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Search: onr:"swepub:oai:DiVA.org:su-189333" > Competitive mapping...

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  • Feuerborn, Tatiana R.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 (author)

Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

  • Article/chapterEnglish2020

Publisher, publication year, extent ...

  • 2020-11-30
  • Springer Science and Business Media LLC,2020
  • printrdacarrier

Numbers

  • LIBRIS-ID:oai:DiVA.org:su-189333
  • https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-189333URI
  • https://doi.org/10.1186/s12864-020-07229-yDOI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-430518URI
  • https://urn.kb.se/resolve?urn=urn:nbn:se:nrm:diva-4082URI

Supplementary language notes

  • Language:English
  • Summary in:English

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  • Subject category:ref swepub-contenttype
  • Subject category:art swepub-publicationtype

Notes

  • 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 and genre

Added entries (persons, corporate bodies, meetings, titles ...)

  • Palkopoulou, EleftheriaSwedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden (author)
  • van der Valk, TomNaturhistoriska riksmuseet,Enheten för bioinformatik och genetik(Swepub:nrm)tomvande (author)
  • von Seth, JohannaNaturhistoriska 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(Swepub:nrm)johavons (author)
  • Munters, Arielle R.Uppsala universitet,Människans evolution(Swepub:uu)arimu328 (author)
  • Pečnerová, PatríciaUniv Copenhagen, Dept Biol, Copenhagen, Denmark (author)
  • Dehasque, MarianneNaturhistoriska 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(Swepub:nrm)marideha (author)
  • Ureña, IreneINIA, Dept Anim Breeding, Madrid, Spain (author)
  • Ersmark, ErikSwedish Museum Nat Hist, Dept Bioinformat & Genet, Stockholm, Sweden; Ctr Palaeogenet, Stockholm, Sweden (author)
  • Kempe Lagerholm, VendelaStockholms 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(Swepub:su)veke2350 (author)
  • Krzewińska, MajaStockholms 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(Swepub:su)mkrze (author)
  • Rodríguez-Varela, RicardoStockholms 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(Swepub:su)rrodr (author)
  • Götherström, AndersStockholms 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(Swepub:su)gother (author)
  • Dalén, LoveNaturhistoriska 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(Swepub:nrm)lovedale (author)
  • Díez-del-Molino, DavidNaturhistoriska 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(Swepub:nrm)davidiez (author)
  • Stockholms universitetInstitutionen för arkeologi och antikens kultur (creator_code:org_t)

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  • In:BMC Genomics: Springer Science and Business Media LLC21:11471-2164

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