Chunk #44 — Online Methods — Expression data preprocessing — Illumina arrays

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Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression.

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Illumina array expression datasets were profiled by HT-12v3, HT-12v4 and HT-12v4 WGDASL arrays. Before analysis, all the probe sequences from the manifest files of those platforms were re-mapped to the GRCh37.p10 human genome build and transcriptome using SHRiMP v2.2.3 aligner56 (http://compbio.cs.toronto.edu/shrimp/), allowing two mismatches. Probes mapping to multiple locations in the genome were removed from further analyses.