NGS-based multi-gene panel analysis in early-onset colorectal cancer patients

Abstract

Background: Colorectal cancer (CRC) keeps an upward incidence and rejuvenation trend in Kazakhstan, as well as worldwide, which is the motive for revising traditional risk factors and searching for cause-effective relationships at the genome level. Genetic nature of early-onset CRC is still unclear. The aim of this study was to determine the spectrum of cancer-related gene mutations among early-onset CRC patients. Method(s): The study included 125 CRC patients aged between 17 and 50 from Kazakhstan. DNAs were extracted from blood using the Gene JET Purification Kit. Next-generation sequencing (NGS) was done on the MiSeq using the Tru Sight Cancer Kit. NGS data were analyzed by the MiSeq Reporter and Variant Studio. SIFT and PolyPhen-2 were used to predict potential pathogenic effects of missense variants on protein structure and function. Result(s): We were able to detect 24 pathogenic/likely pathogenic mutations in 20 (16%) cases, out of which 8 were novel. Out of allmutations, five were detected in the APC gene, three in FANCI, three in BRCA2, two in BRCA1, two inMLH1, and one mutation each, in MSH6,MUTYH, BLM,NBN, ATM,BMPR1A, CHEK2, AIP, and DICER1 genes. The analysis of mutation type has revealed 10 frameshiftmutations, 5 missensemutations, 5 stop-gain mutations, 1 in-frame deletion, and 3mutations involving uncorrected splicing. All mutations were in the heterozygous state.Most of the mutations were not available in the 1000G, ESP6500 and ExAC databases. 5% were available in the dbSNP database, 29.1%in theCOSMIC, and 38.4%in the ClinVar and/or LOVD. Pathogenic mutations in high penetrance CRC genes were higher in patients with family history of cancer (FHC) (21.1%, P=0.0002) and in patients with primary multiple tumors (20.0 %, P=0.0004) compared with patients without/unknown FHC (3.1%). Conclusion(s): Molecular genetic study of CRC in young patients using NGS allows to identify CRC cases with syndromic and sporadic nature, to stratify the level of risk for a particular patient and his/her relatives, to influence on the diagnostic and therapeutic approaches and clinical examinations. The findings from this study show the diagnostic value of the detected pathogenic mutations in key CRC genes from the Kazakhstan population as promising biomarkers for CRC diagnosis in young people.