Germline genetic variants in somatically significantly mutated genes in tumors are associated with renal cell carcinoma risk and outcome

Genome-wide association studies (GWAS) have identified 13 susceptibility loci for renal cell carcinoma (RCC). Additional genetic loci of risk remain to be explored. Moreover, the role of germline genetic variants in predicting RCC recurrence and overall survival (OS) is less understood. In this study, we focused on 127 significantly mutated genes from The Cancer Genome Atlas (TCGA) Pan-Cancer Analysis across 12 major cancer sites to identify potential genetic variants predictive of RCC risk and clinical outcomes. In a three-phase design with a total of 2657 RCC cases and 5315 healthy controls, two single nucleotide polymorphisms (SNPs) that map to PIK3CG (rs6466135:A, OR_meta = 0.85, 95% CI = 0.77-0.94, P_meta = 1.4 × 10^-3) and ATM (rs611646:T, OR_meta = 1.17, 95% CI = 1.05-1.31, P_meta = 3.5 × 10^-3) were significantly associated with RCC risk. With respect to RCC recurrence and OS, two separate datasets with a total of 661 stages I-III RCC patients (discovery: 367; validation: 294) were analyzed. The most significant association was observed for rs10932384:C (ERBB4) with both outcomes (recurrence: HR_meta = 0.52, 95% CI = 0.39-0.68, P_meta = 3.81 × 10-6; OS: HR_meta = 0.50, 95% CI = 0.37-0.67, P_meta = 6.00 × 10-6). In addition, six SNPs were significantly associated with either RCC recurrence or OS but not both (P_meta < 0.01). Rs10932384:C was significantly correlated with mutation frequency of ERBB4 in clear cell RCC (ccRCC) patients (P = 0.003, Fisher's exact test). Cis-eQTL was observed for several SNPs in blood/transformed fibroblasts but not in RCC tumor tissues. In summary, we identified promising genetic predictors of recurrence and OS among RCC patients with localized disease.