RNA-Seq or Exome Seq for Clinical data analysis
2
2
Entering edit mode
6.7 years ago
Karma ▴ 310

My plan is to develop a tool that can predict gene mutation and gene's expression pattern in a user input sample (fastq). From literature survey, I have understood Exome seq is good for calling variants from sample as it call variants from all coding region and RNA-Seq is best for gene / transcript expression data analysis. But, people do go for variant analysis using RNA-seq also. In such case all genomic variants are not captured. Here I have three important question

  1. Can I use RNAseq for identifying the variants for clinical analysis?
  2. Is RNA-Seq clinically more important than exome seq as it is used for both variant calling and identifying transcript expression?
  3. Are Mutations in expressed regions more important than mutations in non-expressed region? Please give your valuable suggestions.

If you need any clarification in the question please reply me here.

Sorry for my language.

Thank you

RNA-Seq Exome next-gen-sequencing • 3.4k views
ADD COMMENT
3
Entering edit mode

I think you have first understand what is exome seq and what is RNA-Seq, also some concepts like tissue specific expression patter, what is actually being sequenced in exome and RNA-Seq etc.

http://www.rna-seqblog.com/a-beginners-glance-at-rna-sequencing-vs-exome-sequencing/

There is also a review Exome versus transcriptome sequencing in identifying coding region variants

ADD REPLY
0
Entering edit mode

Thank you :) @geek_y I have seen this, but still confirming from experts like you. Do you have any suggestions for my 2 and 3 questions

ADD REPLY
0
Entering edit mode

My apologies for being blunt, but I don't think you should be working on a clinical data analysis tools if you don't understand these basic concepts you are asking about. It's probably worth it to first read a lot about what you are planning to do.

ADD REPLY
0
Entering edit mode

Do we need to tell you again about unnecessary upvotes of your comments/questions?

ADD REPLY
0
Entering edit mode

Yeah - I noticed something fishy too. Also check blast alignemnt query coverage - similar pattern of constant upvotes to trivial comments.

ADD REPLY
0
Entering edit mode

After my comment 2 upvotes on the question itself were removed. Odd.

ADD REPLY
0
Entering edit mode

I thought it was strange that I got +6 on a random answer that anyone could have given. In, like, 10 minutes.

ADD REPLY
3
Entering edit mode

So, to summarize, we have

  • fishy
  • odd
  • strange

That's rather remarkable, isn't it?

ADD REPLY
0
Entering edit mode

You got two upvotes for this trivial comment. Who did you arrange to upvote your comments? This is fishy, odd and stranage

ADD REPLY
1
Entering edit mode

In the current context of discussing user behavior, Wouter's comment is not trivial. I'd recommend some maturity in responses please, we are all scientists here.

ADD REPLY
0
Entering edit mode

I wondered about the same. :-p

ADD REPLY
3
Entering edit mode
6.7 years ago
1) No.
2) No.  Variant-calling is less accurate from RNA-seq because there is no guarantee both chromosome copies are expressed (or that either is expressed at that time).
3) No.  Different genes are expressed at different times.  A gene that is only expressed, say, in embryonic development might be critically important but you'd never see it in adult RNA-seq.

So - you need to do WGS or exome-capture for mutations, and RNA-seq for expression.

ADD COMMENT
0
Entering edit mode

Thank You.... Precise and Perfect answer

ADD REPLY
1
Entering edit mode
6.7 years ago

I am not an expert, but

  1. RNA-Seq is useful to understand the tissue specific gene expression and for perturbation studies . BUT, if you want to do a clinical study, at most you would be doing RNA-Seq from saliva/blood and that might not be useful if the variant has effects the heart or pancreas , as you might not even have expression of those tissue specific genes in the blood/saliva sample.

  2. Its been shown in several studies that the non-coding variants have large impact on gene expression, as they are usually enriched in regulatory regions like enhancers, promoters etc.

ADD COMMENT

Login before adding your answer.

Traffic: 2773 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6