Evaluating whole exome sequencing on the Ion Torrent S5™ as a potential diagnostic tool for developmental disorders

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