Hi!
We sequence both blood/fresh frozen and FFPE derived exomes using the Illumina HiSeq2000 and HiSeq4000. After the sample prep the samples are pooled. We have always pooled FFPE derived samples separate from blood/FF derived, since FFPE samples tend to produce a bit less data and we have been worried that the amount of data from these samples would be further reduced when competing with better quality DNA. I have no idea why this would happen though. The molecules bind through their adapter sequences, which are the same and "fresh" regardless of tissue of origin, and the amount of input material on the flow cell is naturally the same. Does anyone have experience on running FFPE and blood/FF samples on the same lane or any idea why we should not do this?
BR, Iikki
We sequence both blood/fresh frozen and FFPE derived exomes using the Illumina HiSeq2000 and HiSeq4000. After the sample prep the samples are pooled. We have always pooled FFPE derived samples separate from blood/FF derived, since FFPE samples tend to produce a bit less data and we have been worried that the amount of data from these samples would be further reduced when competing with better quality DNA. I have no idea why this would happen though. The molecules bind through their adapter sequences, which are the same and "fresh" regardless of tissue of origin, and the amount of input material on the flow cell is naturally the same. Does anyone have experience on running FFPE and blood/FF samples on the same lane or any idea why we should not do this?
BR, Iikki
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