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Old 11-23-2015, 08:15 AM   #1
spliceosome
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Location: US

Join Date: Nov 2015
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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!!

S.
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