Abstract 6624: Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair using highly accurate long- and short-read whole-genome sequencing

Abstract Disentangling the molecular drivers of cancer progression requires a precise understanding of the somatic alterations that take place at the DNA level during tumor development. These include not only small changes like SNVs and indels, but also structural variants, changes in repetitive elements, differential methylation, as well as the haplotype context in which these changes occur. Existing short-read sequencing methods using sequencing by synthesis (SBS) chemistry lack the read length to characterize large structural variants or to span longer repetitive regions as well as to phase variants into haplotypes, while simultaneously lacking the sequencing accuracy to distinguish very low frequency somatic variants from background sequencing error or to sequence through shorter repetitive elements like microsatellites. Long-read PacBio HiFi data addresses the first set of challenges by accurately sequencing long fragments up to 25 kb, while highly accurate short-read sequencing by binding (SBB) chemistry from PacBio addresses the latter by improving raw sequencing accuracy by orders of magnitude, including in homopolymer regions which make up most microsatellites in the human genome. Here we apply these highly accurate long- and short-read sequencing technologies from PacBio to perform whole-genome sequencing of the newly described HG008 matched tumor-normal pair from the Genome in a Bottle (GIAB) consortium. This reference sample includes an adherent, epithelial-like pancreatic adenocarcinoma (PDAC) cell line as the tumor material, with the matched normal obtained from adjacent duodenal and pancreatic tissue. We perform whole-genome sequencing with both PacBio HiFi (35X normal, 80X tumor) and SBB (50X normal, 100X tumor), followed by alignment and tumor-normal variant calling for all variant types. These accurate long- and short-read sequencing technologies offer a more robust and comprehensive picture of somatic variation in this reference sample and contribute to developing this novel benchmark. Citation Format: Alexandra Sockell, Khi Pin Chua, Christopher Kingsley, Dan Nasko, Matthew Boitano, Young Kim, Melanie Wescott, Ian McLaughlin, Primo Baybayan, Jennifer McDaniel, Andrew Shaver, Justin M. Zook, Aaron Wenger. Comprehensive, multi-omic detection of somatic variants from the GIAB HG008 matched tumor-normal pair using highly accurate long- and short-read whole-genome sequencing [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 6624.