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Chunk #54 — ONLINE METHODS — Replication of eQTL signals in independent data sets — Heinzen et al. (2008)14

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Genetic variability in the regulation of gene expression in ten regions of the human brain.
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RNA was extracted using standard Qiagen protocols from the frontal cortex of 93 adult individuals of European ancestry with no defined neuropsychiatric conditions. We downloaded the CEL files for this brain region from Gene Expression Omnibus (GEO) using the accession code GSE30483. We excluded nine individuals who showed evidence of non-European ancestry on the basis of a principal component analysis of the genotypes with respect to HapMap3 populations. Since this study used the same array as our study (Affymetrix Human Exon 1.0 ST), we processed the expression data in the same way as for our data. The DNA for the Heinzen et al.14 study was extracted and analyzed using standard Qiagen protocols using Illumina Infinium HumanHap550 chips, and again we carried out imputation to ~6 million markers in the same way as for our data.