Patterns of damage in genomic DNA sequences from a Neandertal Export

@article{citeulike:1647835, abstract = {High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms. 10.1073/pnas.0704665104}, author = {Briggs, Adrian W. and Stenzel, Udo and Johnson, Philip L. and Green, Richard E. and Kelso, Janet and Prufer, Kay and Meyer, Matthias and Krause, Johannes and Ronan, Michael T. and Lachmann, Michael and Paabo, Svante}, citeulike-article-id = {1647835}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0704665104}, citeulike-linkout-1 = {http://www.pnas.org/cgi/content/abstract/104/37/14616}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17715061}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17715061}, day = {11}, doi = {10.1073/pnas.0704665104}, journal = {Proceedings of the National Academy of Sciences}, keywords = {ancient-dna}, month = {September}, number = {37}, pages = {14616--14621}, posted-at = {2007-09-12 14:23:27}, priority = {2}, title = {Patterns of damage in genomic DNA sequences from a Neandertal}, url = {http://dx.doi.org/10.1073/pnas.0704665104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:1647835 L3 - citeulike-article-id:1647835 N2 - High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms. 10.1073/pnas.0704665104 IS - 37 JF - Proceedings of the National Academy of Sciences EP - 14621 TI - Patterns of damage in genomic DNA sequences from a Neandertal VL - 104 SP - 14616 KW - ancient-dna AU - Briggs, Adrian AU - Stenzel, Udo AU - Johnson, Philip AU - Green, Richard AU - Kelso, Janet AU - Prufer, Kay AU - Meyer, Matthias AU - Krause, Johannes AU - Ronan, Michael AU - Lachmann, Michael AU - Paabo, Svante PY - 2007/09/11/ UR - http://dx.doi.org/10.1073/pnas.0704665104 ER -