August 26, 2006

Ancient autosomal DNA testing

The New Scientist covers this study too:
JURASSIC PARK here we come? Not quite, but we might now be able to sequence the genomes of mammoths and even Neanderthals, thanks to a new way to correct the errors in sequencing ancient DNA that are made because it degrades over time.

When Svante Pääbo's group at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, analysed DNA from 50 to 50,000-year-old bone samples from wolves, a single error stood out: one of DNA's "letters", cytosine, had degraded in such a way that sequencing machines misinterpreted it as the letter thymine. Comparison of ancient DNA with a closely related modern species could allow such errors to be identified and corrected (Proceedings of the National Academy of Sciences, DOI: 10.1073 pnas.0605327103).

This opens the way for sequencing species that died out during the last ice age, says Pääbo.
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0605327103

Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation.


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