What is the difference between Whole Exome Sequencing (WES) & RNA Sequencing (RNA-seq)?

Question

[Wasil]

Hi. I am looking to perform a cohort study to identify differentially expressed proteins between healthy and diseased individuals, in order to develop Ab-based protein biomarker. Which one will be the appropriate method to use: Whole Exome Sequencing or RNA-seq? What is the difference between these two?

Answer 1

[ATpoint]

None, because neither measures protein abundances. RNA-seq measures the abundance of transcripts so we are talking about RNA levels, and WES sequences the exome, so the DNA sequence of the probed exons. The former is commonly used for differential expression analysis, while the latter is ued for calling of variants such as SNPs, Indels and structural variations. RNA abundances can sometimes approximate protein abundances but there is no guarantee it translates linearily. If you want a proteome assessment you will need to perform some kind of mass spectrometry-based experiment. As you mention antibodies (with FACS/IHC) you are after protein-coding genes only. Depending on the final analysis you want to make it could be that (e.g. FACS) the proteins must be on the surface so that would probably change experimental considerations as well. Please be sure to a) scan the literature for experimental suggestions in similar situations, b) talk to a core facility or experienced peers that could assist and counsel you and c) an experienced analyst who is going to analyse all that before doing any experiments. It seems that, with all due respect, you lack essential basic knowledge towards high-throughput assays and its applications/limitations, and a lot of trouble in later analysis can be avoided by a smart and powerful choice and design of the experiment.

[Wasil]

Thank you so much. This was so clear. I will have to study and discuss to have basic understanding of high-throughput methods and experimental designs. Thanks.