RNA-seq differential expression studies: more sequence, or more replication?

RNA-seq is replacing microarrays as the primary tool for gene expression studies. Many RNA-seq studies have used insufficient biological replicates, resulting in low statistical power and inefficient use of sequencing resources.

rna-seqResearchers from the University of Chicago show the explicit trade-off between more biological replicates and deeper sequencing in increasing power to detect differentially expressed (DE) genes. In the human cell line MCF-7, adding more sequencing depth after 10M reads gives diminishing returns on power to detect DE genes, while adding biological replicates improves power significantly regardless of sequencing depth. They also propose a cost-effectiveness metric for guiding the design of large scale RNA-seq DE studies. Their analysis showed that sequencing less reads and perform more biological replication is an effective strategy to increase power and accuracy in large scale differential expression RNA-seq studies, and provided new insights into efficient experiment design of RNA-seq studies.

Cost per 1% power given a particular design = (fixed costs per sample * number of samples + sequencing costs) / power

CONTACT: kpwhite@uchicago.edu

Liu Y, Zhou J, White KP. (2013) RNA-seq differential expression studies: more sequence, or more replication? Bioinformatics [Epub ahead of print]. [abstract]