Go Back   SEQanswers > Applications Forums > Clinical Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Allele frequency in sample below 10% yvancouver Genomic Resequencing 5 11-03-2014 03:38 AM
discrepancies in allele frequencies between 1000 genomes and 5400 exomes AJERYC General 1 10-31-2013 10:01 AM
Allele frequency calculation from cgh data for wes data April21 Illumina/Solexa 1 07-18-2013 04:27 PM
allele frequency threshold GATK m_elena_bioinfo Introductions 3 12-12-2011 11:29 AM
how to fetch the snp allele frequency? dzmtnvmt Bioinformatics 3 06-21-2011 03:44 AM

Thread Tools
Old 06-20-2018, 05:25 AM   #1
Location: Europe

Join Date: Nov 2011
Posts: 52
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.
Attached Images
File Type: jpg example.jpg (62.7 KB, 9 views)

Last edited by puggie; 06-20-2018 at 05:30 AM. Reason: Attached picture
puggie is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 10:43 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO