Evaluating the clinical utility of a SNP-based microarray platform: a comparative study

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Developmental disorders make up a majority of cases seen in genetic clinics at the National Health Laboratory Service (NHLS). Chromosomal microarray analysis (CMA) is the first line testing for individuals with developmental disorders and congenital anomalies. This study compared the clinical utility of single nucleotide polymorphism (SNP) - based array (CytoScan® Optima array) and a comparative genomic hybridization (CGH) array (SurePrint G3 Unrestricted CGH ISCA v2, 8x60 kb microarray) in diagnosis of developmental disorders. This was done by looking at the differences in copy number variant calls, segment size differences and gene content between the two microarrays. The cost to run each type of microarray test for diagnosis was also compared. The copy number variant calls made by the two platforms were comparable. The SNP-based array did provide additional information that would be useful in molecular diagnosis. The final recommendation was for the CGH array and the SNP-based array to be used interchangeably based on clinical requests at the Division of Human Genetics
A research report submitted in partial fulfilment of the requirement for the degree of Master of Science in Medicine (Genomic Medicine) to the Faculty of Health Sciences, University of the Witwatersrand, School of Pathology, Johannesburg, 2023
Developmental disorders, Chromosomal microarray analysis, Single nucleotide polymorphism