Go Back   SEQanswers > Applications Forums > Genomic Resequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Has anyone used MYbaits for targeted resequencing? gary Sample Prep / Library Generation 0 06-19-2013 05:12 AM
Kits for targeted resequencing yaron.goren Genomic Resequencing 1 04-13-2013 05:32 PM
methods for targeted resequencing sasignor Sample Prep / Library Generation 1 06-20-2012 07:59 PM
Directionality in targeted resequencing Harsh Goswami Bioinformatics 14 06-05-2012 06:50 AM
amplification (ligation) bias tea tree oil Illumina/Solexa 0 09-08-2010 07:02 AM

Thread Tools
Old 11-23-2015, 07:15 AM   #1
Junior Member
Location: US

Join Date: Nov 2015
Posts: 1
Default Targeted resequencing for VAF confidence - how avoid amplification bias?

Hi everyone,

I am looking for a good method for targeted resequencing of variants with low coverage (20-50X) in a WES dataset (≥400 targets). Key goal is to gain confidence in size of sub clonal VAFs, and I am somewhat worried about amplification bias in PCR-based methods.

So I am hoping maybe you guys here can advice:
1) What is the dimension of such amplification bias issues (how many % targets are affected and how predictable is it - GC-rich,...)?
2) Can you recommend methods (for example, using UMIs) that could avoid this problem?
3) Third option we are thinking about is re-running the capture libraries at higher depth.

Thank you so so much!!

spliceosome is offline   Reply With Quote

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 03:59 AM.

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