Identification of Clinically Relevant Gene Variants in Colon Adenocarcinoma Samples of Ukrainian Patients Using a Comprehensive Cancer Panel: A Pilot Study

Abstract

The study aimed to identify the clinically relevant gene variants in colon adenocarcinoma samples of Ukrainian patients using the NGS Comprehensive Cancer Panel (CCP) to implement them conveniently in clinical practice. Methods. We have studied 20 samples of Ukrainian patients with colorectal adenocarcinomas of various differentiation grades. To identify the clinically relevant gene variants, the CCP data were filtered using the Franklin by Genoox database. Results. A total of 79 clinically relevant gene variant alterations (SNVs, INDELs) were found in 28 of 409 genes. The largest number of mutations was found in 3 genes, APC, TP53, and KRAS (16, 14, and 8, accordingly). We revealed 4 variants in PTEN and SMAD4, 3 variants in CHEK2, ERBB2, and PIK3CA genes, and 2 variants in AKT1, ATM, DST, IDH1, and TCF12. Mutations for 7 genes, KRAS, TP53, CHEK2, PTEN, AKT1, APC, and SMAD4, were found in more than 1 tumor tissue sample. Tier 1—2 gene variants rate was about 50% of all genetic variants. The therapeutic significance was found in more than 55% of mutations. Additionally, 11 novel genetic mutations in 9 genes have been identified, including G6PD, APC, DST, SINE1, SMAD2, and FLCN. Conclusions. These data suggest a high level of clinical relevance of the NGS CCP approach. Further confirmation on a larger number of samples and using a deeper analysis by other approaches is required.