Powerful eQTL mapping through low coverage RNA sequencing

Mapping genetic variants that regulate gene expression (eQTL mapping) in large-scale RNA sequencing (RNA-seq) studies is often employed to understand functional consequences of regulatory variants. However, the high cost of RNA-Seq limits sample size, sequencing depth, and therefore, discovery power. In this work, we demonstrate that, given a fixed budget, eQTL discovery power can be increased by lowering the sequencing depth per sample and increasing the number of individuals sequenced in the assay. We perform RNA-Seq of whole blood tissue across 1490 individuals at low-coverage (5.9 million reads/sample) and show that the effective power is higher than that of an RNA-Seq study of 570 individuals at high-coverage (13.9 million reads/sample). Next, we leverage synthetic datasets derived from real RNA-Seq data to explore the interplay of coverage and number individuals in eQTL studies, and show that a 10-fold reduction in coverage leads to only a 2.5-fold reduction in statistical power. Our study suggests that lowering coverage while increasing the number of individuals is an effective approach to increase discovery power in RNA-Seq studies.