Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX

Nucleic Acids Research

Volumn 38, Issue 2, 2009, Pages

  Brotherton, Paul ^a,b   Sanchez, Juan J ^c   Cooper, Alan ^a   Endicott, Phillip ^b,d  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c Biology Section Apdo 863 E 41080   (Spain)

^d MUSÉE DE L HOMME   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA FRAGMENT; DOUBLE STRANDED DNA;

ACCESS TO INFORMATION; ACCURACY; ARTICLE; ARTIFACT; CONTROLLED STUDY; DNA DAMAGE; DNA DEGRADATION; DNA EXTRACTION; DNA FINGERPRINTING; DNA SEQUENCE; DNA STRAND; DNA TEMPLATE; FOSSIL HOMININ; GENE AMPLIFICATION; GENE LOCUS; GENE TARGETING; GENETIC ANALYSIS; GENOTYPE; HOMINID; HUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

HOMINIDAE;

EID: 77951146920     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp897     Document Type: Article

References (54)

1. Pääbo, S., Poinar, H., Serre, D., Jaenicke-Despres, V., Hebler, J., Rohland, N., Kuch, M., Krause, J., Vigilant, L. and Hofreiter, M. (2004) Genetic analyses from ancient DNA. Annu. Rev. Genet., 38, 645-679.
2. Handt, O., Krings, M., Ward, R.H. and Pääbo, S. (1996) The retrieval of ancient human DNA sequences. Am. J. Hum. Genet., 59, 368-376.
3. Höss, M., Jaruga, P., Zastawny, T.H., Dizdaroglu, M. and Pääbo, S. (1996) DNA damage and DNA sequence retrieval from ancient tissues. Nucleic Acids Res., 24, 1304-1307.
4. Krause, J., Lalueza-Fox, C., Orlando, L., Enard, W., Green, R.E., Burbano, H.A., Hublin, J.-J., Bertranpetit, J., Hänni, C., de la Rasilla, M. et al. (2007) The derived FOXP2 variant of modern humans was shared with Neanderthals. Curr. Biol., 17, 1908-1912.
5. Lalueza-Fox, C., Römpler, H., Caramelli, D., Stäubert, C., Catalano, G., Hughes, D., Rohland, N., Pilli, E., Longo, L., Condemi, S. et al. (2007) A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science, 318, 1453-1455.
6. Serre, D., Langaney, A., Chech, M., Teschler-Nicola, M., Paunovic, M., Mennecier, P., Hofreiter, M., Possnert, G. and Pääbo, S. (2004) No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol., 2, e57.
7. Bouwman, A.S., Chilvers, E.R., Brown, K.A. and Brown, T.A. (2006) Brief communication: identification of the authentic ancient DNA sequence in a human bone contaminated with modern DNA. Am. J. Phys. Anthropol., 131, 428-431.
8. Krings, M., Stone, A., Schmitz, R.W., Krainitzki, H., Stoneking, M. and Pääbo, S. (1997) Neandertal DNA sequences and the origin of modern humans. Cell, 90, 19-30.
9. Krings, M., Geisert, H., Schmitz, R.W., Krainitzki, H. and Pääbo, S. (1999) DNA sequence of the mitochondrial hypervariable region II from the Neandertal type specimen. Proc. Natl Acad. Sci. USA, 96, 5581-5585.
10. Ovchinnikov, I.V., Götherström, A., Romanova, G.P., Kharitonov, V.M., Lidén, K. and Goodwin, W. (2000) Molecular analysis of Neandertal DNA from the northern Caucasus. Nature, 404, 490-493.
11. Lalueza-Fox, C., Sampietro, M.L., Caramelli, D., Puder, Y., Lari, M., Calafell, F., Martínez-Maza, C., Bastir, M., Fortea, J., de la Rasilla, M. et al. (2005) Neandertal evolutionary genetics: mitochondrial DNA data from the Iberian peninsula. Mol. Biol. Evol., 22, 1077-1081.
12. Meyerhans, A., Vartanian, J.P. and Wain-Hobson, S. (1990) DNA recombination during PCR. Nucleic Acids Res., 18, 1687-1691.
13. Pääbo, S., Irwin, D.M. and Wilson, A.C. (1990) DNA damage promotes jumping between templates during enzymatic amplification. J. Biol. Chem., 265, 4718-4721.
14. Ruano, G., Brash, D.E. and Kidd, K.K. (1991) PCR: the first few cycles. Amplifications, 7, 1-4.
15. Handt, O., Richards, M., Trommsdorff, M., Kilger, C., Simanainen, J., Georgiev, O., Bauer, K., Stone, A., Hedges, R., Schaffner, W. et al. (1994) Molecular genetic analyses of the Tyrolean Ice Man. Science, 264, 1775-1778.
