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Authentication and Assessment of Contamination in Ancient DNA
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“While some guidelines exist for the analysis of ancient genomic data, for example for mapping 162,181,183 or data authentication 56,57,329 , and automated tools embedding critical analytical procedures within open-source pipelines are available 187,188,241,242 , there is still no consensus on a”
From Ancient DNA analysis (2021) · cites this paper as [56]
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ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982
A high-coverage genome sequence from an archaic denisovan individual
Meyer, M., Kircher, M., Gansauge, M.-T., Li, H., Racimo, F., Mallick, S., Schraiber, J. G., Jay, F., Prüfer, K., de Filippo, C., et al. (2012) · Science · doi:10.1126/science.1224344 · Cited by 1,967
Massive migration from the steppe was a source for Indo-European languages in Europe
Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940
mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt193 · Cited by 1,669
Self-citationPopulation genomics of Bronze Age Eurasia
Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550
Self-citationDabney, J., Knapp, M., Glocke, I., Gansauge, M.-T., Weihmann, A., Nickel, B., Valdiosera, C., García, N., Pääbo, S., Arsuaga, J.-L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314445110 · Cited by 1,443
Ancient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357
Self-citationGenome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023
Recalibrating equus evolution using the genome sequence of an early middle pleistocene horse
Orlando, L., Ginolhac, A., Zhang, G., Froese, D., Albrechtsen, A., Stiller, M., Schubert, M., Cappellini, E., Petersen, B., Moltke, I., et al. (2013) · Nature · doi:10.1038/nature12323 · Cited by 841
Self-citationNuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins
Meyer, M., Arsuaga, J.-L., de Filippo, C., Nagel, S., Aximu-Petri, A., Nickel, B., Martínez, I., Gracia, A., de Castro, J. M. B., Carbonell, E., et al. (2016) · Nature · doi:10.1038/nature17405 · Cited by 584
Flagged first, then by citations
Research works printed but not linked: 66
- Ermini L, Der Sarkissian C, Willerslev E, Orlando L (2015) Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 79:4–20. https://doi.org/10.1016/j.jhevol.2014.06.015 · DOI
- Llamas B, Fehren-Schmitz L, Valverde G et al (2016) Ancient mitochondrial DNA provides high-resolution time scale of the peopling of the. Am Sci Adv. https://doi.org/10.1126/sciadv.1501385 · DOI · Paper page
- Librado P, Der Sarkissian C, Ermini L et al (2015) Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. Proc Natl Acad Sci U S A 112:E6889–E6897. https://doi.org/10.1073/pnas.1513696112 · DOI
- Frantz LAF, Mullin VE, Pionnier-Capitan M et al (2016) Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 352:1228–1231. https://doi.org/10.1126/science.aaf3161 · DOI · Paper page
- MacHugh DE, Larson G, Orlando L (2016) Taming the past: ancient DNA and the study of animal domestication. Annu Rev Anim Biosci. https://doi.org/10.1146/annurev-animal-022516-022747 · DOI
- Der Sarkissian C, Ermini L, Schubert M et al (2015) Evolutionary genomics and conservation of the endangered Przewalski’s horse. Curr Biol 25:2577–2583. https://doi.org/10.1016/j.cub.2015.08.032 · DOI
- Da Fonseca RR, Smith BD, Wales N, et al (2015) The origin and evolution of maize in the Southwestern United States. Nat Plants. doi: https://doi.org/10.1038/nplants.2014.3 · DOI
- Bos KI, Schuenemann VJ, Golding GB et al (2011) A draft genome of Yersinia pestis from victims of the Black Death. Nature. https://doi.org/10.1038/nature10675 · DOI
- Wagner MR, Lundberg DS, Coleman-Derr D et al (2015) Corrigendum to Wagneret al.: natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett. https://doi.org/10.1111/ele.12400 · DOI
- Ramos-Madrigal J, Smith BD, Moreno-Mayar JV et al (2016) Genome sequence of a 5,310-year-old maize cob provides insights into the early stages of maize domestication. Curr Biol 26:3195–3201. https://doi.org/10.1016/j.cub.2016.09.036 · DOI
- Rasmussen S, Allentoft ME, Nielsen K et al (2015) Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163:571–582. https://doi.org/10.1016/j.cell.2015.10.009 · DOI
- Hofreiter M, Serre D, Poinar HN et al (2001) Ancient DNA. Nat Rev Genet 2:353–359. https://doi.org/10.1038/35072071 · DOI · Paper page
- Briggs AW, Stenzel U, Johnson PL et al (2007) Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A 104:14616–14621. https://doi.org/10.1073/pnas.0704665104 · DOI · Paper page
- Green RE, Malaspinas A-S, Krause J et al (2008) A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell 134:416–426. https://doi.org/10.1016/j.cell.2008.06.021 · DOI
