http://genetics.plosjournals.org/perlserv/?request...This is a research article evaluating data from two recent (2006) publications of portions of the Neanderthal genome sequence. The authors conclude that: "these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors". Which just goes to show that you shouldn't believe everything you read 
References:
Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, et al. (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314: 1113-1118.
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.
Wall JD, Kim SK (2007) Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genet 3(10): e175. doi:10.1371/journal.pgen.0030175
