Distinguishing tumor vs. clonal hematopoiesis (CH)–derived <i>TP53</i> and <i>BRCA1/2</i> alterations in ovarian cancer liquid biopsies with a predictive algorithm to inform clinical decision-making.

Abstract

5592 Background: CH results from mutations in hematopoietic stem cells and can occur in clinically relevant genes that are detected in liquid biopsy (LBx) of solid tumor patients. TP53 and less frequently BRCA1/2 can be detected in tumor and as CH potentially confounding interpretation of LBx results. Using an algorithmic method for CH prediction in a cohort of tubo-ovarian carcinoma (OC) LBx, we evaluated the prevalence of CH and non-CH alterations in TP53 and BRCA1/2 genes, CH frequency by circulating tumor DNA tumor fraction (ctDNA TF) and concordance in samples with paired tissue biopsies. Methods: Patients (pts) with a diagnosis of OC and LBx via FoundationOne Liquid CDx were included. ctDNA was quantified via TF. A machine learning model incorporating fragmentomics and other sequencing features was trained using LBx samples with equal-depth sequencing of plasma and white blood cells for short variant origin prediction (VOP) with output probabilities of origin (germline, tumor-somatic, or CH). Oncogenic short variants (i.e. mutations [mut]) with probability of being CH &gt;0.5 were classified as CH and with probability &lt;0.5 as tumor. Detection of CH and tumor TP53 mut in paired tissue samples (FoundationOne CDx) was evaluated (n=355). Results: 1,405 pts met criteria for study inclusion. 498 (35%) had TF≥1%. Overall, TP53 mut was detected in 74% (origin 30% tumor only, 23% CH only, and 21% both CH and tumor TP53 mut), and 26% had no detected TP53 mut Prevalence of VOP TP53 mut groups varied by TF with TF&lt;1% having more pts with no detected TP53 mut (35% vs 9%) or only CH TP53 mut (33% vs 4%) and fewer pts with only tumor TP53 mut (18% vs 51%) or both CH and tumor TP53 mut (13% vs 36%) than TF≥1%. The emerging drug target TP53 Y220C was predicted to be CH in 42/68 (62%) LBx samples. Of the 333 individual TP53 mut predicted to be CH on LBx, 310 (93%) were not detected in corresponding tissue. Of the 200 TP53 mut predicted to be tumor on LBx, 176 (88%) were detected in paired tumor tissue. Overall, 9% of pts had at least one germline BRCA1/ 2mut, 4% had no germline BRCA1/2 mut but had a tumor-somatic BRCA1/2 alteration (51 with mut, 4 with truncating rearrangements or copy number loss), and 1% had only CH BRCA1/2. Of patients with non-germline BRCA1/2 mut, 12/63 (19%) had only CH-derived BRCA1/2 mut. Conclusions: &gt;60% of OC LBx with TP53 mut, including TP53 Y220C, had evidence of CH contributing to cell free DNA. TF &lt;1% was associated with higher rates of CH only TP53 mut, but tumor-derived variants in TP53 and other genes were still detected. The majority (93%) of TP53mut predicted to be CH were not detected in tissue biopsies of paired samples. While the majority of LBx with a BRCA1/2 mut had germline or tumor-somatic muts, 6% of BRCA1/2 mut LBx only harbored BRCA1/2 mut predicted to be CH. Together, CH prediction and TF can be used to correctly contextualize LBx findings to support informed clinical decision making.