Chunk #48 — Methods — Detection of SNPs in Affymetrix probe-binding regions

Source

Joint mouse-human phenome-wide association to test gene function and disease risk.

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To find probe sequences affected by variants (SNPs and small indels) within probe binding regions of the Affymetrix Mouse Genome 430 2.0 array, we mapped all probes to the mouse reference genome using Blat. Probe regions were then examined for the presence of SNPs or small indels.