Development of an accessible gene expression bioinformatics pipeline to identify driver mutations of colorectal cancer

Van Den Driest, Lisa and Johnson, Caroline H. and Rattray, Nicholas J. W. and Rattray, Zahra (2022) Development of an accessible gene expression bioinformatics pipeline to identify driver mutations of colorectal cancer. Alternatives to Laboratory Animals, 50 (4). pp. 282-292. ISSN 2632-3559 (https://doi.org/10.1177/02611929221107546)

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Abstract

Colorectal cancer (CRC) is a global cause of cancer-related mortality driven by genetic and environmental factors which influence therapeutic outcomes. The emergence of next-generation sequencing technologies enables the rapid and extensive collection and curation of genetic data for each cancer type into clinical gene expression biobanks. We report the application of bioinformatics tools for investigating the expression patterns and prognostic significance of three genes that are commonly dysregulated in colon cancer: adenomatous polyposis coli ( APC); B-Raf proto-oncogene ( BRAF); and Kirsten rat sarcoma viral oncogene homologue ( KRAS). Through the use of bioinformatics tools, we show the patterns of APC, BRAF and KRAS genetic alterations and their role in patient prognosis. Our results show mutation types, the frequency of mutations, tumour anatomical location and differential expression patterns for APC, BRAF and KRAS for colorectal tumour and matched healthy tissue. The prognostic value of APC, BRAF and KRAS genetic alterations was investigated as a function of their expression levels in CRC. In the era of precision medicine, with significant advancements in biobanking and data curation, there is significant scope to use existing clinical data sets for evaluating the role of mutational drivers in carcinogenesis. This approach offers the potential for studying combinations of less well-known genes and the discovery of novel biomarkers, or for studying the association between various effector proteins and pathways.

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