Exploring clonal hematopoiesis (CH) of short variants (SVs) detected in liquid biopsies (LBx) in genes relevant to non-small cell lung cancer (NSCLC).

Abstract

e20675 Background: Clonal hematopoiesis (CH) results from fitness-enhancing mutations in hematopoietic stem cells. Although many CH SVs are in heme-related genes, some are in genes with solid tumor relevance ( TP53, ATM and CHEK2 ). In this study we report the prevalence of CH SVs in driver genes, emerging targets, and other clinically relevant genes in NSCLC. Methods: For 1813 pan-cancer LBx (572 NSCLC), plasma cell-free DNA and white blood cell (WBC) DNA were sequenced in parallel at equal depth with FoundationOne Liquid CDx. A novel variant origin prediction (VOP) algorithm trained and validated using WBC was used to classify origins for SVs detected in 21,456 NSCLC LBx submitted 8/2020-7/2024. Three possible variant origins were predicted using sequencing features including fragmentomics: germline, tumor-somatic, and CH. Results: Classic NSCLC driver SVs were not detected in WBC except for a KRAS G12D SV in a NSCLC patient (contrasted with 80 KRAS G12X SVs classified as tumor-somatic), and a KRAS G12S and a MET ex14 skipping SV in WBC from non-NSCLC patients. In contrast, other mutations in driver genes ( EGFR T415K, A743T, E829K, V843I, and A864V; KRAS V14I, I24N, A59G, and A146T; BRAF class 2/3 mutations) were more likely to be CH. Table shows SVs detected in WBCs and predicted to be CH-derived in the wider NSCLC LBx cohort. SVs in genes representing emerging targets or having clinical implications in NSCLC were detected in WBC at the following frequencies: 54 (3.0%) NF1 , 16 (0.9%) TP53 Y220C, 8 (0.4%) RB1 , 4 (0.2%) STK11 , 3 (0.2%) KEAP1 , and 3 (0.2%) SMARCA4 . In the larger NSCLC LBx cohort, frequencies of LBx with predicted tumor-somatic SVs vs only CH SVs detected were: NF1 (4.3% vs 3.9%), TP53 Y220C (0.5% vs 1.2%), RB1 (5.6% vs 0.3%), STK11 (7.6% vs 0.4%), KEAP1 (7.0% vs 0.3%), and SMARCA4 (3.6% vs 0.2%). Conclusions: This study shows that detection of currently targetable driver SVs in NSCLC is not confounded by CH in LBx, except rare KRAS G12X and MET ex14 skipping mutations. However, some emerging targets such as TP53 Y220C, BRAF class 2 mutations, STK11, and SMARCA4 SVs are CH-derived at appreciable rates. Ruling out CH origin through tissue testing, equal depth WBC sequencing, or algorithmic prediction of CH origin may be advisable. SVs in targetable genes CH SVs in WBC, non-NSCLC (n = 1241) CH SVs in WBC, NSCLC (n = 572) Tumor-somatic SVs, not detected in WBC, NSCLC (n = 572) NSCLC LBx with VOP-predicted CH SVs (n=21,456)n (%) NSCLC LBx with VOP-predicted tumor-somatic SVs (n=21,456) n (%) EGFR L858R, G719X, S768I, L861Q, ex19 deletions, ex20 insertions 0 0 70 6 (0.0%) 1940 (9.0%) EGFR, other 3 2 28 87 (0.4%) 667 (3.1%) BRAF V600E 0 0 7 8 (0.0%) 206 (1.0%) BRAF, other, class 2/3 8 2 7 130 (0.6%) 391 (1.8%) MET ex14 skipping 1 0 5 18 (0.1%) 256 (1.2%) MET, other 1 0 1 23 (0.1%) 51 (0.2%) KRAS G12X 1 1 80 14 (0.1%) 2891 (13.5%) KRAS, other 1 3 14 43 (0.2%) 696 (3.2%) ERBB2 0 0 6 9 (0.0%) 305 (1.4%)