Abstract 3391: Clonality and allelic imbalance of driver genes in a large retrospective cohort of colorectal cancer patients
Authors: Henry Walch, Paolo Manca, Jierui Xu, Christopher Fong, Justin Jee, Karl Pichotta, Adam Price, Allison L. Richards, Mark Donoghue, Jinru Shia, Efsevia Vakiani, Neil H. Segal, Andrea Cercek, Nikolaus Schultz, Francisco Sanchez-Vega, Walid K. Chatila, Rona Yaeger
Journal: Cancer Research (2025)

Abstract Intro: The genomic alteration landscape of colorectal cancers (CRCs) is heterogeneous, which can have implications for treatments and outcomes. In this analysis, we investigated tumor sequencing data from a large cohort of CRC patients to unpack the relevance of clonality and allelic imbalance heterogeneity. Methods: We analyzed a cohort of 6789 CRC patients treated at Memorial Sloan Kettering Cancer Center from 2014 to 2024. Every patient had a tumor/normal pair sequenced with MSK-IMPACT, a targeted sequencing assay that profiles genomic alterations across 341-505 cancer genes. The FACETS copy number algorithm was used to determine whole-genome duplication (WGD) status, as well as assess allelic imbalance and the clonality of mutations. Of the 6789 tumors, 5520 passed FACETS QC criteria. Tumors were classified as microsatellite stable (MSS), microsatellite instable (MSI), and POLE-mutant (POLE). Overall survival was calculated from time of diagnosis to last follow up. Results: The median age at diagnosis of our cohort was 56 years. Left-sided primary tumors were the most common (38.0%) and the majority of patients were stage IV (50.3%). The most frequent molecular subtype was MSS (87.6%), followed by MSI (11.4%) and POLE (1.0%). Within the MSS cohort, we investigated the clonality and allelic imbalance of mutations in canonical CRC genes, such as TP53, APC, KRAS, BRAF, and PIK3CA. Across all genes, clonal mutations demonstrated significantly higher rates of allelic imbalance favoring the mutant allele relative to subclonal mutations. Consistent with the other genes, tumors with a single clonal APC mutation had higher rates of allelic imbalance favoring the mutant allele when compared to those with a single subclonal mutation (81.5% vs 63.1%, p&amp;lt;0.001). However, this difference was not seen in tumors with more than 1 APC mutation. Tumors with a clonal TP53 mutation had higher median FGA estimates relative to subclonal TP53 mutant tumors in both WGD- (42% vs 28%, p&amp;lt;0.001) and WGD+ (77% vs 69%, p=0.011) tumors. TP53 clonal mutant tumors were enriched for loss across several chromosomal arms, whereas TP53 wild-type tumors were enriched for gains of chromosome 12, which contains both MDM2 and KRAS (32.4% vs 10.8%, p&amp;lt;0.001). Among patients with left-sided primary tumors and KRAS mutations, presence of KRAS gain was associated with a higher risk of death (HR=1.58, 95%CI:1.17-2.12, p=0.003) Conclusions: The presence of allelic imbalance in CRC might contribute to the clonal expansion of mutations important for early tumorigenesis, particularly in the absence of multiple mutations leading to loss of the wild-type allele, as is the case with APC. Further, stratification by TP53 mutation clonality demonstrated its role in regulating genomic instability. Copy number alterations might shape CRCs fate toward a higher dependency on the TP53 or RAS pathway, with possible prognostic implications. Citation Format: Henry Walch, Paolo Manca, Jierui Xu, Christopher Fong, Justin Jee, Karl Pichotta, Adam Price, Allison L. Richards, Mark Donoghue, Jinru Shia, Efsevia Vakiani, Neil H. Segal, Andrea Cercek, Nikolaus Schultz, Francisco Sanchez-Vega, Walid K. Chatila, Rona Yaeger. Clonality and allelic imbalance of driver genes in a large retrospective cohort of colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 3391.