- Gilbert MTP, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, Higham TFG, Richards MP, O’Connell TC, Tobin DJ, Janaway RC, Cooper A (2004) Ancient mitochondrial DNA from hair. Curr Biol 14:R463–R464 · DOI
- Pilli E, Modi A, Serpico C et al (2013) Monitoring DNA contamination in handled vs. directly excavated ancient human skeletal remains. PLoS One. https://doi.org/10.1371/journal.pone.0052524 · DOI
- Korlević P, Gerber T, Gansauge M-T et al (2015) Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. BioTechniques 59:87–93. https://doi.org/10.2144/000114320 · DOI · Paper page
- Guschanski K, Krause J, Sawyer S et al (2013) Next-generation museomics disentangles one of the largest primate radiations. Syst Biol 62:539–554. https://doi.org/10.1093/sysbio/syt018 · DOI
- Pruvost M, Schwarz R, Correia VB et al (2007) Freshly excavated fossil bones are best for amplification of ancient DNA. Proc Natl Acad Sci U S A 104:739–744. https://doi.org/10.1073/pnas.0610257104 · DOI · Paper page
- Champlot S, Berthelot C, Pruvost M et al (2010) An efficient multistrategy DNA decontamination procedure of PCR reagents for hypersensitive PCR applications. PLoS One. https://doi.org/10.1371/journal.pone.0013042 · DOI
- Serre D, Langaney A, Chech M, et al (2004) No evidence of Neandertal mtDNA contribution to early modern humans. PLoS Biol. https://doi.org/10.1371/journal.pbio.0020057 · DOI
- Brown S, Higham T, Slon V et al (2016) Identification of a new hominin bone from Denisova Cave, Siberia using collagen fingerprinting and mitochondrial DNA analysis. Sci Rep. https://doi.org/10.1038/srep23559 · DOI · Paper page
- Briggs AW, Good JM, Green RE et al (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325:318–321. https://doi.org/10.1126/science.1174462 · DOI
- Sawyer S, Renaud G, Viola B et al (2015) Nuclear and mitochondrial DNA sequences from two Denisovan individuals. Proc Natl Acad Sci U S A 112:15696–15700. https://doi.org/10.1073/pnas.1519905112 · DOI
- Krause J, Briggs AW, Kircher M et al (2010) A complete mtDNA genome of an early modern human from Kostenki, Russia. Curr Biol 20:231–236. https://doi.org/10.1016/j.cub.2009.11.068 · DOI · Paper page
- Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362:709–715. https://doi.org/10.1038/362709a0 · DOI · Paper page
- Seguin-Orlando A, Schubert M, Clary J et al (2013) Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes. PLoS One. https://doi.org/10.1371/journal.pone.0078575 · DOI · Paper page
- Wales N, Ramos Madrigal J, Cappellini E et al (2016) The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. J Archaeol Sci. https://doi.org/10.1016/j.jas.2016.05.014 · DOI
- Seguin-Orlando A, Hoover CA, Vasiliev SK et al (2015) Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns. Sci Technol Archaeol Res. https://doi.org/10.1179/2054892315Y.0000000005 · DOI · Paper page
- Wall JD, Kim SK (2007) Inconsistencies in Neanderthal genomic DNA sequences. PLoS Genet 3:1862–1866. https://doi.org/10.1371/journal.pgen.0030175 · DOI
- Prüfer K, Meyer M (2015) Anthropology. Comment on “Late Pleistocene human skeleton and mtDNA link Paleoamericans and modern Native Americans”. Science. https://doi.org/10.1126/science.1260617 · DOI
- Weiß CL, Dannemann M, Prüfer K, Burbano HA (2015) Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data. eLife. https://doi.org/10.7554/eLife.10005 · DOI
- Schubert M, Ermini L, Der Sarkissian C et al (2014) Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. Nat Protoc 9:1056–1082. https://doi.org/10.1038/nprot.2014.063 · DOI · Paper page
- Kircher M (2012) Analysis of high-throughput ancient DNA sequencing data. Methods Mol Biol 840:197–228. https://doi.org/10.1007/978-1-61779-516-9_23 · DOI · Paper page
- Schubert M, Lindgreen S, Orlando L (2016) AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. https://doi.org/10.1186/s13104-016-1900-2 · DOI
- Renaud G, Stenzel U, Kelso J (2014) leeHom: adaptor trimming and merging for Illumina sequencing reads. Nucleic Acids Res. https://doi.org/10.1093/nar/gku699 · DOI
- Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170 · DOI · Paper page
- O’Connell J, Schulz-Trieglaff O, Carlson E et al (2015) NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics 31:2035–2037. https://doi.org/10.1093/bioinformatics/btv057 · DOI
- Sturm M, Schroeder C, Bauer P (2016) SeqPurge: highly-sensitive adapter trimming for paired-end NGS data. BMC Bioinformatics. https://doi.org/10.1186/s12859-016-1069-7 · DOI
- Zhang J, Kobert K, Flouri T, Stamatakis A (2014) PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30:614–620. https://doi.org/10.1093/bioinformatics/btt593 · DOI · Paper page
