Paleogenomics Using the 454 Sequencing Platform

Next Generation Genome Sequencing: Towards Personalized Medicine

Volumn , Issue , 2008, Pages 183-199

  Gilbert, M Thomas P ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

454; Ancient DNA; Paleogenomics

Indexed keywords

EID: 66249115790     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527625130.ch14     Document Type: Chapter

References (47)

1. Noonan, J., Hofreiter, M., Smith, D., Priest, J.R., Rohlan, N., Rabeder, G., Krause, J., Detter, J.C. et al. (2005) Genomic sequencing of Pleistocene cave bears. Science, 309, 597-599.
2. Haddrath, O. and Baker, A.J. (2001) Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. Proceedings of the Royal Society of London, Series B: Biological Sciences, 268, 939-945.
3. Cooper, A., Lalueza-Fox, C., Anderson, S., Rambaut, A.,Austin, J. andWard, R. (2001) Complete mitochondrial genome of two extinct moas clarify ratite evolution. Nature, 409, 704-707.
4. Krause, J., Dear, P., Pollack, J.L., Slatkin, M., Spriggs, H., Barnes, I., Lister, A.M., Ebersberger, I. et al. (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of the Elephantidae. Nature, 439, 724-727.
5. Rogaev,E.I.,Moliaka,Y.K.,Malyarchuk,B.A., Kondrashov, F.A., Derenko, M.V., Chumakov, I. and Grigorenko, A.P. (2006) Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biology, 4, e73.
6. Margulies, M., Egholm, M., Altman,W.E., Attiya, S., Bader, J.S., Bemben, L.A., Berka, J., Braverman, M.S. et al. (2005) Genome sequencing in microfabricated highdensity picolitre reactors. Nature, 437, 376-380.
7. Poinar, H.N., Schwarz, C., Qi, J., Shapiro, B.,Macphee, R.D.E., Buiges, B., Tikhonov, A., Huson, D.H. et al. (2006) Metagenomics to palaeogenomics: large-scale sequencing of mammoth DNA. Science, 311, 392-394.
8. Green, R.E., Krause, J., Ptak, S.E., Briggs, A.W., Ronan, M.T., Simons, J.F., Du, L., Egholm, M. et al. (2006) Analysis of one million base pairs of Neanderthal DNA. Nature, 444, 330-336.
9. Noonan, J., Coop, G., Kudaravalli, S., Smith, D., Krause, J., Alessi, J., Chen, F., Platt, D. et al. (2005) Sequencing and analysis of Neanderthal genomic DNA. Science, 314, 1113-1118.
10. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature, 362, 709-715.
11. Smith, C., Chamberlain, A.T., Riley, M.S., Cooper, A., Stringer, C.B. and Collins, M.J. (2001) Neanderthal DNA: not just old but old and cold? Nature, 410, 772-773.
12. Smith, C., Chamberlain, A.T., Riley, M.S., Stringer, C. and Collins, M.J. (2003) The thermal history of human fossils and the likelihood of successful DNA amplification. Journal of Human Evolution, 45, 203-217.
13. Cano, R.J., Poinar, H. and Poinar, G.O. Jr. (1992) Isolation and partial characterization of DNA from the bee Problebeia dominicana (Apidae: Hymenoptera) in 25-40 million year old amber. Medical Science Research, 20, 249-251.
14. DeSalle, R., Gatesy, J., Wheeler, W. and Grimaldi, D. (1992) DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science, 257, 1933-1936.
15. Woodward, S.R., Weyand, N.J. and Bunnell, M. (1994) DNA sequence from Cretaceous period bone fragments. Science, 266, 1229-1232.
16. Kim, S., Soltis, D.E., Soltis, P.S. and Suh, Y. (2004) DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae). American Journal of Botany, 91, 615-620.
17. Pääbo, S. (1989) Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proceedings of the National Academy of Sciences of the United States of America, 86, 1939-1943.
18. Pääbo, S., Higuchi, R. and Wilson, A. (1989) Ancient DNA and the polymerase chain reaction. The Journal of Biological Chemistry, 264, 9709-9712.
19. Hofreiter, M., Jaenicke, V., Serre, D., von Haeseler, A. and Pääbo, S. (2001) DNA sequences from multiple amplifications reveal artefacts induced by cytosine deamination in ancient DNA. Nucleic Acids Research, 29, 4793-4799.
20. Gilbert, M.T.P., Hansen, A.J., Willerslev, E., Rudbeck, L., Barnes, I., Lynnerup, N. and Cooper, A. (2003) Characterisation of genetic miscoding lesions caused by post mortem damage. American Journal of Human Genetics, 72, 48-61.
21. Binladen, J., Wiuf, C., Gilbert, M.T.P., Bunce, M., Barnett, R., Larson, G., Greenwood, A.D., Haile, J. et al. (2006) Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics, 172, 733-741.
22. Stiller, M., Green, R.E., Ronan, M., Simons, J.F., Du, L., He, W., Egholm, M., Rothberg, J.M. et al. (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct largescale sequencing of ancient DNA. Proceedings of the National Academy of Sciences of the United States of America, 103, 13578-13584.
23. Gilbert, M.T.P., Binladen, J., Miller, C., Wiuf, C., Willerslev, E., Poinar, H., Carlson, J.E., Leebens-Mack, J.H. et al. (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Research, 35, 1-10.
