Selective enrichment of damaged DNA molecules for ancient genome sequencing

Genome Research

Volumn 24, Issue 9, 2014, Pages 1543-1549

  Gansauge, Marie Theres ^a   Meyer, Matthias ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; MITOCHONDRIAL DNA; SINGLE STRANDED DNA; URACIL; DEOXYURIDINE PHOSPHATE;

ARTICLE; CONTROLLED STUDY; DNA CONTAMINATION; DNA DAMAGE; DNA EXTRACTION; DNA LIBRARY; DNA SEQUENCE; DNA STRAND; ESCHERICHIA COLI; GENETIC SELECTION; HOMO NEANDERTHALENSIS; HUMAN; HUMAN GENOME; INFANT; MICROBIAL CONTAMINATION; NONHUMAN; SEQUENCE ANALYSIS; ANIMAL; CHEMISTRY; GENETICS; GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; SENSITIVITY AND SPECIFICITY;

ANIMALS; BASE SEQUENCE; DEOXYURACIL NUCLEOTIDES; DNA CONTAMINATION; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; NEANDERTHALS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

EID: 84907210065     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.174201.114     Document Type: Article

References (40)

1. Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, et al. 2007. Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci 104: 14616-14621.
2. Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, et al. 2009. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325: 318-321.
3. Briggs AW, Stenzel U, MeyerM, Krause J, Kircher M, Pääbo S. 2010. Removal of deaminated cytosines and detection of in vivomethylation in ancient DNA. Nucleic Acids Res 38: e87.
4. Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PL, Xuan Z. 2010. Targeted investigation of the Neandertal genome by array-based sequence capture. Science 328: 723-725.
5. Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, Allentoft ME, Sikora M, Rasmussen M, Gravel S, Guillen S, Nekhrizov G, et al. 2013. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries. Am J Hum Genet 93: 852-864.
6. Dabney J, Meyer M. 2012. Length and GC-biases during sequencing library amplification: a comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries. Biotechniques 52: 87-94.
7. Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, Valdiosera C, Garcia N, Pääbo S, Arsuaga JL, et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci 110: 15758-15763.
8. Ermini L, Olivieri C, Rizzi E, Corti G, Bonnal R, Soares P, Luciani S, Marota I, De Bellis G, Richards MB, et al. 2008. Complete mitochondrial genome sequence of the Tyrolean Iceman. Curr Biol 18: 1687-1693.
9. Fu Q, Meyer M, Gao X, Stenzel U, Burbano HA, Kelso J, Pääbo S. 2013a. DNA analysis of an early modern human from Tianyuan Cave, China. Proc Natl Acad Sci 110: 2223-2227.
10. Fu Q, Mittnik A, Johnson PL, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, et al. 2013b. A revised timescale for human evolution based on ancient mitochondrial genomes. Curr Biol 23: 553-559.
11. Gansauge MT, Meyer M. 2013. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA. Nat Protoc 8: 737-748.
12. Gilbert MT, Kivisild T, Gronnow B, Andersen PK, Metspalu E, Reidla M, Tamm E, Axelsson E, Gotherstrom A, Campos PF, et al. 2008. Paleo- Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland. Science 320: 1787-1789.
13. Golovanova LV, Hoffecker JF, Kharitonov VM, Romanova GP. 1999. Mezmaiskaya Cave: a Neanderthal occupation in the Northern Caucasus. Curr Anthropol 40: 77-86.
14. Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, et al. 2008. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134: 416-426.
15. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. 2010. A draft sequence of the Neandertal genome. Science 328: 710-722.
16. Hofreiter M, Jaenicke V, Serre D, von Haeseler A, Pääbo S. 2001. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res 29: 4793-4799.
17. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, Forster M, et al. 2012. New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing. Nat Commun 3: 698.
18. Kircher M, Sawyer S, Meyer M. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 40: e3.
19. Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S. 2010a. A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol 20: 231-236.
20. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. 2010b. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464: 894-897.
21. Lalueza-Fox C, Sampietro ML, Caramelli D, Puder Y, Lari M, Calafell F, Martinez-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.
22. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 25: 1754-1760.
23. Lindahl T. 1993. Instability and decay of the primary structure of DNA. Nature 362: 709-715.
24. Meyer M, Briggs AW, Maricic T, Hober B, Hoffner B, Krause J, Weihmann A, Pääbo S, Hofreiter M. 2008. From micrograms to picograms: quantitative PCR reduces the material demands of high-throughput sequencing. Nucleic Acids Res 36: e5.
25. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338: 222-226.
26. Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga JL, Martinez I, Gracia A, de Castro JM, Carbonell E, et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature 505: 403-406.
27. Olalde I, Allentoft ME, Sanchez-Quinto F, Santpere G, Chiang CW, DeGiorgio M, Prado-Martinez J, Rodriguez JA, Rasmussen S, Quilez J, et al. 2014. Derived immune and ancestral pigmentation alleles in a 7, 000-year-old Mesolithic European. Nature 507: 225-228.
28. Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, et al. 2014. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res 24: 454-466.
29. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43-49.
30. Raghavan M, Skoglund P, Graf KE, Metspalu M, Albrechtsen A, Moltke I, Rasmussen S, Stafford TW Jr, Orlando L, Metspalu E, et al. 2014. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505: 87-91.
31. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, et al. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468: 1053-1060.
32. Rohland N, Hofreiter M. 2007. Ancient DNA extraction from bones and teeth. Nat Protoc 2: 1756-1762.
33. Sawyer S, Krause J, Guschanski K, Savolainen V, Pääbo S. 2012. Temporal patterns of nucleotide misincorporations and DNA fragmentation in ancient DNA. PLoS ONE 7: e34131.
34. Shapiro B, HofreiterM. 2014. A paleogenomic perspective on evolution and gene function: new insights from ancient DNA. Science 343: 1236573.
35. Skinner AR, Blackwell BAB, Martin S, Ortega A, Blickstein JIB, Golovanov LV, Doronichev VB. 2005. ESR dating at Mezmaiskaya Cave, Russia. Appl Radiat Isot 62: 219-224.
36. Skoglund P, Malmstrom H, Raghavan M, Stora J, Hall P, Willerslev E, Gilbert MT, Gotherstrom A, Jakobsson M. 2012. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336: 466-469.
37. Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S, Krause J, Jakobsson M. 2014a. Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proc Natl Acad Sci 111: 2229-2234.
38. Skoglund P, Storáb J, Götherström A, Jakobsson M. 2014b. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J Archaeol Sci 40: 4477-4482.
39. Stoneking M, Krause J. 2011. Learning about human population history from ancient and modern genomes. Nat Rev Genet 12: 603-614.
40. Zaremba-Niedzwiedzka K, Andersson SGE. 2013. No ancient DNA damage in actinobacteria from the Neanderthal bone. PLoS ONE 8: e62799.