Utility of Next-Generation Sequencing in Renal Neoplasia, Including Tumors With Clear Cytoplasm and Rare Phenotypes (ELOC/MITF Alterations and Mismatch Repair Deficiency).

Abstract

To define the clinical utility of next-generation sequencing (NGS) of renal tumors, including carbonic anhydrase 9-positive renal neoplasia with clear cell features (ccRCN) that include ELOC (for expansion of gene symbols, use search tool at www.genenames.org) and MTOR/TSC1/TSC2-mutated renal cell carcinoma (RCC) with fibromyomatous stroma (ELOC-RCCfms and M/TSC-RCCfms, respectively), as these tumors often have overlapping features. Renal tumors (n=234) diagnosed between August 1, 2021, and June 15, 2025, were submitted for genomic profiling using Clinical Laboratory Improvement Amendments-validated 515-gene (n=30), 30-gene (n=175), and smaller (<5 gene, n=29) next-generation sequencing panels. Available histologic and NGS data was reviewed to render a final integrated diagnosis and determine clinical utility. Next-generation sequencing was requested solely for diagnostic indications in most cases (209 of 234 [89%]), with 66% of cases (154 of 234) showing a clinically impactful genomic profile. The highest utility was among ccRCN and high-grade RCC/RCC, type not otherwise specified (NOS) in which only 8 of 79 (10%) and 17 of 57 (30%) remained unclassifiable, respectively. Some rare phenotypes included variants associated with hereditary disease, uncommon presentations, multiple driver alterations, mismatch repair deficiency (n=3), and rare MITF p.E318K alterations (n=3). The cohort of ccRCN included 12 ELOC-RCCfms (p.Y79C/S: 9 of 12; p.A100E, 2 of 12; p.L104Q: 1 of 12). GPNMB was expressed in M/TSC-RCCfms (10 of 10, 100%) and lacked appreciable expression in most ccRCN tested (n=25), including ELOC-RCCfms. Next-generation sequencing-based molecular profiling had clinical utility in two-thirds of patients, and the greatest benefit was within the broad category of ccRCN. Our results suggest that GPNMB expression was helpful in separating ELOC-RCCfms from M/TSC-RCCfms. Other benefits of NGS include subtyping high-grade RCC/RCC type not otherwise specified and identification of rare phenotypes.