Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Identification of Novel Mutations in Colorectal Cancer Patients using Ampliseq Comprehensive Cancer Panel

Version 1 : Received: 14 April 2021 / Approved: 15 April 2021 / Online: 15 April 2021 (08:10:42 CEST)

A peer-reviewed article of this Preprint also exists.

Almuzzaini, B.; Alghamdi, J.; Alomani, A.; AlGhamdi, S.; Alsharm, A.A.; Alshieban, S.; Sayed, A.; Alhejaily, A.G.; Aljaser, F.S.; Abudawood, M.; Almajed, F.; Samman, A.; Balwi, M.A.A.; Aziz, M.A. Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel. J. Pers. Med. 2021, 11, 535. Almuzzaini, B.; Alghamdi, J.; Alomani, A.; AlGhamdi, S.; Alsharm, A.A.; Alshieban, S.; Sayed, A.; Alhejaily, A.G.; Aljaser, F.S.; Abudawood, M.; Almajed, F.; Samman, A.; Balwi, M.A.A.; Aziz, M.A. Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel. J. Pers. Med. 2021, 11, 535.

Journal reference: J. Pers. Med. 2021, 11, 535
DOI: 10.3390/jpm11060535

Abstract

Discovery of novel variants from data derived from local population provides confident targets for developing biomarkers for personalized medicine. Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. We identified the need to generate high quality sequencing data from local population and understand the pattern of occurrence of variants in colorectal cancer patients. In this report, we used archived samples from Saudi Arabia and used Ampliseq Comprehensive Cancer panel to identify novel somatic variants. We report a comprehensive analysis of next generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in large intestine. APC, RET and EGFR genes were most frequently mutated. Higher number of variants were identified in left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population.

Keywords

Colorectal cancer; personalized medicine; biomarker; variant

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