What is a good way to compare the WES and panel seq results from the same set of samples?
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5.8 years ago
sm.hashemin ▴ 90

What is a good way to compare the WES and panel seq results from the same set of samples? These are tumor samples and somatic mutations are important for us. Is there a way to get statistics of pairwise (sample1 WES vs Panel) AF consistancy?

exome sequencing VCF Panel-seq • 1.0k views
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5.8 years ago
Amitm ★ 2.3k

hi, Most of the time gene panel based seq. have much higher coverage (read depth) and hence there may not be a direct consistency of a standard WES vs. gene panel seq. results for the same sample.

Nonetheless, all that you 'saw' in WES, should be 'detectable' in the panel seq. Also, the variant allele frequency for all such cases would be in the same range. Some caveats -

  1. The DNA in both cases: Were they extracted from separate tissue chunks, or one extraction and then the aliquot has been used twice.
  2. Hopefully the WES and panel seq. are on the same seq. tech. platform.
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