Inaugural Article: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA

@article{citeulike:841703, abstract = {Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation. 10.1073/pnas.0605327103}, author = {Stiller, M. and Green, R. E. and Ronan, M. and Simons, J. F. and Du, L. and He, W. and Egholm, M. and Rothberg, J. M. and Keats, S. G. and Ovodov, N. D. and Antipina, E. E. and Baryshnikov, G. F. and Kuzmin, Y. V. and Vasilevski, A. A. and Wuenschell, G. E. and Termini, J. and Hofreiter, M. and Jaenicke-Despres, V. and Paabo, S. }, citeulike-article-id = {841703}, doi = {http://dx.doi.org/10.1073/pnas.0605327103}, journal = {PNAS}, keywords = {ancient-dna}, month = {September}, number = {37}, pages = {13578--13584}, posted-at = {2008-02-28 15:30:18}, priority = {2}, title = {Inaugural Article: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA}, url = {http://dx.doi.org/10.1073/pnas.0605327103}, volume = {103}, year = {2006} }

TY - JOUR ID - citeulike:841703 L3 - citeulike-article-id:841703 N2 - Whereas evolutionary inferences derived from present-day DNA sequences are by necessity indirect, ancient DNA sequences provide a direct view of past genetic variants. However, base lesions that accumulate in DNA over time may cause nucleotide misincorporations when ancient DNA sequences are replicated. By repeated amplifications of mitochondrial DNA sequences from a large number of ancient wolf remains, we show that C/G-to-T/A transitions are the predominant type of such misincorporations. Using a massively parallel sequencing method that allows large numbers of single DNA strands to be sequenced, we show that modifications of C, as well as to a lesser extent of G, residues cause such misincorporations. Experiments where oligonucleotides containing modified bases are used as templates in amplification reactions suggest that both of these types of misincorporations can be caused by deamination of the template bases. New DNA sequencing methods in conjunction with knowledge of misincorporation processes have now, in principle, opened the way for the determination of complete genomes from organisms that became extinct during and after the last glaciation. 10.1073/pnas.0605327103 IS - 37 JF - PNAS EP - 13584 TI - Inaugural Article: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA VL - 103 SP - 13578 KW - ancient-dna AU - Stiller, M AU - Green, RE AU - Ronan, M AU - Simons, JF AU - Du, L AU - He, W AU - Egholm, M AU - Rothberg, JM AU - Keats, SG AU - Ovodov, ND AU - Antipina, EE AU - Baryshnikov, GF AU - Kuzmin, YV AU - Vasilevski, AA AU - Wuenschell, GE AU - Termini, J AU - Hofreiter, M AU - Jaenicke-Despres, V AU - Paabo, S PY - 2006/09/12/ UR - http://dx.doi.org/10.1073/pnas.0605327103 ER -