Concordance of parent-of-origin predictions for hereditary cancer variants using proband-only analysis.

Abstract

10595 Background: Determining the parental origin of germline variants is a critical gap in clinical genetics, essential for risk management, variant classification, and cascade genetic testing. Traditional methods rely on testing family members, which can be time-consuming and impractical when relatives are unavailable, deceased, or unwilling to participate. Parent-of-Origin-Aware Genomic Analysis (POAga) offers a transformative solution by enabling accurate assignment of any autosomal variant to either parent with 99% accuracy using only a blood sample from the proband. This method integrates methylation and sequence data from Oxford Nanopore long-read sequencing with chromosome-length haplotypes generated from Strand-seq, leveraging the accurate phasing of imprinted differentially methylated regions (iDMRs) that occur on each autosome to infer the parent of origin (PofO) of variants across the genome. This study aims to validate POAga across multiple hereditary cancer syndromes, including high-penetrance conditions such as hereditary breast and ovarian cancer (HBOC) and Lynch syndrome, as well as rarer syndromes with PofO effects and other genes associated with breast and gastrointestinal malignancies. Methods: Blood samples from carriers of pathogenic variants in ATM , BRCA1 , BRCA2 , CDH1 , MLH1 , MSH2 , MSH6 , PMS2 , EPCAM , PALB2 , SDHD , SDHAF2 and TP53 with known parental segregation, are currently being ascertained and undergoing whole-genome analysis to determine the analytic validity of POAga. These samples span diverse demographics, including variations in age, sex, ethnicity, and cancer status. PofO predictions are made according to previously described methods (Akbari V, Hanlon VCT, et al . Cell Genom. 2022 Dec 21;3(1):100233) under an REB-approved protocol. Results: To date, 188 individuals carrying 189 pathogenic variants with known parental segregation have been analyzed. The distribution of variants includes BRCA2 (n=31), MLH1 (n=23), MSH2 (n=22), BRCA1 (n=22), SDHD (n=21), MSH6 (n=20), PALB2 (n=14), PMS2 (n=13), ATM (n=9), CDH1 (n=9), SDHAF2 (n=2), EPCAM (n=2) and TP53 (n=1). PofO assignment was successful for 172 of 189 (91%) variants. Only one sample with an MLH1 variant was misassigned, while all other cases demonstrated concordance between the predicted and known parental origin (188 of 189, 99.5% accuracy). Conclusions: These results support the ability of POAga to accurately infer the parental origin of pathogenic variants in diverse hereditary cancer syndromes using only blood sample from the proband. Ongoing validation will further assess its feasibility in real-world clinical settings and refine its clinical translation. POAga represents a powerful advancement in hereditary cancer genetics, with the potential transform how we conduct genetic cancer risk assessments for patients and families.