Svante Pääbo’s update on Neandertal DNA contamination and a completed mitochondrial genome

Got to hand it to Blaine Bettinger, of the Genetic Genealogist, for catching this news on GenomeWeb Daily New. In a nutshell, it is a report of what Svante Pääbo‘s talked about at the Biology of Genomes meeting at Cold Spring Harbor Laboratory. Pääbo, if you don’t know, is one of the main researchers behind sequencing the Neandertal genome. He’s spent a lot of his life perfecting the recovering and sequencing of ancient DNA, from Egyptian mummies to ice-age bears.

In late 2006, he was a co-author of a paper reporting that he and his team have sequenced 1 million bases of the Neandertal genome. The paper, “Analysis of one million base pairs of Neanderthal DNA,” was generally well received. But a PLoS Genetics paper titled, “Inconsistencies in Neanderthal Genomic DNA Sequences,” found a lot of problems with results and raised concerns that a lot of the issues are possibly due to modern human DNA contaminants and/or a high rate of sequencing errors. Pääbo has looked into this and in his talk,

“mentioned that about 10 percent of the DNA library they initially sequenced consisted of modern human DNA. But over the last two years, they have been guarding against contamination by generating DNA libraries in a clean room and by barcoding the Neandertal DNA.”

He and his team have also been able to sequence the complete Neandertal mitochondrial genome. They didn’t do this just one time. They did it 35 times, which not only increases the accuracy of the sequence by conferring it many more times, but also weeds out the possibility contamination exists. This has been possible because Pääbo has utilized pyrosequencing, a newish method developed by 454 Life Sciences. Pyrosequencing can handle several contiguous sites in parallel, whereas traditional chain termination methods can’t.

The completed mitochondrial genome of the Neandertal is approximately 16 kilobases long and differs from the Cambridge Reference Sequence of the modern human mitochondrial genome at 133 positions. Blaine has tried to seek out the actual sequence, but with little luck. I hope that they will soon put up the sequence on GenBank for us to play around with!

2 thoughts on “Svante Pääbo’s update on Neandertal DNA contamination and a completed mitochondrial genome

  1. While Paabo et al. could have compared the Neandertal sequence to the Cambridge Reference, what was reported in the GenomeWeb Daily News article was that there were 133 differences between the Neandertal sequence and those of “almost all modern humans” – which is much more vague.

  2. It occurs to me that those of us that are Type II diabetics are suffering from Neandertal Revenge……an intolerance for carbohydrates that we inherited from our hunter-gatherer ancestors. I have to admit that my own lateral profile resembles the fossil image.

    Dennis D’Inzeo
    Aguadilla, Puerto Rico

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