Table 5.
Risk loci for ER-negative breast cancer identified in the EUGENE gene-based analysis and not in previous GWAS
| Locus Index | Gene | Chr | Start | N sentinel eQTL | Gene-based P-valuea | Sentinel eQTL with strongest association in adjusted GWAS | OncoScore | ||
|---|---|---|---|---|---|---|---|---|---|
| Tested | with P < 0.05 in adjusted GWAS* | Variant | P-valueb | ||||||
| 1 | INHBB | 2 | 121103719 | 3 | 2 | 1.13E−07 | rs6542583 | 5.37E−06 | 25.82 |
| 2 | TNFSF10 | 3 | 172223298 | 4 | 3 | 4.93E−07 | rs2041692 | 5.66E−07 | 86.01 |
| 3 | VPS52 | 6 | 33218049 | 2 | 1 | 1.01E−06 | rs17215231 | 2.73E−07 | 17.45 |
| 4 | GTF2IRD2B | 7 | 74508364 | 1 | 1 | 8.52E−07 | rs2259337 | 8.52E−07 | 0 |
aGene-based association P-value obtained when the EUGENE gene-based test was applied to the adjusted GWAS results
bP-value in the Milne et al. GWAS3, adjusted for (i) the association with the sentinel risk variants identified in this study using the COJO-COND test; and (ii) the LD-score intercept