Integrative Analysis of Germline Rare Variants in Clear and Non-Clear Cell Renal Cell Carcinoma

IMPORTANCERCC encompasses a set of histologically distinct cancers with a high estimated genetic heritability, of which only a portion is currently explained. Previous rare germline variant studies in RCC have usually pooled clear and non-clear cell RCCs and have not adequately accounted for population stratification that may significantly impact the interpretation and discovery of certain candidate risk genes. OBJECTIVETo evaluate the enrichment of germline PVs in established cancer-predisposing genes (CPGs) in clear cell and non-clear cell RCC patients compared to cancer-free controls using approaches that account for population stratification and to identify unconventional types of germline RCC risk variants that confer an increased risk of developing RCC. DESIGN, SETTING, AND PARTICIPANTSIn 1,436 unselected RCC patients with sufficient data quality, we systematically identified rare germline PVs, cryptic splice variants, and copy number variants (CNVs). From this unselected cohort, 1,356 patients were ancestry-matched with 16,512 cancer-free controls, and gene-level enrichment of rare germline PVs were assessed in 143 CPGs, followed by an investigation of somatic events in matching tumor samples. MAIN OUTCOMES AND MEASURESGene-level burden of rare germline PVs, identification of secondary somatic events accompanying the germline PVs, and characterization of less-explored types of rare germline PVs in RCC patients. RESULTSIn clear cell RCC (n = 976 patients), patients exhibited significantly higher prevalence of PVs in VHL compared to controls (OR: 39.1, 95% CI: 7.01-218.07, p-value:4.95e-05, q-value:0.00584). In non-clear cell RCC (n = 380 patients), patients carried enriched burden of PVs in FH (OR: 77.9, 95% CI: 18.68-324.97, p-value:1.55e-08, q-value: 1.83e-06) and MET (OR: 1.98e11, 95% CI: 0-inf, p-value: 2.07e-05, q-value: 3.50e-07). In a CHEK2-focused analysis with European cases and controls, clear cell RCC patients (n=906 European patients) harbored nominal enrichment of the previously reported low-penetrance CHEK2 variants, p.Ile157Thr (OR:1.84, 95% CI: 1.00-3.36, p-value:0.049) and p.Ser428Phe (OR:5.20, 95% CI: 1.00-26.40, p-value:0.045) while non-clear cell RCC patients (n=295 European patients) exhibited nominal enrichment of CHEK2 LOF germline PVs (OR: 3.51, 95% CI: 1.10-11.10, p-value: 0.033). RCC patients with germline PVs in FH, MET, and VHL exhibited significantly earlier age of cancer onset compared to patients without any germline PVs in CPGs (Mean: 46.0 vs 60.2 years old, Tukey adjusted p-value < 0.0001), and more than half had secondary somatic events affecting the same gene (n=10/15, 66.7%, 95% CI: 38.7-87.0%). Conversely, patients with rare germline PVs in CHEK2 exhibited a similar age of disease onset to patients without any identified germline PVs in CPGs (Mean: 60.1 vs 60.2 years old, Tukey adjusted p-value: 0.99), and only 30.4% of the patients carried secondary somatic events in CHEK2 (n=7/23, 95% CI: 14.1-53.0%). Finally, rare pathogenic germline cryptic splice variants underexplored in RCC were identified in SDHA and TSC1, and rare pathogenic germline CNVs were found in 18 patients, including CNVs in FH, SDHA, and VHL. CONCLUSIONS AND RELEVANCEThis systematic analysis supports the existing link between several RCC risk genes and elevated RCC risk manifesting in earlier age of RCC onset. Our analysis calls for caution when assessing the role of germline PVs in CHEK2 due to the burden of founder variants with varying population frequency in different ancestry groups. It also broadens the definition of the RCC germline landscape of pathogenicity to incorporate previously understudied types of germline variants, such as cryptic splice variants and CNVs. KEY Points QuestionCan we improve the assessment of germline genetic risk determinants for clear cell and non-clear cell renal cell carcinoma (RCC) with approaches that are aware to population-stratification and RCC histological subtypes? FindingsIn this systematic case-control study of 1,356 RCC patients and 16,512 ancestry-matched cancer-free controls strictly controlling for population stratification, clear-cell RCC patients exhibited a significantly higher prevalence of rare germline pathogenic variants (PVs) in VHL, and non-clear cell RCC patients carried significantly more rare germline PVs in FH and MET. European clear-cell RCC patients harbored a nominally significant enrichment of two low-penetrance CHEK2 variants (p.Ser428Phe and p.Ile157Thr) while European non-clear RCC patients carried a nominally significant enrichment of rare germline loss-of-function (LOF) variants in CHEK2. Subsequent somatic analyses identified secondary somatic events in genes significantly enriched for germline PVs (VHL, FH, MET), and these variant carriers presented with earlier age of disease onset, but CHEK2 germline variant carriers harbored relatively fewer somatic events in CHEK2 and did not present with earlier age of onset. Finally, we identified 6 RCC patients with rare germline cryptic splice and copy number variants that impacted known kidney cancer risk genes, increasing the diagnostic yield of pathogenic variants in RCC risk genes from 2.1% to 2.5%. MeaningClear and non-clear RCCs have distinct germline pathogenic variant enrichment patterns and somatic variants. Accurate risk assessment of CHEK2 in RCC requires careful adjustment for population stratification. In addition, previously underappreciated forms of germline variants may explain a portion of the missing heritability in RCC.