OPGP Affymetrix CytoHD Variants (blue=Gain; red=Loss; solidbox=AFFY_FILTER; solidline=MULTI_ALGO; dashedline=ONLY_CHAS)

The Ontario Population Genomics Platform (OPGP) was conceived as an opportunity to establish a collection of fully consented, Ontario-based population control DNA samples and corresponding immortalized cell lines, as a resource for researchers in Ontario and elsewhere. Blood-dervied DNA from 873 samples was genotyped using the Affymetrix CytoScanHD array and analyzed for copy number variation (CNV). A primary set of 71,178 calls were made by ChAS (Chromosome Analysis Suite) using minimum size and probe cutoffs of 1kb and 8 markers, respectively. Additionally we generated CNV calls using IPN (iPattern), NXS (Nexus) and PTK (Partek) that we used to annotate our primary dataset. Three groups of variants were generated depending on the following criteria. The AFFY_FILTER set of variants represent those defined by Affymetrix as clinically relevant variants. These are losses which are a minimum of 25kb in size and contain a minimum of 25 probes and gains which are a minimum of 50kb and contain a minimum of 50 probes. The MULTI_ALGO set of variants represent those which have been identified using the ChAS algorithm and at least 1 additional algorithm to call the variant (min 1kb, 8 probes). The ONLY_CHAS set of variants represent those which have been identified by the ChAS algorithm only (min 1kb, 8 probes).