16. Wang, G.C. and Wang, Y. (1997) Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl. Environ. Microbiol., 63, 4645-4650.
17. 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 Acid Res., 35, 5717-5728.
18. Hansen, A., Willerslev, E., Wiuf, C., Mourier, T. and Arctander, P. (2001) Statistical evidence for miscoding lesions in ancient DNA templates. Mol. Biol. Evol., 18, 262-265.
19. Gilbert, M.T.P., Hansen, A.J., Willerslev, E., Rudbeck, L., Barnes, I., Lynnerup, N. and Cooper, A. (2003) Characterization of genetic miscoding lesions caused by post-mortem damage. Am. J. Hum. Genet., 72, 48-61.
20. Gilbert, M.T.P., Shapiro, B.A., 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. J. Archaeol. Sci., 32, 1053-1060.
21. Lalueza-Fox, C., Krause, J., Caramelli, D., Catalano, G., Milani, L., Sampietro, M.L., Calafell, F., Martínez-Maza, C., Bastir, M., García-Tabernero, A. et al. (2006) Mitochondrial DNA of an Iberian Neandertal suggests a population affinity with other European Neandertals. Curr. Biol., 16, R629-R630.
22. Binladen, J., Wiuf, C., Gilbert, M.T.P., Bunce, M., Larson, G., Barnett, R., Hansen, A.J. and Willerslev, E. (2006) Comparing miscoding lesion damage in mitochondrial and nuclear ancient DNA. Genetics, 172, 733-741.
23. 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 Res., 29, 4793-4799.
24. Lalueza-Fox, C., Gigli, E., de la Rasilla, M., Fortea, J., Rosas, A., Bertranpetit, J. and Krause, J. (2008) Genetic characterization of the ABO blood group in Neandertals. BMC Evol. Biol., 8, 342.
25. Bandelt, H.J. (2005) Mosaics of ancient mitochondrial DNA: positive indicators of nonauthenticity. Eur. J. Hum. Genet., 13, 1106-1112.
26. Caramelli, D., Lalueza-Fox, C., Vernesi, C., Lari, M., Casoli, A., Mallegni, M., Chiarelli, B., Dupanloup, I., Bertranpetit, J., Barbujani, G. et al. (2003) Evidence for a genetic discontinuity between Neandertals and 24, 000-year-old anatomically modern Europeans. Proc. Natl Acad. Sci. USA, 100, 6593-6597.
27. García-Bour, J., Pérez-Pérez, A., Alvarez, S., Fernández, E., López-Parra, A.M., Arroyo-Pardo, E. and Turbón, D. (2004) Early population differentiation in extinct aborigines from Tierra del Fuego-Patagonia: ancient mtDNA sequences and Y-chromosome STR characterization. Am. J. Phys. Anthropol., 123, 361-370.
28. Endicott, P., Gilbert, M.T., Stringer, C., Lalueza-Fox, C., Willerslev, E., Hansen, A.J. and Cooper, A. (2003) The genetic origins of the Andaman Islanders. Am. J. Hum. Genet., 72, 178-184.
29. Haak, W., Forster, P., Bramanti, B., Matsumura, S., Brandt, G., Tanzer, M., Villems, R., Renfrew, C., Gronenborn, D., Alt, K.W. et al. (2005) Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science, 310, 1016-1018.
30. Endicott, P., Metspalu, M., Stringer, C., Macaulay, V., Cooper, A. and Sanchez, J.J. (2006) Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations. PLoS ONE, 1, e81.
31. Barik, S.S., Sahani, R., Prasad, B.V.R., Endicott, P., Metspalu, M., Sarkar, B.N., Bhatacharya, S., Annapooma, P.C.H., Sreenath, J., Sun, D. et al. (2008) Detailed mtDNA genotypes permit a reassessment of the settlement and population structure of the Andaman Islands. Am. J. Phys. Anthropol., 136, 19-27.
32. Green, R.E., Krause, J., Ptak, S.E., Briggs, A.W., Ronan, M.T., Simons, J.F., Du, L., Egholm, M., Rothberg, J.M., Paunovic, M. et al. (2006) Analysis of one million base pairs of Neanderthal DNA. Nature, 444, 330-336.
33. Stiller, M., Green, R.E., Ronan, M., Simons, J.F., Du, L., He, W., Egholm, M., Rothberg, J.M., Keates, S.G., Ovodov, N.D. et al. (2006) Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc. Natl Acad. Sci. USA, 103, 13578-13584.
34. Gilbert, M.T., Binladen, J., Miller, W., Wiuf, C., Willerslev, E., Poinar, H., Carlson, J.E., Leebens-Mack, J.H. and Schuster, S.C. (2007) Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis. Nucleic Acids Res., 35, 1-10.
