BACKGROUND: Colorectal cancer is still the second leading cause of cancer-related deaths and thus biomarkers allowing prediction of the resistance of patients to therapy and estimating their prognosis are needed. We designed a panel of 558 genes with pharmacogenomics records related to 5-fluorouracil resistance, genes important for sensitivity to other frequently used drugs, major oncodrivers, and actionable genes. We performed a target enrichment sequencing of DNA from tumors and matched blood samples of patients, and compared the results with patient prognosis stratified by systemic adjuvant chemotherapy. RESULTS: The median number of detected variants per tumor sample was 18.5 with 4 classified as having a high predicted functional effect and 14.5 moderate effect. APC, TP53, and KRAS were the most frequent mutated genes (64%, 59%, and 42% of mutated samples, respectively) followed by FAT4 (23%), FBXW7, and PIK3CA (16% for both). Patients with advanced stage III had more frequently APC, TP53, or KRAS mutations than those in stages I or II. KRAS mutation counts followed an increasing trend with grade (G1 < G2 < G3). The response to adjuvant therapy was worse in carriers of frameshift mutations in APC or 12D variant in KRAS, but none of these oncodrivers had prognostic value. Carriage of somatic mutations in any of the genes ABCA13, ANK2, COL7A1, NAV3, or UNC80 had prognostic relevance for worse overall survival (OS) of all patients. In contrast, mutations in FLG, GLI3, or UNC80 were prognostic in the same direction for patients untreated, and mutations in COL6A3, LRP1B, NAV3, RYR1, RYR3, TCHH, or TENM4 for patients treated with adjuvant therapy. The first association was externally validated. From all germline variants with high or moderate predicted functional effects (median 326 per patient), > 5% frequency and positive Manhattan plot based on 3-year RFS, rs72753407 in NFACS, rs34621071 in ERBB4, and rs2444274 in RIF1 were significantly associated with RFS, OS or both. CONCLUSIONS: The present study identified several putative somatic and germline genetic events with prognostic potential for colorectal cancer that should undergo functional characterization.

• Keywords
• Carcinoma, Colorectal, Drug, Oncodriver, Pharmacogene, Prognosis, Resistance, Sequencing,
• MeSH
• Drug Resistance, Neoplasm genetics   MeSH
• Adult MeSH
• F-Box-WD Repeat-Containing Protein 7 genetics   MeSH
• Pharmacogenetics methods   MeSH
• Fluorouracil therapeutic use   MeSH
• Class I Phosphatidylinositol 3-Kinases MeSH
• Colorectal Neoplasms * genetics   drug therapy   pathology   MeSH
• Middle Aged MeSH
• Humans MeSH
• Mutation genetics   MeSH
• Biomarkers, Tumor genetics   MeSH
• Tumor Suppressor Protein p53 genetics   MeSH
• Prognosis MeSH
• Adenomatous Polyposis Coli Protein genetics   MeSH
• Proto-Oncogene Proteins p21(ras) genetics   MeSH
• Aged MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Male MeSH
• Aged MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• APC protein, human MeSH Browser
• F-Box-WD Repeat-Containing Protein 7 MeSH
• Fluorouracil MeSH
• Class I Phosphatidylinositol 3-Kinases MeSH
• KRAS protein, human MeSH Browser
• Biomarkers, Tumor MeSH
• Tumor Suppressor Protein p53 MeSH
• PIK3CA protein, human MeSH Browser
• Adenomatous Polyposis Coli Protein MeSH
• Proto-Oncogene Proteins p21(ras) MeSH
• TP53 protein, human MeSH Browser