Chunk #33 — Online Methods (Limit 3,000 words, at end of manuscript, currently 2,064) — Creating gene expression predictors for the dorso-lateral pre-frontal cortex — eQTL Data
A 1% minor allele frequency (MAF) cut-off was applied. Variants were filtered to remove any SNPs in high LD (r2>0.9), indels, and all variants with ambiguous ref/alt alleles. All protein coding genes on chromosomes 1–22 with at least one cis-SNP after these QC steps were included in this analysis (15,362 genes in total). SNPs in trans have been shown not to provide a substantial improvement in prediction accuracy15 and were not included here.
