Leveraging high variant allele frequencies (VAF) of DNA damage repair (DDR) mutations (muts) in liquid biopsy (LBx) as a surrogate for germline testing: Implications for precision medicine.

Abstract

10576 Background: LBx based next-generation sequencing (NGS) provides a minimally invasive means to detect true DDR muts as well as DDR muts that represent clonal hematopoiesis of indeterminate potential (CHIP), and in certain cases identifying high VAF DDR muts of suspected germline origin. Herein, we aim to address the knowledge gap in interpreting these findings to guide germline testing. Methods: We retrospectively collected data on patients (pts) with cancer who underwent LBx with FoundationOneLiquid CDx (311 gene panel) from 2022-2024 and tissue biopsy (TBx) based NGS using either Caris Life Sciences or FoundationOne CDx. A panel of 22 muts directly involved in the DDR pathway were designated as DDR muts. Findings from LBx and TBx were reported using descriptive statistics. Best objective clinical responses were evaluated using RECIST v1.1. Results: The study cohort consisted of 637 pts tested using LBx, with the majority being male (62.6%; n=399) and white (81%; n=517). On LBx, 203 pts (31.8%; n=203/637) were identified to have one or more DDR muts. Paired testing with LBx and Tbx was available for 221 pts of which 28 pts (12.6%) had ‘true CHIP’ (identified on LBx but not on TBx), all contributed by ATM and CHEK2 (50% each; n=14/28). Of pts who had paired LBx and TBx (n=221), 24 pts (10.8%) had the same DDR mut on both, suggesting likely somatic origin (True DDRs), the most common being ATM (25%; n=6/24), PALB2 (12.5%; n=3/24) and CDK12 (12.5%; n=3/24). Using a linear mixed-effects model to account for patient- and gene-level variability in VAF, true DDRs had a significantly (p < 0.001) higher VAF (median: 46.8, IQR: 49.6, n = 26) compared to true CHIP DDRs (median: 0.24, IQR: 0.29, n = 31). LBx revealed potential germline implications based on high VAF in 7.9% pts (n=50/637) of which 45 pts had DDR muts. Genetic referrals were initiated in 48% (n=24/50) with subsequent confirmatory germline testing done for 66.6% (n=16/24), all confirming germline muts (table 1). Notably, for the 52% (n=26/50) without genetic referrals, 73% (n=19/26) lacked documentation of a referral discussion. Out of the 50 pts with muts likely of germline origin, 19 were enrolled in phase-1 clinical trials, with 6 receiving matched therapies targeting DDR muts (PARP and ATR inhibitors). Of these, 1 had a partial response (CHEK2) and 3 had stable disease (1-MUTYH, 2-PALB2). Conclusions: LBx can be used as a potential surrogate indicator of likely germline muts as evidenced by high VAFs. Our findings underscore the need for improved interpretation of LBx reports to guide timely genetic referrals and confirmatory germline testing. Gene Median VAF (IQR) BAP1 (n=1) 52.4% (52.4-52.4) MUTYH (n=2) 51.3% (50.7–51.9) CHEK2 (n=2) 51.0% (50–52) ATM (n=2) 50.2% (49.8–50.6) BRCA2 (n=4) 50.0% (48.5–52.2) PALB2 (n=2) 48.4% (46.7–50.2) MSH6 (n=1) 46.6% (46.6-46.6)