Background

Most single nucleotide polymorphisms (SNPs) associated with disease traits by genome-wide association studies (GWAS) are in non-coding regions of the genome. One way in which these SNPs may influence disease risk is via effects on expression of nearby genes as expression quantitative trait loci (eQTL). Public resources such as the Genotype-Tissue Expression (GTEx) Project allow scientists to easily query large datasets from multiple tissues from humans without disease for eQTL relationships between SNP variants and specific RNA transcripts in various organ tissues from healthy individuals. However, in many cases, investigators may want to understand whether an eQTL relationship extends to specific tissues from specific individuals; for example, either in tissues not queried by these databases or in individuals with a disease condition. Because the mechanistic basis for many eQTL effects is allele-specific expression (ASE), we developed a protocol for assaying ASE in brain tissue from human subjects with Parkinson’s disease (PD) who are heterozygous for the eQTL SNP in question, affecting the target gene GPNMB. This protocol builds on the ASE method described by Mayba et al. (2014) by enriching for the desired transcripts via an RNA CaptureSeq (Mercer et al., 2014) step and by adapting the protocol to assay human brain tissue as opposed to cultured cells. Furthermore, our protocol can be adapted to multiple complex traits and tissues to advance our mechanistic understanding of many non-coding risk variants with eQTL effects.