Brain expression quantitative trait locus mapping informs genetic studies of psychiatric diseases

Genome-wide association study (GWAS) can be used to identify genes that increase the risk of psychiatric diseases. However, much of the disease heritability is still unexplained, suggesting that there are genes to be discovered. Functional annotation of the genetic variants may increase the power of GWAS to identify disease genes, by providing prior information that can be used in Bayesian analysis or in reducing the number of tests. Expression quantitative trait loci (eQTLs) are genomic loci that regulate gene expression. Genetic mapping of eQTLs can help reveal novel functional effects of thousands of single nucleotide polymorphisms (SNPs). The present review mainly focused on the current knowledge on brain eQTL mapping, and discussed some major methodological issues and their possible solutions. The frequently ignored problems of batch effects, covariates, and multiple testing were emphasized, since they can lead to false positives and false negatives. The future application of eQTL data in GWAS analysis was also discussed.