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Allele frequency discrepancies in Illumina data?

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  • Allele frequency discrepancies in Illumina data?

    Dear forum members,

    We are using the TST-15 Illumina panel and occasionally detect variant frequencies that appear not to be of biological relevance. I.e. frequencies in the range of 60-90%. A simple calculation should give a maximum of 50% frequency when having pure tumor cells due to the wild type allele.

    Such discrepancies between tumor cell content and variant frequencies we observe both for deletions and single base mutations. (example in attachment shows deletion with frequency of almost 80%)

    What is your opinion concerning these issues, PCR bias so on and so forth?

    Any input is appreciated.
    Attached Files
    Last edited by puggie; 06-20-2018, 05:30 AM. Reason: Attached picture
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