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.
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.