Abstract Cancer arises from the progressive accumulation of genomic alterations. The Cancer Genome Atlas (TCGA), a landmark consortium project, has comprehensively characterized 33 cancer types through multi-omics profiling of over 11,000 tumor-normal pairs. However, most TCGA-based studies had relied on whole-exome sequencing (WES), which covers only ∼1-2% of the genome, leaving the majority of the genomic landscape unexplored. To achieve a more comprehensive understanding of cancer genomes, the Broad Institute and Inocras collaboratively analyzed TCGA whole-genome sequencing (WGS) data encompassing over 8,000 tumors across more than 30 cancer types, which were initially analyzed by whole-exome sequencing. To fully leverage this resource, we applied CancerVision, an automated and streamlined bioinformatics pipeline developed by Inocras for clinical-grade WGS interpretation. CancerVision detects diverse genomic variants, including single-nucleotide variants (SNVs), insertions/deletions (indels), somatic copy number alterations (SCNAs), structural variants (SVs), and germline mutations, while also inferring homologous recombination deficiency (HRD) and mutational signatures. Using CancerVision, we performed a comprehensive, harmonized reanalysis of the TCGA WGS dataset and benchmarked our results against the bioinformatics pipelines from the Broad Institute and the official TCGA exome data. Across representative cohorts, ovarian cancer (CNV-driven), thyroid cancer (SNV-driven), and glioblastoma (mixed), CancerVision achieved high concordance, often uncovering additional high-confidence genomic alterations not captured in the existing TCGA resource. By integrating these results, we expand the known landscape of somatic variants, improve driver gene detection, and demonstrate the power of whole-genome-based analytics for actionable insights in precision oncology. Citation Format: Chunyang Bao, Hansol Park, Gang-Hee Lee, Ryul Kim, Won-Chul Lee, Jonghoon Lee, Yoonsuh Lee, Beomki Lee, David Lehotzky, Ron Solan, Antonia Kowalewski, Xavi Loinaz, Vasuki Narasimha Swamy, David I. Heiman, Samantha Van Seters, Saveliy Belkin, Sam Wiseman, Andrew D. Cherniack, Luis Antonio Corchete Sanchez, Brian P. Danysh, Zachary Everton, Chip Stewart, Haruna Tomono, Gengchao Wang, Esther Rheinbay, Gad Getz, Young Seok Ju. Comprehensive mutation profiling from The Cancer Genome Atlas (TCGA) whole-genome sequencing datasets abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 7270.
Bao et al. (Fri,) studied this question.