Results of NGS analysis of multiple genetic variants in colorectal cancer tissues

Abstract

Background: Colorectal cancer (CRC) is one of the leading causes of cancer-related morbidity and mortality worldwide and develops through the accumulation of genetic alterations involving multiple genes. In Mongolia, the substantial burden of CRC, limited treatment options, and scarcity of studies investigating its molecular genetic characteristics highlight the need to improve molecular diagnostics and expand personalized treatment options. Aim: To identify genetic variants in tumor tissues from patients with CRC and compare them with variants detected in matched adjacent normal tissues. Materials and Methods: This cross-sectional study was conducted between August 2023 and May 2024 in collaboration with the National Cancer Center of Mongolia, the Mongolian Institute of Human Genetics, and Happy Veritas Hospital. Eleven patients who underwent surgical treatment for CRC at the Department of General Surgery were enrolled. Paired tumor and adjacent normal tissue samples were collected from each patient and analyzed. Targeted next-generation sequencing (NGS) was performed using the MGISEQ-200 platform, covering 2,881 targeted positions across 53 cancerassociated genes. Sequencing data were processed through a bioinformatics pipeline involving quality control, alignment to the reference genome, variant calling, and filtering. BWA-MEM, GATK Mutect2, and Variant Effect Predictor (VEP) were used to identify and annotate genetic variants. Variants were comparatively evaluated according to their occurrence in tumor and adjacent normal tissues, potential functional consequences, and clinical significance. Results: A total of 60 genetic variant observations were identified across 11 paired CRC and adjacent normal tissue samples, including 56 single-nucleotide variants (SNVs; 93.3%) and four insertions or deletions (INDELs; 6.7%). Of these, 36 observations (60.0%) were recorded in tumor tissues and 24 (40.0%) in adjacent normal tissues. Eleven amino acid-altering variants were identified in tumor tissues. Variants in PDGFRA (90.9%), TP53 (54.5%), APC (36.4%), PTEN (27.3%), KIT (18.2%), and KRAS (9.1%) were detected in tumor tissues. The frequencies of variants in PDGFRA, TP53, and PTEN were higher in tumor tissues than in adjacent normal tissues, although the differences were not statistically significant (p > 0.05; FDR ≥ 0.75). Variants detected in APC, KRAS, TP53, PTEN, and MLH1 were associated with molecular pathways involved in colorectal carcinogenesis, including Wnt/β-catenin, MAPK, p53, PI3K–AKT–mTOR, and DNA mismatch repair pathways. The KRAS p.Gly13Asp (G13D) variant was identified as a clinically relevant alteration for evaluating response to anti-EGFR targeted therapy. Conclusion: Variants in PDGFRA, TP53, and PTEN were more frequently observed in CRC tissues than in adjacent normal tissues; however, the differences were not statistically significant. Variants in KRAS, KIT, and CDKN2A were detected exclusively in tumor tissues. The KRAS p.Gly13Asp variant may have clinical relevance in evaluating the selection of anti-EGFR targeted therapy.