detecting mutations in ncRNA from exome or whole genome sequencing data

[jongwook0712]

I assume that RNA-seq is the best application for detecting non-coding RNA mutations.

However, are there ways to detect mutations in annotated non-coding RNAs using data generated from WGS or exome sequencing?

Thanks

[Richard Finney]

Actually, high coverage whole genome with accurate long reads is the best method.
There is the phenomena of "rna-editing" in RNA. Some rna wet lab processing methods may not detect non coding RNA; for instance some rna-seq methods target polyadenylated reads and some non coding RNA may be polyadenylated. Some RNA may be shorter than the read length; these won't get "harvested". I'm guessing (I just dont know), some RNAs by not hang around long enough to get detected, they may immediately get used. The role of non coding RNAs still needs much more study. The impact of mutations is, of course, difficult to determine. If one could show that the folding is impacted, then that would be some suggestive evidence that the impact is detrimental. Proving it would be difficult.

Regardless, rna-seq is pretty good for finding some mutations in non coding RNAs. You may with to use targeted sequencing of the DNA regions in question to verify mutations.

[jongwook0712]

could you elaborate more on the "harvesting of short RNAs"?

[Richard Finney]

I'm no expert on what goes on before the fastq files. That's where I pick it up. It's the current border between "computer guy" and "wet lab guy". It's good to know a little bit of the problems on the other side, though. The best I can do is refer you to the internet : http://en.wikipedia.org/wiki/RNA-Seq#Methods . The wikipedia entry is a pretty good overview.