Patterns of Somatic Variants in Colorectal Adenoma and Carcinoma Tissue and Matched Plasma Samples from the Hungarian Oncogenome Program

SIMPLE SUMMARY: Colorectal cancer is a highly lethal cancer type with a high incidence and mortality rate in Hungary. To explore the genetic background behind this epidemiological challenge, an emerging number of studies have aimed to explore colorectal carcinomas, but less is known about adenomas; therefore, we aimed to analyze tissue biopsies from both sample types in a comprehensive way by whole-exome sequencing (WES). As liquid biopsy has certain advantages over tissue sampling, we included matched plasma-originated cfDNA samples and examined the differences between colorectal cancer and adenomas by WES and targeted sequencing. According to our WES results, a high correlation was found between matched tissue and plasma variant allele frequencies. Liquid biopsy is a suitable starting material for WES and also for targeted panel sequencing, with the latter providing higher coverage depth; therefore, plasma-derived cfDNA may gradually become the first choice for genetic characterization of CRC patients in the future. ABSTRACT: Analysis of circulating cell-free DNA (cfDNA) of colorectal adenoma (AD) and cancer (CRC) patients provides a minimally invasive approach that is able to explore genetic alterations. It is unknown whether there are specific genetic variants that could explain the high prevalence of CRC in Hungary. Whole-exome sequencing (WES) was performed on colon tissues (27 AD, 51 CRC) and matched cfDNAs (17 AD, 33 CRC); furthermore, targeted panel sequencing was performed on a subset of cfDNA samples. The most frequently mutated genes were APC, KRAS, and FBN3 in AD, while APC, TP53, TTN, and KRAS were the most frequently mutated in CRC tissue. Variants in KRAS codons 12 (AD: 8/27, CRC: 11/51 (0.216)) and 13 (CRC: 3/51 (0.06)) were the most frequent in our sample set, with G12V (5/27) dominance in ADs and G12D (5/51 (0.098)) in CRCs. In terms of the cfDNA WES results, tumor somatic variants were found in 6/33 of CRC cases. Panel sequencing revealed somatic variants in 8 out of the 12 enrolled patients, identifying 12/20 tumor somatic variants falling on its targeted regions, while WES recovered only 20% in the respective regions in cfDNA of the same patients. In liquid biopsy analyses, WES is less efficient compared to the targeted panel sequencing with a higher coverage depth that can hold a relevant clinical potential to be applied in everyday practice in the future.