A sequence of errors

An upcoming article (early view available here) by Wall and Kim (2007) in PLOS Genetics questions the validity of the nuclear Neanderthal sequence data that was published by Green et al. (2006) and Noonan et al. (2006). Aside from an abstract light on the detail and the misuse of the word data as singular rather than plural (I've been nailed for this so many times, I'm like a Pavlovian puppy with it).

This article is really a metadata analysis of the previous sequence analysis presented in these articles. The authors obviously favor Noonan's data more than Green's. They imply that data presented in the Green article may have been seriously contaminated by modern human DNA or sequencing errors and this led to the more recent convergence time and some of the other results from the article. Both of these latter occurences are common laboratory pratfalls, which are often overlooked in the literature.

Contamination with modern humans occurs because PCR is really non-discriminatory and willl amplify anything that gets into the sample. So in the case of any ancient DNA a number of precautions need to be underaken. Sequencing errors are more numerous in the scientific literature. If you look at mtDNA studies, which is by far the most extensively (some might say excessively) used genomic research in humans you find an error rate around 60% due to human error (Forster 2003) or phantom mutations (Brandstatter et al. 2005). This is generally easily resolved just by investigating the transistion to transversion ratio. In humans transistions are more common than transversions and so just by analogy you could assume the same to be true for Neanderthals. Sequences can also be misread by the sequencer when the laser misdetects a base pair and so on the chromatogram the basepair may be mislabeled. This is more common at the front and back ends of the sequence. You can then investigate this by hand reading the chromatogram, however if you are dealing with 1,000s to 100,000s of base pairs this is probably not feasible. The alternative is to have multiple labs investigate the same stretch and come to a consensus, which is costly and means you have to share the glory.

Overall, I agree with the conclusion of the article, that the amplification of Neanderthal DNA is a major scientific breakthrough but that these resulting data need to be carefully verified before they are rushed to publication.

References Cited

Brandstatter A, Sanger T, Lutz-Bonengel S, Parson W, Beraud-Colomb E, Wen B, Kong QP, Bravi CM, Bandelt HJ. 2005. Phantom mutation hotspots in human mitochondrial DNA.
Electrophoresis 26:3414–3429.

Forster P. 2003. To err is human. Ann Hum Genet 67:2–4.

Green RE, Krause J, Ptak SE, Briggs AW, Ronan MT, et al. (2006) Analysis of one
million base pairs of Neanderthal DNA. Nature 16: 330-336.

Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, et al. (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113-1118.

Wall JD, Kim SK (2007) Inconsistencies in Neanderthal genomic
DNA sequences. doi:10.1371/journal.pgen.0030175.eor