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Single-Stranded DNA Amplification Protocol Key to 15-Fold Coverage Boost


A team intent on unraveling the genetic secrets of archaic hominins has come up with a new strategy for amplifying single, rather than double, strands of DNA, making it possible to sequence ancient genomes to far greater depth than was previously possible. And because the strategy is specialized for dealing with old and/or somewhat degraded DNA, its developers say it could prove useful not only for sequencing ancient genetic material, but also for performing more sensitive forensic studies.

"We generated protocols from scratch that take into account the special preservation conditions of ancient DNA, such as fragmentation and strand breaks," said Matthias Meyer, a Max Planck Institute for Evolutionary Anthropology researcher, during a telephone briefing.

As described in Science, Meyer and his colleagues applied the approach to sequence the genome of a female from an archaic group known as the Denisovans to more than 30-fold coverage, on average. Genomic DNA for the study came from a fragment of finger bone found in a Siberian cave in 2010 that is believed to be tens of thousands of years old.

Prior to this, the Denisova genome had been sequenced to around 1.9 times coverage, on average, using DNA from the same finger bone shard and a DNA repair-based method developed in 2010.

With its newest sequencing method, though, the team "succeeded in developing a more efficient way of extracting information from the few DNA fragments that are preserved in the bone," Meyer said.

And by dramatically bumping up the depth of coverage for the archaic hominin genome, the team was able to do much more detailed studies on archaic admixture with modern humans and to delve into genetic features that have arisen in the modern human lineage since the split from the Denisovans and a related archaic group, the Neandertals.

"We've sort of taken the next technical step, if you like," added Svante Pääbo, director of the evolutionary genetics department at Max Planck, "in that we have determined this genome sequence from this little finger bone to a quality that's equal to what you would determine a genome sequence in me or you today."

Having gotten over this latest hurdle in sequencing ancient DNA, Pääbo said that there is now "no difference in what we can learn genetically about a person that lived 50,000 years ago and from a person today, provided that we have well-enough preserved bones."

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