The Neandertal genome and ancient DNA authenticity Export

@article{citeulike:5391418, abstract = {Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large-scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar 'boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired.}, author = {Green, Richard E. and Briggs, Adrian W. and Krause, Johannes and Prufer, Kay and Burbano, Hernan A. and Siebauer, Michael and Lachmann, Michael and Paabo, Svante}, citeulike-article-id = {5391418}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/emboj.2009.222}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/emboj2009222a}, day = {06}, doi = {10.1038/emboj.2009.222}, issn = {0261-4189}, journal = {The EMBO Journal}, keywords = {anthropology, data-mining, divergence, fossils, genetics, genome, hominidae, humans, methods, mitochondrial, nuclear, phylogenomics, primates}, month = {August}, number = {17}, pages = {2494--2502}, posted-at = {2009-10-06 09:58:04}, priority = {2}, publisher = {Nature Publishing Group}, title = {The Neandertal genome and ancient DNA authenticity}, url = {http://dx.doi.org/10.1038/emboj.2009.222}, volume = {28}, year = {2009} }

TY - JOUR ID - citeulike:5391418 L3 - citeulike-article-id:5391418 N2 - Recent advances in high-thoughput DNA sequencing have made genome-scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large-scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar 'boot-strap' approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired. IS - 17 JF - The EMBO Journal SN - 0261-4189 EP - 2502 TI - The Neandertal genome and ancient DNA authenticity PB - Nature Publishing Group VL - 28 SP - 2494 KW - anthropology KW - data-mining KW - divergence KW - fossils KW - genetics KW - genome KW - hominidae KW - humans KW - methods KW - mitochondrial KW - nuclear KW - phylogenomics KW - primates AU - Green, Richard AU - Briggs, Adrian AU - Krause, Johannes AU - Prufer, Kay AU - Burbano, Hernan AU - Siebauer, Michael AU - Lachmann, Michael AU - Paabo, Svante PY - 2009/08/06/ UR - http://dx.doi.org/10.1038/emboj.2009.222 ER -