24. Brotherton, P., Endicott, P., Sanchez, J.J., Beaumont, M., Barnett, R., Austin, J. and Cooper, A. (2007) Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Research, 35, 5717-5728.
25. Briggs, A.W., Stenzel, U., Johnson, P.L.F., Green, R.E.,Kelso, J., Prüfer, K.,Meyer, M., Krause, J. et al. (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 104, 14616-14621.
26. Gilbert, M.T.P., Willerslev, E., Hansen, A.J., Rudbeck, L., Barnes, I., Lynnerup, N. and Cooper, A. (2003) Distribution patterns of postmortem damage in human mitochondrial DNA. American Journal of Human Genetics, 72, 32-47.
27. Gilbert, M.T.P., Shapiro, B., Drummond, A. and Cooper, A. (2005) Post mortem DNA damage hotspots in Bison (Bison bison and B. bonasus) provide supporting evidence for mutational hotspots in human mitochondria. Journal of Archaeological Science, 32, 1053-1060.
28. Hofreiter, M., Serre, D., Poinar, H.N., Kuch, M. and Pääbo, S. (2001) Ancient DNA. Nature Reviews. Genetics, 2, 353-358.
29. Gilbert, M.T.P., Rudbeck, L., Willerslev, E., Hansen, A.J., Smith, C., Penkman, K.E.H., Prangenberg, K., Nielsen-Marsh, C.M. et al. (2005) Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy. Journal of Archaeological Science, 32, 783-795.
30. Gilbert, M.T.P., Hansen, A.J., Willerslev, E., Turner-Walker, G. and Collins, M. (2006) Insights into the processes behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA. International Journal of Osteoarchaeology, 16, 156-164.
31. Salamon, M., Tuross, N., Arensburg, B. and Weiner, S. (2005) Relatively well preserved DNA is present in the crystal aggregates of fossil bones. Proceedings of the National Academy of Sciences of the United States of America, 102, 13783-13788.
32. Malmström, H., Stora, J., Dalén, L., Holmlund, G. and Götherström, A. (2005) Extensive human DNA contamination in extracts from ancient dog bones and teeth. Molecular Biology and Evolution, 22, 2040-2047.
33. Malmström, H., Svensson, E., Holmlund, G., Gilbert, M.T.P. and Götherström, A. (2007) More on contamination: asymmetric molecular behaviour as a mean to identify authentic ancient human DNA. Molecular Biology and Evolution, 24, 998-1004.
34. Kemp, B. and Glenn Smith, D. (2005) Use of bleach to eliminate contaminating DNA from the surface of bones and teeth. Forensic Science International, 154, 53-61.
35. Turner-Walker, G., Nielsen-Marsh, C.M., Syversen, U., Kars, H. and Collins, M.J. (2002) Sub-micron spongiform porosity is the major ultra-structural alteration occurring in archaeological bone. International Journal of Osteoarchaeology, 12, 407-414.
36. Leonard, J.A., Shanks, O., Hofreiter, M., Kreuz, E., Hodges, L., Ream, W., Wayne, R.K. and Fleischer, R.C. (2007) Animal DNA in PCR reagents plagues ancient DNA research. Journal of Archaeological Science, 34, 1361-1366.
37. Nicholson, G.J., Tomiuk, J., Czarnetzki, A., Bachmann, L. and Pusch, C.M. (2002) Detection of bone glue treatment as a major source of contamination in ancient DNAanalyses. American Journal of Physical Anthropology, 118, 117-120.
38. Wall, J.D. and Kim, S.K. (2007) Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genetics, 3, e175.
39. D'Abbadie, M., Hofreiter, M., Vaisman, A., Loakes, A., Gasparutto, D., Cadet, J., Woodgate, R., Pääbo, S. et al. (2007) Molecular breeding of polymerases for amplification of ancient DNA. Nature Biotechnology, 25, 939-943.
40. Gilbert, M.T.P. and Willerslev, E. (2007) Rescuing ancient DNA. Nature Biotechnology, 25, 872-874.
41. Gilbert, M.T.P., Tomsho, L.P., Rendulic, S., Packard, M., Drautz, D.I., Sher, A., Tikhonov, A., Dalén, L. et al. (2007) Wholegenome shotgun sequencing of mitochondria from ancient hair shafts. Science, 317, 1927-1930.
42. Collins, M.J., Waite, E.R. and van Duin, A.C.T. (1999) Predicting protein decomposition: the case of aspartic-acid racemization kinetics. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 354, 51-64.
43. Wilson, M.R., Polanskey, D., Butler, J., DiZinno, J.A., Replogle, J. and Budowle, B. (1995) Extraction, PCR amplification and sequencing of mitochondrial DNA from human hair shafts. BioTechniques, 18, 662-669.
44. Jehaes, E., Gilissen, A., Cassiman, J.J. and Decorte, R. (1998) Evaluation of a decontamination protocol for hair shafts before mtDNA sequencing. Forensic Science International, 94, 65-71.
45. Gilbert, M.T.P., Menez, L., Janaway, R.C., Tobin, D.J., Cooper, A. and Wilson, A.S. (2006) Resistance of degraded hair shafts to contaminant DNA. Forensic Science International, 156, 208-212.
46. Frederico, L.A.Kunkel, T.A. and Shaw, B.R. (1990) A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry, 29, 2532-2537.
47. SEQUENCHER v4.7 Build 2947 (2006) Gene Codes Corporation, Ann Arbor, MI, USA.