Svante Päabo has a mission: The genome sequence of the Neanderthal. Amongst the attendants of the congress his report and strong opinions on the possibility, usefulness and quality of the sequence data could be heard at several occasions. His plenary lecture addressed most of the concerns that I had heard earlier, about degradation, contamination and sequencing quality. He promised the 1x coverage genome for the turn of the year. This corresponds to a large number of runs of 454-sequencers because the vast amount of DNA in the available samples bacterial. The “junk” would probably make a nice metagenomics project on its own.

Bacterial sequences should sufficiently different from but what about human DNA contamination? The trick to ensure a high quality extraction builds on the availability of the mitochondrial genome of the Neanderthal. By comparing it to the known and well established mitochondrial sequences in an extraction, one can measure the ratio of contaminant human DNA and he showed that indeed, only few extractions were really usable. The openness in error reporting certainly convinced me.

The precautions go much further and includes the use of special linker sequences for Neanderthal to ensure that there is no carry over of DNA from within the sequencing machines.

From everything I saw today, it seems as if a good portion of the Neanderthal genome will be available in a reasonable amount of time. But will we get to see more human fossils sequenced? Svante Päabo’s answer to the question after the talk was sobering. In his opinion, degradation of the DNA will make it impossible to sequence older hominids like Australopithecus. But even specimen from the human lineage younger than the 40.000 year old Neanderthals will not be available because it will be impossible to separate contaminated samples from pure ones due to the lack of a mitochondrial standard.

That was this morning but an article in PLoS ONE now reports the isolation the mitochondrial sequence of a Cro-Magnon and validation of the originality by comparing it with all seven people that were in contact with the sample. That could mean that Svante Päabo’s a little too pessimistic. But he surely wouldn’t mind to err.