I'm working on the microbiome and I can only use tissues which are fixed with formalin and embedded in paraffin. Is it possible to apply NGS (next generation sequencing) on FFPE (formalin fixed paraffin embedded) tissues? I'm particularly concerned about contamination that could affect the results.

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    – tyersome
    Commented Oct 5, 2020 at 23:05

1 Answer 1


It's a little hard to tell based on your question, but it seems that you want to do Illumina sequencing of FFPE tissue samples. This is quite routine, Illumina sells kits for it.

I do not know how the FFPE process affects microbial cells, but people have published recently on doing metagenomic analysis of FFPE tissue samples. This suggests to me that it is possible.

If "any contamination" is a problem, then maybe there are additional roadblocks; low-level contamination is a routine problem in metagenomics, which is exacerbated by complicated, old, or low-input sample types. I would suggest treating it the way you would treat any other metagenomic sample, and try to exclude the possibility of contamination through methods and account for it in data analysis.

  • $\begingroup$ Thank you very much , yes i have fears about paraffin and its remove could cause any artificial mutations in the DNA , it can be a real problem for the sequencing process. $\endgroup$ Commented Oct 5, 2020 at 19:24
  • $\begingroup$ People have been doing FFPE sequencing on Illumina instruments for years. Literally a decade, I believe. $\endgroup$
    – swbarnes2
    Commented Oct 5, 2020 at 21:13
  • $\begingroup$ @swbarnes2 oh yes, it is quite routine as i said. I think that the only question is how viable/mature it is for metagenomic sequencing. $\endgroup$ Commented Oct 6, 2020 at 2:31

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