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  • 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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