Abstract 5352: Identification of novel potentially pathogenic SNPs and associated genes in esophageal cancer: Insights from whole exome sequencing

Abstract Esophageal carcinoma (EC) is a prevalent malignancy and a leading cause of mortality, yet limited biomarkers exist to aid in prognosis and guide therapy. In this study, to pinpoint critical markers that could improve prognostic accuracy and reveal potential therapeutic targets, we employed whole exome sequencing (WES), to identify novel and potentially pathogenic single nucleotide polymorphisms (SNPs) and their associated genes in a cohort of EC patients (n=10). WES and subsequent data analysis were conducted as a commercial service at Macrogen. Genomic DNA was sequenced on the Illumina NovaSeq 6000 platform, and sequences were mapped to the human genome (hg38) using BWA. PCR duplicates were removed with Picard's Mark Duplicates, followed by recalibration and variant calling using GATK. Variants were filtered and annotated with SnpEff, dbSNP, ClinVar, ESP6500, and the 1000 Genomes Project. SNP pathogenicity was assessed using in-silico tools (SIFT, LRT, Mutation Taster, FATHMM, and PROVEAN). Genes associated with variants were prioritized/listed based on their frequency across the cohort. STRING analysis was conducted to examine protein interactions and enriched biological processes associated with key genes harboring multiple variants. We identified a total of 912, 214 SNPs in our cohort, of which 703 were classified as potentially pathogenic, including 331 novel SNPs that have not been reported in any population to date. Genes along-with associated variants were prioritized based on their highest frequency of occurrence across the cohort, including those with ≥2 distinct or repeated variants (Genes: RPS4X, PSMC1, HOMER2, PPAT, TPM3, RANBP9, NALCN, PTPN11, ARIH2, BMPR1B, HOXA13, PRKAA2, SCN8A, HDAC1, LRP2, HNRNPA3, FECH, PSMC5, MTMR2, ABCB1, RPL23, ITPR1, COL5A2, TBL1XR1, ITGB1, ZFAND1, PBX2, TCP1, HNRNPD, CALM2, PEX5, PCBD2, CACNA1E, FOXO1, GPD2, KARS, ABCC2, AFG3L2, CHCHD2, HNRNPA1). STRING analysis further highlighted crucial protein-protein interactions and biological processes in which these genes are involved, including (GO:0010604: Positive regulation of macromolecule metabolic process) , (GO:0048522: Positive regulation of cellular process), (GO:0051173: Positive regulation of nitrogen compound metabolic process), (GO:0045935: Positive regulation of nucleobase-containing compound metabolic process), (GO:0048518 Positive regulation of biological process), (GO:0009987 Cellular process), and (GO:0010557 Positive regulation of macromolecule biosynthetic process). These findings highlight potentially actionable genetic alterations in our cohort that could be developed as biomarkers for EC. Future studies are warranted to validate these variants in larger cohorts and investigate their mechanistic roles in EC progression through a range of in-silico and in-vitro validations. Citation Format: Waqas A. Abbasi, Sajida Qureshi, Muhammad A. Qureshi, Mohammed S. Quraishy. Identification of novel potentially pathogenic SNPs and associated genes in esophageal cancer: Insights from whole exome sequencing [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 5352.