Phase 1

LIBD RNA-seq Project

We identified expression quantitative trait loci (eQTLs) in the DLPFC of 412 subjects (age > 13, 175 patients with schizophrenia and 237 unaffected controls) using RNA sequencing (RNA-seq) and genotype data. The RNA-seq data was quantified across five convergent feature summarizations including at the gene, exon, junction, transcript, and expressed region (ER) levels. The eQTL modeling tested for additive genetic effects on expression while adjusting for sex, ancestry (multidimensional scaling components), and expression heterogeneity (principal components). Significant eQTLs were those SNP-feature pairs with a false discovery rate (FDR) less than 1%.

The "DLPFC - All" database is those FDR-significant eQTLs that further had the best SNP-feature pair replicated in two independent sets of DLPFC samples. Replication consisted of the SNP feature pair having the same allelic direction and p < 0.01 in the the CommonMind Consortium and same allelic direction in the GTEx project.

The "DLPFC - Control" database consisted of identifying eQTLs in the 237 control samples (age p > 13) using the same adjustment strategy (genetic and expression principal components) across all five feature summarizations.

These results can be viewed and visualized using the eQTL browser. Users can search for eQTL relationships by gene symbol or Ensembl ID or by SNP rs number. Individual eQTLs can be visualized as boxplots with additional annotation information.