It’s common wisdom that formalin-preserved samples can’t be DNA sequenced because formalin degrades DNA beyond use . However, a paper recently appeared in Genome Research, describing successful whole genome sequencing of formalin-prepared samples.
If it is possible to sequence DNA from formalin-fixed specimens, then that opens up a world of genetic studies through space and time using museum specimens.
However, the samples in the Genome Research paper, besides being formalin fixed, were also paraffin-embedded, and probably deep-frozen, as they were cancer research archival samples. Paraffin embedding and deep-freezing may also be required for successful sequencing of formalin fixed samples. Thus, perhaps the method won’t work for samples stored for 75 years at room temperature.
I don’t have the expertise to say. Any of our more molecularly savvy readers care to venture?
If there is any DNA left behind, say after a short formalin fix followed by ethanol storage, then DNA sequencing of formalin-preserved samples should be the equivalent of ancient DNA approaches, no?
CITATION: Scheinin, Ilari et al. 2014. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Research 24: 2022-2032. doi: 10.1101/gr.175141.1
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Kurt Schwenk
If the specimen was paraffin embedded, then it had to have been dehydrated, run through clearing agents and heated for infiltration. These are extremely harsh treatments, particularly the heat (approx. 60 deg. C) that would only have served to denature the DNA further. As such, it is likely that unsectioned tissues from museum specimens would work better (unless there is something about the histological preparation of the tissue that is a necessary part of the DNA extraction).
Thomas Sanger
I was about to write nearly the same thing that Kurt said. The nucleic acids are in the tissue regardless of how you treat them. We even do in situ hybridization on paraffin embedded tissues which is RNA-based. We also regularly recover RNA of deep sequencing quality from 12um frozen sections that were laser captured from tissue lightly fixed in paraformaldehyde. If I had to guess what the typical problem with recovering DNA from museum specimens is I would error on the side of over-fixing of the tissue creating too much cross linking for the typical DNA extraction to work efficiently. Unfortunately, I don’t immediately see the details of the fixation and storage described in the paper you highlighted.
Thomas Sanger
One other thought, while I am far from a sequencing jockey I would also guess that there is an important difference in sequencing techniques that needs to be highlighted. Using Illumina sequencing technology these authors were likely recovering relatively short reads that may be relatively forgiving to fragmented DNA. When I think about people working with museum collections I would imagine that they are trying to recover much longer amplicons using standard PCR and Sanger sequencing, which would become difficult if the DNA has become degraded during preservation or extraction.