The CSHL team contributed a technology developed by Hannon, postdoc Emily Hodges, Ph.D., and others at CSHL in 2007. "We call it "Array capture re-sequencing," says Hannon, "and it enables us to extract from genomes important information, on a very selective basis, rapidly, very accurately, and at low cost. We always anticipated that it might help in the analysis of evolutionary relationships, so when Svante offered us the opportunity to apply it to a Neandertal sample, we were very excited and grateful for the opportunity."
The technique enabled Hannon's CSHL team, working with Pbo's team in Leipzig, to greatly amplify intact bits of DNA from a Neandertal sample that was 99.8% contaminated -- mainly by bacterial DNA-- and regarded by Pbo as not likely to yield useful data. The sample studied was considerably more impure than that used as the basis for Pbo's full Neandertal genome sequence. "Our technology is particularly useful in enabling us to work with the most contaminated samples," says Hannon. "We identify and then greatly amplify just those portions of the target DNA called exons. Exons are stretches of DNA that encode proteins. They comprise only a small fraction of the total genome of modern humans, about 1%."
The Neandertal genome, like that of modern humans, contains about 3 billion base-pairs of nucleotides often referred to metaphorically as "letters" in the genome's "book of life." The Hannon-Pbo collaboration focused on obtaining the most accurate possible sequence of only 14,000 protein-coding segments within the full genome. "These," Hannon explains, "are exons that give rise to the 14,000 proteins that we know are different in modern humans and chimpanzees." The question was what those 14,000 proteins would look li
|Contact: Peter Tarr|
Cold Spring Harbor Laboratory