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Powerful eQTL mapping through low-coverage RNA sequencing
oleh: Tommer Schwarz, Toni Boltz, Kangcheng Hou, Merel Bot, Chenda Duan, Loes Olde Loohuis, Marco P. Boks, René S. Kahn, Roel A. Ophoff, Bogdan Pasaniuc
| Format: | Article |
|---|---|
| Diterbitkan: | Elsevier 2022-07-01 |
Deskripsi
Summary: 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 eQTL studies. 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 1,490 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 moderate coverage (13.9 million reads/sample). Next, we leverage synthetic datasets derived from real RNA-seq data (50 million reads/sample) 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 to identify eQTLs. Our work suggests that lowering coverage while increasing the number of individuals in RNA-seq is an effective approach to increase discovery power in eQTL studies.