Abstract 5037: Accelerated somatic mutation calling for whole-exome sequencing of tumor samples

Abstract Background: Integrating next-generation sequencing (NGS) data into clinical practice faces several challenges. High-throughput sequencing generates massive amounts of data that need to be processed quickly to deliver timely clinical insights. Additionally, formalin-fixed paraffin embedded (FFPE) tissue is the primary resource for tumor molecular profiling in clinical settings. However, nucleic acids extracted from FFPE are prone to chemical alterations and technical artifacts during sequencing. Therefore, distinguishing tumor-specific variants from artifacts and germline variation with a low false discovery rate rapidly with high accuracy remains challenging. Methods: We recently developed MuSE2, an advanced somatic mutation caller for cancer genomics that integrates a nucleotide-specific Markov substitution model for molecular evolution, a tumor-specific error model to determine tier-based cutoffs for selecting SNVs, and an optimized multi-threaded processing pipeline. It was demonstrated significantly enhanced accuracy and up to 8-80 folds faster performance compared to other common variant callers. Next, we evaluated the performance of our variant calling pipeline on FFPE derived whole exome sequencing data as part of a liquid biopsy test from patients with colorectal cancer at MD Anderson (n=808). We benchmarked our consensus calls from two out of three of the following callers, MuSE2, Strelka2, and MuTecT2, using a patient matched Medical Diagnostic Lab genetic panel sequencing as the ground truth. Our consensus calls performed well in both panel 1 (n=126 genes, F1=0.726) and panel 2 (n=146 genes, F1=0.773). Results: MuSE2 achieves high sensitivity when combined with existing callers for both whole exome sequencing (WES, F1=0.88 0.04) and whole genome sequencing (WGS, F1=0.93 0.02). Furthermore, the calls had optimal performance when benchmarking the top driver genes in colorectal cancer (TP53, F1=0.95, KRAS, F1=0.99, PIK3CA, F1=0.74, and BRAF, F1=0.88). However, for less frequent genes the performance drops indicating additional measures are required to remove potential technical artifacts. Conclusion: Our results suggest that a consensus mutation calling strategy including MuSE2 achieves high efficiency without compromising accuracy for clinical tumor sequencing. This is an urgent matter as genetic screening is considered a fundamental aspect of translational cancer research and is entering cancer care standard practice. 2, 134 characters (max allowed = 2, 600) Citation Format: Jessica Castrillon Lal, Shuangxi Ji, Ruonan Li, Scott Kopetz, Wenyi Wang. Accelerated somatic mutation calling for whole-exome sequencing of tumor samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5037.