742 | 0.0344 | 7.2917 | 2.4113 |
| Cytokine & Chemokine Signaling | Nanostring metabolic |
Somatic | 25 | 24 | 0.9615 | 0.7742 | 0.0344 | 7.2917 | 2.4113 |
| E2F _TARGETS |
MSigDB Hallmark |
Somatic | 25 | 24 | 0.9615 | 0.7742 | 0.0344 | 7.2917 | 2.4113 |
| PI3K | Nanostring metabolic |
Somatic | 25 | 24 | 0.9615 | 0.7742 | 0.0360 | 7.2917 | 2.4113 |