28. Comparison of different SNP microarray designs and whole genome sequencing for cytogenetic testing

      Since the landmark consensus statement paper published in 20101, microarray testing has become the primary tool for detection of chromosomal aberrations of various sizes. In fact, high-density SNP arrays have now become one of the most popular forms of cytogenetic testing due to their ability to detect regions of homozygosity (which is clinically useful) in addition to detection of copy number variants (CNVs). We have performed extensive analytical analysis of the designs from 10 SNP arrays offered by Thermo Fisher/Affymetrix and Illumina. The analysis includes number and coverage statistics on distribution of heterozygous probes for detection of AOH events and coverage and distribution of probes genome-wide, in regions marked by ClinGen as Pathogenic or Likely Pathogenic, in OMIM and OMIM Morbid genes, and in specific genes with high association with constitutional as well as oncology testing. We present the results of this comparison between the different SNP array platforms and compare these results with Whole Genome Sequencing at different read-depths. The comparison is designed to identify the best value today for cytogenetic testing and project for the future as cost of sequencing continues to decline. Finally, we have compared the performance of SNP array and WGS data empirically by having the same sample processed on different platforms. The conclusion of the analysis indicates that new SNP arrays designed for large scale genotyping studies can offer the best price/performance value at this time and likely for the next few years before being displaced by WGS. 1Miller DT, Adam MP, Aradhya S, et al. Consensus statement: chromosomal microarray is a first-tier clinical diagnostic test for individuals with developmental disabilities or congenital anomalies. Am J Hum Genet. 2010;86(5):749–764.
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