- Magoč T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963. https://doi.org/10.1093/bioinformatics/btr507 · DOI · Paper page
- Mielczarek M, Szyda J (2016) Review of alignment and SNP calling algorithms for next-generation sequencing data. J Appl Genet 57:71–79. https://doi.org/10.1007/s13353-015-0292-7 · DOI
- Li HH, Durbin RR (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324 · DOI · Paper page
- Kerpedjiev P, Frellsen J, Lindgreen S, Krogh A (2014) Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-15-100 · DOI
- Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923 · DOI · Paper page
- Nomiyama H, Fukuda M, Wakasugi S et al (1985) Molecular structures of mitochondrial-DNA-like sequences in human nuclear DNA. Nucleic Acids Res 13:1649–1658. https://doi.org/10.1093/nar/13.5.1649 · DOI
- Lopez JV, Yuhki N, Masuda R et al (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39:174–190 · DOI
- Li H, Handsaker B, Wysoker A et al (2008) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079 · DOI · Paper page
- Dozmorov MG, Adrianto I, Giles CB et al (2015) Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data. BMC Bioinformatics. https://doi.org/10.1186/1471-2105-16-S13-S10 · DOI
- McKenna A, Hanna M, Banks E et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110 · DOI · Paper page
- Briggs AW, Stenzel U, Meyer M et al (2010) Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. https://doi.org/10.1093/nar/gkp1163 · DOI · Paper page
- Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot5448 · DOI
- Krause J, Unger T, Noçon A et al (2008) Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evol Biol. https://doi.org/10.1186/1471-2148-8-220 · DOI
- Pedersen JS, Valen E, Velazquez AMV et al (2014) Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res 24:454–466. https://doi.org/10.1101/gr.163592.113 · DOI · Paper page
- Gokhman D, Lavi E, Prüfer K et al (2014) Reconstructing the DNA methylation maps of the Neandertal and the Denisovan. Science 344:523–527. https://doi.org/10.1126/science.1250368 · DOI · Paper page
- Hanghøj K, Seguin-Orlando A, Schubert M et al (2016) Fast, accurate and automatic ancient nucleosome and methylation maps with epiPALEOMIX. Mol Biol Evol 33:3284–3298. https://doi.org/10.1093/molbev/msw184 · DOI
- Schuenemann VJ, Singh P, Mendum TA et al (2013) Genome-wide comparison of medieval and modern Mycobacterium leprae. Science 341:179–183. https://doi.org/10.1126/science.1238286 · DOI · Paper page
- Parks M, Lambert D (2015) Impacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study. BMC Genomics. https://doi.org/10.1186/s12864-015-1219-8 · DOI
- Green RE, Briggs AW, Krause J et al (2009) The Neandertal genome and ancient DNA authenticity. EMBO J 28:2494–2502. https://doi.org/10.1038/emboj.2009.222 · DOI · Paper page
- Zhang H, Paijmans JLA, Chang F et al (2013) Morphological and genetic evidence for early Holocene cattle management in northeastern China. Nat Commun. https://doi.org/10.1038/ncomms3755 · DOI
- Weissensteiner H, Pacher D, Kloss-Brandstätter A et al (2016) HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res 44:W58–W63. https://doi.org/10.1093/nar/gkw233 · DOI
- Racimo F, Renaud G, Slatkin M (2016) Joint estimation of contamination, error and demography for nuclear DNA from ancient humans. PLoS Genet. https://doi.org/10.1371/journal.pgen.1005972 · DOI · Paper page
- Skoglund P, Storå J, Götherström A, Jakobsson M (2013) Accurate sex identification of ancient human remains using DNA shotgun sequencing. J Archaeol Sci. https://doi.org/10.1016/j.jas.2013.07.004 · DOI · Paper page
- Abecasis GR, Auton A, Brooks LD, et al with 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65. https://doi.org/10.1038/nature11632 · DOI · Paper page
- Louvel G, Der Sarkissian C, Hanghøj K, Orlando L (2016) metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data. Mol Ecol Resour 16:1415–1427. https://doi.org/10.1111/1755-0998.12546 · DOI · Paper page
- Renaud G, Hanghøj K, Willeslev E, Orlando L (2016) gargammel: a sequence simulator for ancient DNA. Bioinformatics 33(4):577–579. https://doi.org/10.1093/bioinformatics/btw670 · DOI · Paper page
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Orlando, L., Allaby, R., Skoglund, P., Der Sarkissian, C., Stockhammer, P. W., Ávila-Arcos, M. C., Fu, Q., Krause, J., Willerslev, E., Stone, A. C., et al. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-020-00011-0 · Cited by 411
Self-citation
Metadata
- Authors
- Renaud, G., Schubert, M., Sawyer, S., & Orlando, L.
- Venue
- Methods in Molecular Biology
- Publisher
- Springer New York
- Published
- 2019
- Pages
- 163-194
- ISSN
- 1064-3745
- 1940-6029
- Cited by
- 23
- References
- 17
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
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