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Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis.

Abstract：

:Single-cell RNA-sequencing (scRNA-Seq) is a compelling approach to directly and simultaneously measure cellular composition and state, which can otherwise only be estimated by applying deconvolution methods to bulk RNA-Seq estimates. However, it has not yet become a widely used tool in population-scale analyses, due to its prohibitively high cost. Here we show that given the same budget, the statistical power of cell-type-specific expression quantitative trait loci (eQTL) mapping can be increased through low-coverage per-cell sequencing of more samples rather than high-coverage sequencing of fewer samples. We use simulations starting from one of the largest available real single-cell RNA-Seq data from 120 individuals to also show that multiple experimental designs with different numbers of samples, cells per sample and reads per cell could have similar statistical power, and choosing an appropriate design can yield large cost savings especially when multiplexed workflows are considered. Finally, we provide a practical approach on selecting cost-effective designs for maximizing cell-type-specific eQTL power which is available in the form of a web tool.

journal_name

Nat Commun

journal_title

Nature communications

authors

Mandric I,Schwarz T,Majumdar A,Hou K,Briscoe L,Perez R,Subramaniam M,Hafemeister C,Satija R,Ye CJ,Pasaniuc B,Halperin E

doi

10.1038/s41467-020-19365-w

subject

Has Abstract

pub_date

2020-10-30 00:00:00

pages

5504

issue

1

issn

2041-1723

pii

10.1038/s41467-020-19365-w

journal_volume

11

pub_type

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