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Old 06-20-2018, 06:25 AM   #1
puggie
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Location: Europe

Join Date: Nov 2011
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Default 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.
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Last edited by puggie; 06-20-2018 at 06:30 AM. Reason: Attached picture
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