Is whole-exome sequencing from paraffin-embedded tissues possible?

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I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

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Christian Cole

Yes. There are several papers which talk about FFPE sample. Google for them.

Victor Martinez-Glez

Not exome, but NGS panels (40 genes-HaloPlex-MiSeq) using DNA extracted from paraffin works well

Ferenc Fazakas

No. Your DNA is fragmented, dont expect fragments longer than 200-350 bp, which means that most of your exons will be lost.

Jason K Wall

Yes, this is most definitely possible. Life Technologies has products that are specifically designed for creating sequencing libraries from FFPE samples. Rohan has it right that the DNA is fragmented prior to assembly for sequencing anyway, so as long as your DNA is not EXTENSIVELY degraded (more of a problem with RNA and whole transcriptome sequencing), you'll be fine.