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

Lisa van den Driest, Caroline H Johnson, Nicholas JW Rattray, Zahra Rattray

Research output: Working paperWorking Paper/Preprint


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.

In this study we used a combination of bioinformatics tools to investigate the expression patterns and prognostic significance of two genes, adenomatous polyposis coli (APC) and B-Raf proto-oncogene (BRAF), that are commonly dysregulated in colon cancer. Subsequently, we investigated the pathways and biomolecular effectors implicated in APC and BRAF function.

Our results show mutation types, frequency, anatomical location and differential expression patterns for APC and BRAF between colorectal tumour and matched healthy tissue. The prognostic values of APC and BRAF was investigated as a function of expression level in CRC and other cancer types.

In the era of precision medicine and with significant advancements in biobanking and data curation, there is significant scope to use existing clinical datasets for evaluating the role of mutational drivers in carcinogenesis. This offers the potential for studying combinations of less well-known genes and the discovery of novel biomarkers or studying the association between various effector proteins and pathways.
Original languageEnglish
Place of PublicationCold Spring Harbor
Number of pages16
Publication statusPublished - 15 Nov 2021


  • bioinformatics
  • colon cancer
  • cancer
  • driver mutations
  • biomarkers
  • prognosis


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