Ffpe False Positive Variant Calls
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8.5 years ago
richardc.gsc ▴ 150

Hi All,

When I look in the literature about the FFPE causing changes to DNA, it seems to always cite a spike in C>T and G>A changes due to the FFPE process. See for example, these papers...

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1866966/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1850907/

However, in my recent illumina sequencing of some FFPE samples I don't see an increase in C>T and G>A, but I see a huge spike that is specific to FFPE sample in another substitution (I don't want to say specifically what we observe, since I don't know how important it is).

Has anyone else out there either confirmed that they see a spike in C>T or G>A changes specific to FFPE, or seen a spike in a different substitution?

snps • 2.0k views
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