Neanderthal genomics

I went to a talk today by a researcher from the Max Planck Institute for Evolutionary Anthropology in Germany today. The topic was "Neandertal Genomics" and it was the first research talk I've been to ever where I felt like I was listening to science fiction. Many researchers, particularly those in Svante Pääbo's lab at the Max Planck Institute, have had great success over the past decade or so in extracting and sequencing DNA from the bones of extinct animals. Among these successes are the sequencing of mitochondrial DNA from Homo neanderthalensis, which has been extinct for about 30,000 years or so. The Max Planck is now carrying out an ambitious plan to sequence a 1x copy of the entire Neanderthal nuclear genome, based on a new technology called 454 sequencing, which differs radically from conventional PCR. In this method, short fragments of DNA from the insides of Neanderthal bones are split into single strands, and attached to tiny beads, each suspended in its own tiny drop of oil. Miniature PCR reactions are apparently carried out in each of these tiny oil drops, so that millions of copies of the sequence are now affixed to the surface of each bead. These beads are then placed into a glass plate covered in hundreds of thousands of tiny holes, so that each contains a single bead, and then the machine sequences all these short fragments simultaneously. In one run, the machine produces 250,000 sequences. Each of these is about 100 base pairs long, and most of these sequences turn out to be unidentifiable or of fungi. But some subset of these are identifiable hominid sequences, out of which some fragment are apparently identifiable as Neanderthal sequences and are not contamination from modern human DNA. Over the next few years, they plan to obtain enough Neanderthal sequences to be equivalent to the number of base pairs in the entire genome (this is called a 1x copy, and it will contain at least some redundancy, and never the entire genome itself). I was a bit unclear how they were expecting to actually be able to reliably distinguish Neanderthal nuclear DNA from that of Homo sapiens, and the presentation skipped a lot of details about the 454 sequencing process. But I wish them the best of luck.

More information here.