Identifying potential biomarkers for colorectal cancer diagnosis using an RNA-seq analysis workflow
Date
2021
Authors
Kader, Zubayr
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Abstract
In South Africa, colorectal cancer (CRC) is the second most common cancer
in men and the third most common cancer in women, located at the lower
end of the digestive system, in the colon and rectum, and is most accurately
diagnosed through colonoscopy procedures. The prevalence of CRC is on the
rise globally as well as locally, yet participation rates for screening tools remain
low. In the present study, bioinformatics which is a multidisciplinary field that
is focused on interpreting biology through the analysis of gene sequences and
protein expression, was employed to explore the molecular biology of patient
CRC data as well as to identify dysregulated genes as potential biomarkers
to be used as an alternative screening tool. This was performed by creating
an RNA-Seq analysis workflow, that identified differentially expressed genes
that were further used in functional analysis to identify biological processes
and pathways relating to CRC onset and progression in patients. The genes
were tested as biomarkers in silico using statistical tests and blood expression
data and the genes identified included COL11A1, INHential tissue biomarkers, and MMP1, CTHRC1, KRT17
and IGBA, CLDN1, ETV4
and FOXQ1 as potFBP1 as potential blood biomarkers. The identified biomarkers require
future wet lab validation and illustrates the potential for a novel CRC screening
test to reduce the dependency on traditional tools that are ineffective due to
poor patient participation and associated cost.
Description
A dissertation submitted in fulfilment of the requirements for the degree of Master of Science to the Faculty of Science, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2021
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Citation
Kader, Zubayr (2020) Identifying potential biomarkers for colorectal cancer diagnosis using an RNA-Seq analysis workflow, University of the Witwatersrand, Johannesburg, <http://hdl.handle.net/10539/32292>