SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Strelka: Somatic small-variant calling workflow for matched tumor-normal samples ctsa Bioinformatics 15 12-15-2014 01:38 AM
Database of tumor-normal reads desmo Bioinformatics 2 03-27-2014 10:21 AM
Any program reports somatic CNVs with tumor fraction? ymc Bioinformatics 2 07-30-2013 08:07 PM
UnifiedGenotyper between tumor and normal kasthuri Bioinformatics 3 07-21-2012 08:47 AM
Tumor/Normal comparison tool for VCF? NGSNewbie1 Bioinformatics 9 06-14-2012 08:46 PM

Reply
 
Thread Tools
Old 11-04-2013, 10:34 PM   #1
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default Calling tumor CNVs without normal as control?

http://www.foundationone.com/about-f..._Technical.pdf

I noticed that the recently IPOed Foundation Medicine only used tumor sample to find mutations, CNVs and rearrangements by sequencing 200+ genes panel.

I think their approach is fine with mutations/indels but sequencing normal as well to differentiate the true somatic ones might be slightly better. For rearrangement/fusion genes, they are using some introns sequence for that. I think RNA-seq can cover more fusion cases than this approach, is that right?

The only thing that bugs me a lot is their claim about CNVs. Isn't that without the normal control, GC bias can't be removed?
ymc is offline   Reply With Quote
Old 11-05-2013, 01:11 AM   #2
bw.
Member
 
Location: San Francisco, CA

Join Date: Mar 2012
Posts: 21
Default

Also curious about this. Perhaps they are using pooled normals?
If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results using ExomeCNV.
bw. is offline   Reply With Quote
Old 11-06-2013, 01:36 AM   #3
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default

Quote:
Originally Posted by bw. View Post
Also curious about this. Perhaps they are using pooled normals?
If library prep & sequencer are the same, and the pooled samples are copy-number neutral, it should be possible to get decent results using ExomeCNV.
If I understand correctly, pooled normal only helps for calling CNVs on normal samples in the context of ExomeCNV.

I presume they aren't very nosy about accuracy. As long as it works in their clinical trials, then it is ok. One error can bite their ass though....
ymc is offline   Reply With Quote
Reply

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 01:24 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO