SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Unannotated sequence ikim De novo discovery 6 05-30-2013 11:30 AM
How to quantify expression values of unannotated transcripts? icebsd RNA Sequencing 8 06-07-2012 11:06 PM
Tophat and unannotated transcripts honey Bioinformatics 1 07-02-2011 07:58 AM
PubMed: Transcript assembly and quantification by RNA-Seq reveals unannotated transcr Newsbot! Literature Watch 2 06-11-2010 06:56 AM

Reply
 
Thread Tools
Old 02-13-2017, 12:04 PM   #1
lre1234
Senior Member
 
Location: US

Join Date: Aug 2011
Posts: 106
Default How many unannotated SNPs?

Hi All,
I have a quick question. I'm doing some exome sequencing, and after all of the mapping, and annotating steps, I'm starting to go through the downstream analysis. One thing that I am looking at are the SNPs that are annotated (dbSNP, exac, TCGA, and other databases) versus what is not in those databases. One thing that I am finding is that of ~25000 variants pulled out of the exome data, only ~150 are not present (i.e. unannotated/novel). This seems like a very small amount. I'm not sure how many I would expect to get, but a few years ago when doing some exome seq I was getting about 3-5% of all SNPs to be unannotated. Out of curiosity, what are other people getting these days. Is it possible that with the vast amount of samples that have been sequenced, we are reaching the point where almost all variants will have been identified, with the exception of those few very rare or private ones?

This is more of a curiosity thing than anything else.....
lre1234 is offline   Reply With Quote
Old 02-13-2017, 10:36 PM   #2
wdecoster
Member
 
Location: Antwerp, Belgium

Join Date: Oct 2015
Posts: 97
Default

The population you are studying will hugely influence this. If you are working on commonly sequenced individuals such as European Americans the frequency of "known" variants will be much compared to an isolated less-studied population.
wdecoster is offline   Reply With Quote
Old 02-15-2017, 04:49 AM   #3
lre1234
Senior Member
 
Location: US

Join Date: Aug 2011
Posts: 106
Default

I'm working with a standard Caucasian population group. Nothing of a isolated population which I agree would probably have a higher % of 'novel' variants.

Generally, though for anyone that has done some exomes in the last few months, how many (or what %) of the identified variants were not in dbSNP/1000genomes/ExAc/or other databases? Just a general curiosity.
lre1234 is offline   Reply With Quote
Reply

Tags
exome analsys, snp annotation

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO