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Competitive mapping...
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets
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- Feuerborn, Tatiana R. (author)
- Stockholms universitet,Institutionen för arkeologi och antikens kultur,University of Copenhagen, Denmark; Swedish Museum of Natural History, Sweden; Centre for Palaeogenetics, Sweden,Univ Copenhagen, Globe Inst, Copenhagen, Denmark; Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden
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- Palkopoulou, Eleftheria (author)
- Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden
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- van der Valk, Tom (author)
- Naturhistoriska riksmuseet,Enheten för bioinformatik och genetik
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- von Seth, Johanna (author)
- Naturhistoriska riksmuseet,Stockholms universitet,Zoologiska institutionen,Swedish Museum of Natural History, Sweden; Centre for Palaeogenetics, Sweden,Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden,Enheten för bioinformatik och genetik
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- Munters, Arielle R. (author)
- Uppsala universitet,Människans evolution
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- Pečnerová, Patrícia (author)
- Univ Copenhagen, Dept Biol, Copenhagen, Denmark
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- Dehasque, Marianne (author)
- Naturhistoriska riksmuseet,Stockholms universitet,Zoologiska institutionen,Swedish Museum of Natural History, Sweden; Centre for Palaeogenetics, Sweden,Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden,Enheten för bioinformatik och genetik
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- Ureña, Irene (author)
- INIA, Dept Anim Breeding, Madrid, Spain
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- Ersmark, Erik (author)
- Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden
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- Kempe Lagerholm, Vendela (author)
- Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden
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- Krzewińska, Maja (author)
- Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden
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- Rodríguez-Varela, Ricardo (author)
- Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden
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- Götherström, Anders (author)
- Stockholms universitet,Institutionen för arkeologi och antikens kultur,Centre for Palaeogenetics, Sweden,Stockholm Univ, Dept Archaeol & Class Studies, Archaeol Res Lab, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden
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- Dalén, Love (author)
- Naturhistoriska riksmuseet,Stockholms universitet,Zoologiska institutionen,Swedish Museum of Natural History, Sweden; Centre for Palaeogenetics, Sweden,Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden,Enheten för bioinformatik och genetik
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- Díez-del-Molino, David (author)
- Naturhistoriska riksmuseet,Stockholms universitet,Zoologiska institutionen,Swedish Museum of Natural History, Sweden; Centre for Palaeogenetics, Sweden,Swedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden; Stockholm Univ, Dept Zool, Stockholm, Sweden,Enheten för bioinformatik och genetik
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(creator_code:org_t)
- 2020-11-30
- 2020
- English.
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
- Related links:
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https://doi.org/10.1...
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https://bmcgenomics....
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https://uu.diva-port... (primary) (Raw object)
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https://nrm.diva-por... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://urn.kb.se/re...
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Abstract
Subject headings
Close
- Background: After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data.Results: Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses.Conclusions: We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
Subject headings
- TEKNIK OCH TEKNOLOGIER -- Miljöbioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Environmental Biotechnology (hsv//eng)
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Keyword
- Ancient DNA
- DNA contamination removal
- Palaeogenomics
- Competitive mapping
- Livets mångfald
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Feuerborn, Tatia ...
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Palkopoulou, Ele ...
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van der Valk, To ...
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von Seth, Johann ...
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Munters, Arielle ...
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Pečnerová, Patrí ...
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show more...
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Dehasque, Marian ...
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Ureña, Irene
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Ersmark, Erik
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Kempe Lagerholm, ...
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Krzewińska, Maja
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Rodríguez-Varela ...
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Götherström, And ...
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Dalén, Love
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Díez-del-Molino, ...
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- About the subject
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- ENGINEERING AND TECHNOLOGY
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ENGINEERING AND ...
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and Environmental Bi ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Genetics
- Articles in the publication
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BMC Genomics
- By the university
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Stockholm University
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Uppsala University
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Swedish Museum of Natural History