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.