A characterization of cis - and trans -heritability of RNA-Seq-based gene expression

Insights into individual differences in gene expression and its heritability ( h 2 ) can help in understanding pathways from DNA to phenotype. We estimated the heritability of gene expression of 52,844 genes measured in whole blood in the largest twin RNA-Seq sample to date (1497 individuals including 459 monozygotic twin pairs and 150 dizygotic twin pairs) from classical twin modeling and identity-by-state-based approaches. We estimated for each gene h 2 total , composed of cis-heritability ( h 2 cis , the variance explained by single nucleotide polymorphisms in the cis -window of the gene), and trans -heritability ( h 2 res , the residual variance explained by all other genome-wide variants). Mean h 2 total was 0.26, which was significantly higher than heritability estimates earlier found in a microarray-based study using largely overlapping (>60%) RNA samples (mean h 2 = 0.14, p = 6.15 × 10 −258 ). Mean h 2 cis was 0.06 and strongly correlated with beta of the top cis expression quantitative loci (eQTL, ρ = 0.76, p < 10 −308 ) and with estimates from earlier RNA-Seq-based studies. Mean h 2 res was 0.20 and correlated with the beta of the corresponding trans -eQTL ( ρ = 0.04, p < 1.89 × 10 −3 ) and was significantly higher for genes involved in cytokine-cytokine interactions ( p = 4.22 × 10 −15 ), many other immune system pathways, and genes identified in genome-wide association studies for various traits including behavioral disorders and cancer. This study provides a thorough characterization of cis - and trans - h 2 estimates of gene expression, which is of value for interpretation of GWAS and gene expression studies.