Abstract 7191: Targeted genomic and epigenomic dual analysis of the same region for an entire single gene
Authors: Grace Q. Zhao, Heng Wang, Alexandra Harris, Yingmin Wang, Yingzhen Wang, Ling Su, Ashraf Wahba, Josh Wang, Yun Bao, Carole Durand, Bram Herman, Tiffany Dorsey, Shengrong Lin, Xiaolin Wu, Stefan Ambs
Journal: Cancer Research (2025)

Abstract Omics analysis for cancer research is increasingly focusing on integrating both genomic and epigenomic data. While most studies often limit methylation analysis to promoter regions and genomic analysis to exons, research suggests the importance of examining omics information for entire genes, including UTRs and introns. Current whole-genome technologies for simultaneous genomic and epigenomic analysis require costly deep sequencing for low tumor content and may suffer from limited coverage in high CG content regions. To address these challenges, we developed a novel strategy that enables simultaneous genomic alteration and methylation dual analysis of the same region within a single gene, offering an affordable solution with improved uniformity, including high CG regions. ARID1A, a critical component of the SWI/SNF complex, is frequently mutated in breast cancer. Low ARID1A expression is associated with poor outcomes in luminal A and HER2-positive subtypes, making it an ideal candidate for investigating genomic alterations and potential methylation-related gene inactivation. To achieve this, we utilized the novel strategy for simultaneous genomic and epigenomic analysis using the Agilent Avida Duo target enrichment system. This approach allowed us to sequentially capture and analyze both genomic and methylation information across the same promoter, intron, and exon regions of the entire gene from a single DNA input without sample splitting. Moreover, the sequencing depth can be independently optimized for each modality. To optimize sequencing budget and coverage uniformity, we divided the panels (90kb) into high-quality and low-complexity regions, primarily introns, and experimented with different panel mixture ratios. With 10ng of fragmented gDNA, we achieved good coverage for both genomic (&amp;gt;1000x unique molecules) and methylation (&amp;gt;100x unique molecules) analysis, using less than 5M PE reads (sequencing clusters) for each omics in the Avida Duo workflow. For uniformity, the percentage of regions with coverage greater than 0.2x of the mean coverage is &amp;gt;90%. Our pilot studies, using tumor genomic DNA, formalin-fixed paraffin-embedded (FFPE) tissue from various cancer types, and cell-free DNA (cfDNA) control samples, successfully demonstrated the feasibility of our approach for simultaneous targeted genomic and epigenomic analysis of the same region within the entire single gene, even with limited DNA input. For Research Use Only. Not for use in diagnostic procedures. Citation Format: Grace Q. Zhao, Heng Wang, Alexandra Harris, Yingmin Wang, Yingzhen Wang, Ling Su, Ashraf Wahba, Josh Wang, Yun Bao, Carole Durand, Bram Herman, Tiffany Dorsey, Shengrong Lin, Xiaolin Wu, Stefan Ambs. Targeted genomic and epigenomic dual analysis of the same region for an entire single gene [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 7191.