Humanrefseq 8 expression beadchip

As Parkinson Disease (PD) is a disorder of the central nervous system, we selected eQTL data in brain for a case study from Gibbs et al.21 (link) and Myers et al.22 (link). In Gibbs et al.’s study, four frozen tissue samples of the cerebellum (CRBLM), frontal cortex (FCTX), caudal pons (PONS) and temporal cortex (TCTX) were obtained from 150 neurologically normal Caucasian subjects resulting in 600 tissue samples. SNP genotyping was performed using Infinium HumanHap 550 beadchips (Illumina) for 561,466 SNPs. Profiling of 22,184 mRNA transcripts was performed using HumanRef-8 (link) Expression BeadChips (Illumina). For each of the four brain regions, a regression analysis was performed using Plink23 (link). After eQTL analysis in each brain regions, we integrated the results. In Myers et al.’s study, whole-genome genotyping for 366,140 SNPs and expression analysis of 14,078 genes were carried out on a series of 193 neurologically normal human brain samples using the Affymetrix GeneChip Human Mapping 500 K Array Set and Illumina HumanRefseq-8 Expression BeadChip platforms. A one-degree-of-freedom allelic test of association analysis was performed using Plink23 (link). We integrated the results from these 2 studies. Finally, we got 51,131 significant correlations between 22,740 SNPs and 7,161 genes with the threshold of FDR < 0.05.

We used the brain eQTL data reported by Myers et al.^{22 (link)} in this study. Briefly, human brain tissues (cortex) of 193 normal human subjects were obtained. All of the individuals were of European of ancestry and had no clinical history of neurologic and neuropsychiatric diseases. DNA and RNA were extracted using standard procedures. Genotyping was performed using Affymetrix GeneChip (Human Mapping 500K Array Set) and gene expression was measured using Illumina HumanRefseq-8 Expression BeadChip. PLINK was used to test the association between the genotyped genetic variants and gene expression using linear regression. More details about sample description, genotyping, expression quantification and statistical analyses can be found in the original paper of Myers et al.^{22 (link)}.

We used human brain tissue data for this disease gene mining study. The data were obtained from a series of 193 neuropathologically normal human brain samples using the Affymetrix GeneChip Human Mapping 500 K Array Set and Illumina HumanRefseq-8 Expression BeadChip platforms [28] (link). The eQTLs were determined by Matrix eQTL [29] (link). In this study, the cis-eQTL definition was a SNP within the gene body +1 Mb up/down stream of the gene body. We calculated cis-eQTLs and trans-eQTLs and performed FDR adjustment (q value < 0.1) separately; then we combined the cis-eQTLs and trans-eQTLs. Finally, we obtained 25,866 significant SNP-gene association pairs of 3709 genes. The results can be downloaded from the seeQTL database [30] (link).