35. Maniatis, T., Fritsch, E.F. and Sambrook, J. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
36. Frohman, M.A., Dush, M.K. and Martin, G.R. (1988) Rapid production of full-length cDNAs from rare transcripts by amplification using a single gene-specific oligonucleotide primer. Proc. Natl Acad. Sci. USA, 85, 8998-9002.
37. O'Hara, O., Dorit, R.I. and Gilbert, W. (1989) One-sided PCR: the amplification of cDNA. Proc. Natl Acad. Sci. USA, 86, 5673-5677.
38. Walsh, P.S., Erlich, H.A. and Higuchi, R. (1992) Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl., 1, 241-250.
39. Richards, M., Sykes, B. and Hedges, R. (1995) Authenticating DNA extracted from ancient skeletal remains. J. Arch. Sci., 22, 291-299.
40. Thomas, M.G., Jones, A.L., Osman, F., Weale, M.E., Egarter-Vigl, E. and Pramstaller, P.P. (2001) Y-chromosome Variation in the Iceman and Modern Europeans. The Iceman, Sud-Tyrol Archaeological Museum, Bolzano.
41. Rollo, F., Ermini, L., Luciani, S., Marota, I., Olivieri, C. and Luiselli, D. (2006) Fine characterization of the Iceman's mtDNA haplogroup. Am. J. Phys. Anthropol., 130, 557-564.
42. Ermini, L., Olvieri, C., Rizzi, E., Corti, G., Bonnal, R., Soares, P., Luciani, S., Marota, I., De Bellis, G., Richards, M.B. et al. (2008) Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr. Biol., 18, 1-7.
43. Endicott, P., Sanchez, J.J., Pichler, I., Brotherton, P., Brooks, J., Egarter-Vigl, E., Cooper, A. and Pramstaller, P. (2009) Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed single-base-extension assay: the singular maternal history of the Tyrolean Iceman. BMC Genet., 10, 29.
44. Tamm, E., Kivisild, T., Reidla, M., Metspalu, M., Smith, D.G., Mulligan, C.J., Bravi, C.M., Rickards, O., Martinez-Labarga, C., Khusnutdinova, E.K. et al. (2007) Beringian standstill and spread of Native American founders. PLoS ONE, 2, e829.
45. Kong, Q.P., Yao, Y.G., Sun, C., Bandelt, H.J., Zhu, C.L. and Zhang, Y.P. (2003) Phylogeny of East Asian mitochondrial DNA lineages inferred from complete sequences. Am. J. Hum. Genet., 73, 671-676.
46. Sampietro, M.L., Gilbert, M.T.P., Lao, O., Caramelli, D., Lari, M., Bertranpetit, J. and Lalueza-Fox, C. (2006) Tracking down human contamination in ancient human teeth. Mol. Biol. Evol., 23, 1801-1807.
47. Malmstrom, H., Svensson, E.M., Gilbert, M.T.P., Willerslev, E., Gotherstrom, A. and Holmlund, G. (2007) More on contamination: the use of asymmetric molecular behaviour to identify authentic ancient human DNA. Mol. Biol. Evol., 24, 998-1004.
48. Wall, J.D. and Kim, S.K. (2007) Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genet., 3, 1862-1866.
49. Malmström, H., Storå, J., Dalén, L., Holmlund, G. and Götherström, A. (2005) Extensive human DNA contamination in extracts from ancient dog bones and teeth. Mol. Biol. Evol., 22, 2040-2047.
50. Clark, J.M. (1988) Novel non-templated nucleotide addition reactions catalyzed by prokaryotic and eukaryotic DNA polymerases. Nucleic Acids Res., 16, 9677-9686.
51. Strauss, B.S. (1991) The 'A rule' of mutagen specificity: a consequence of DNA polymerase bypass of non-instructional lesions? Bioessays, 13, 79-84.
52. Shibutani, S., Takeshita, M. and Grollman, A.P. (1997) Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the "A rule". J. Biol. Chem., 272, 13916-13922.
53. Berthet, N., Roupioz, Y., Constant, J.F., Kotera, M. and Lhomme, J. (2001) Translesional synthesis on DNA templates containing the 2(-deoxyribonolactone lesion. Nucleic Acids Res., 29, 2725-2732.
54. Green, R.E., Malaspinas, A.S., Krause, J., Briggs, A.W., Johnson, P.L., Uhler, C., Meyer, M., Good, J.M., Maricic, T., Stenzel, U. et al. (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134, 416-426.