Abstract 5287: Parent-of-Origin-Aware genomic analysis in hereditary cancer: identifying the side of the family at risk using only the proband’s blood sample

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Abstract Background: Determining the parent of origin (PofO) of a variant in hereditary cancer guides counseling, risk management, recurrence risk assessment, and variant classification. In conditions involving genes with PofO effects, such as SDHD, SDHAF2 and MAX, this information can determine whether disease will manifest. Current approaches rely on family-based testing, yet uptake among eligible first-degree relatives remains low, with fewer than 30% undergoing testing, creating a major barrier in hereditary cancer.To address this gap, we developed Parent-of-Origin-Aware Genomic Analysis (POAga), a method that integrates chromosome-scale haplotyping with DNA methylation at differentially imprinted regions to assign PofO without parental data. To validate POAga, we applied it to individuals with hereditary cancer and known segregation of their pathogenic variants, and compared the predicted PofO with the established segregation to assess concordance and limitations. Methods: Blood samples are being collected from individuals with pathogenic variants in hereditary cancer genes, representing broad ranges of ages, ancestries, and cancer histories. Parental segregation was previously known or established through confirmatory testing. Predicted PofO is compared with true segregation to assess concordance. All samples undergo Strand-seq and long-read sequencing under an REB-approved protocol. Results: To date, 285 samples with 290 pathogenic variants have been analyzed across the following genes: BRCA2 (n=46), BRCA1 (n=42), MSH2 (n=34), SDHD (n=29), MLH1 (n=27), MSH6 (n=26), PMS2 (n=20), PALB2 (n=15), TP53 (n=14), ATM (n=14), CDH1 (n=9), CHEK2 (n=3), EPCAM (n=2), SDHAF2 (n=2), MUTYH (n=2), CDKN2A (n=1), POT1 (n=1), RAD51D (n=1), and SDHC (n=1). PofO was assigned for 250 variants, with 98.4% concordance (246/250). PofO could not be determined for 40 variants (13.8%, 40/290), mainly due to insufficient allele-specific methylation at imprinted regions or extended homozygosity that impeded phasing. Misassignments were rare and mainly due to stochastic phasing errors, unresolved inversions, or random allelic methylation at imprinted regions. Conclusion: POAga achieves clinical-grade accuracy in assigning PofO from a single blood sample in hereditary cancer. This directly addresses a major barrier in clinical genetics, particularly when parental samples are unavailable. For genes with PofO effects, this information can determine whether disease will manifest. By enabling reliable segregation without parental testing, POAga helps direct clinical efforts toward those truly at risk and improves the clinical interpretation of variants. Ongoing analyses will refine its performance and support its adoption as a transformative tool in hereditary cancer genomics. Citation Format: Lilian Cordova, Vahid Akbari, Tiffany Leung, Kieran O’Neill, Katherine Dixon, Alexandra Roston, Eugene Cheung, Chuyi Zheng, Millicent Sharman, Alshanee Sharma, Steve Bilobram, Yaoqing Shen, Janine Senz, Yanni Wang, Daniel Chan, Alexandra Fok, Jennifer Nuk, Quang Hong, Robin Coope, Eric Chuah, Simon Chan, Hyun-Wu Lee, Yongjun Zhao, Miruna Bala, Karen Mungall, Andrew Mungall, Richard Moore, Nur Diana Binte Ishak, Siao Ting Chong, Ee Ling Chew, Ashley McDonald, Anna Martinez, Gregory Kelly, Rosella Delgado, Caitlin Orr, Joanne Yuen Yie Ngeow, Kara N. Maxwell, Stephen B. Gruber, Dean Regier, Alice Virani, Louis Lefebvre, Fabio Feldman, Marco Marra, Sophie Sun, Stephen Yip, Peter Lansdorp, Steven John Jones, Kasmintan Schrader. Parent-of-Origin-Aware genomic analysis in hereditary cancer: identifying the side of the family at risk using only the proband’s blood sample [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 5287.

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