Evaluating whole exome sequencing on the Ion Torrent S5™ as a potential diagnostic tool for developmental disorders
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Date
2020
Authors
Flynn, Kaitlyn Ashley
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Abstract
Developmental disorders (DD) are a group of heterogeneous disorders characterised
by delayed physical and mental development. It is thought that 25-50% of DD have a
genetic aetiology, yet a majority of patients remain undiagnosed through current
testing procedures. In South Africa, chromosomal karyotyping (diagnostic rate of 3%)
and MLPA (diagnostic rate of 5-10%) are the routine diagnostic testing approach for
patients presenting with DD. Globally, experts are recommending WES as a first-line
diagnostic test for DD, mainly due to its superior diagnostic rate (±40%), and the fact
that it outperforms CMA (current gold-standard) for evaluation of unexplained DD.
However, the utility of this test has not been investigated in a limited resource setting.
This study aimed to implement a WES pipeline and investigate the diagnostic rate,
clinical utility, and associated financial and computational costs, using the Thermo
Fisher Ion Torrent S5™ NGS instrument. This was done by performing WES on seven
DD patients and one sequencing control DNA sample. Data analysis was performed
across three investigative platforms namely Moon (Diploid); an in-house, bespoke
bioinformatics pipeline, and VarAFT; and all were complemented with manual analysis
to identify possible putative disease-causing mutations. Identified variants were
validated with Sanger sequencing. Of the seven patients tested we identified disease causing mutations in six individuals and validated said variants in five individuals. We
determined that WES of a single patient cost approximately ZAR13,000.00 (laboratory
cost and data analysis). The diagnostic rate was greater than 70% for this project and
significant clinical interventions were identified for most patients. We refined a
bioinformatic workflow for the effective analysis of WES data to identify putative
disease-causing mutations in South African DD patients and concluded that WES
would be a highly beneficial tool in the investigation of DD within the local context
Description
A dissertation submitted in fulfilment of the requirements for the degree of Master of Science in Medicine to the Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, 2020