Forum:Possible Analysis from Data - RNA-Seq and Whole Genome Sequence

Question

[thekid2018]

Hello Everyone,

I am new to the land of NGS and I have been tasked with some work that involves sequencing of paired : normal vs tumor samples by RNA-Seq and Whole Genome Sequencing.

As much as I have read and understood about NGS, I believe these are the data types that will be available for me to work with, could someone tell me if I missed something:

RNA-Seq----> SNPs, RNA edits, Isoforms, ncRNA, Gene Expression, Novel/Fusion transcripts.

Whole Genome Seq (WGS)----> SNPs, Indels, CNVs, LOH, SVs

Also could someone tell me how to determine the mutation rates for each sample either from RNA-Seq or WGS (normal vs tumor)??

Thank you,
Vip

[mikhail.shugay]

It seems to me that, strictly speaking, RNA-Seq alone couldn't distinguish sequence variants (especially somatic mutations) and RNA edits without complementary WGS data. As for the mutation rates, RNA-Seq could miss some mutations or provide wrong frequency estimates due to gene expression bias.