All probe sequences were queried against an HG19 database using a nucleotide version of the Basic Local Alignment Search Tool. The Basic Local Alignment Search Tool results were compared with the original array manifest, an Illumina update to the array manifest, and the Broad Institute updates to the manifest. The genomic coordinates matched between the Basic Local Alignment Search Tool results and the existing manifests for 95.12% of probes. 2.23% of probes were updated based on the new Basic Local Alignment Search Tool results. 2.11% retained their original mapping. The remaining 0.54% were split between the Broad Institute reference and the Illumina update or the probe was removed from the data set (Supplementary Table 1).
