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

Feuerborn, Tatiana R ; Palkopoulou, Eleftheria ; van der Valk, Tom ; von Seth, Johanna ; Munters, Arielle R ; Pečnerová, Patrícia LU orcid ; Dehasque, Marianne ; Ureña, Irene ; Ersmark, Erik and Lagerholm, Vendela Kempe , et al. (2020) In BMC Genomics 21.
Abstract

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... (More)

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.

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publishing date
type
Contribution to journal
publication status
published
keywords
DNA Contamination, DNA, Ancient, Genome, Genomics, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA
in
BMC Genomics
volume
21
article number
844
pages
10 pages
publisher
BioMed Central (BMC)
external identifiers
  • pmid:33256612
  • scopus:85096938959
ISSN
1471-2164
DOI
10.1186/s12864-020-07229-y
language
English
LU publication?
no
id
0dbc2c67-0793-4bda-b84e-2c3ec9e5354b
date added to LUP
2024-10-10 15:59:50
date last changed
2025-02-28 16:37:55
@article{0dbc2c67-0793-4bda-b84e-2c3ec9e5354b,
  abstract     = {{<p>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.</p><p>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.</p><p>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.</p>}},
  author       = {{Feuerborn, Tatiana R and Palkopoulou, Eleftheria and van der Valk, Tom and von Seth, Johanna and Munters, Arielle R and Pečnerová, Patrícia and Dehasque, Marianne and Ureña, Irene and Ersmark, Erik and Lagerholm, Vendela Kempe and Krzewińska, Maja and Rodríguez-Varela, Ricardo and Götherström, Anders and Dalén, Love and Díez-Del-Molino, David}},
  issn         = {{1471-2164}},
  keywords     = {{DNA Contamination; DNA, Ancient; Genome; Genomics; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA}},
  language     = {{eng}},
  month        = {{11}},
  publisher    = {{BioMed Central (BMC)}},
  series       = {{BMC Genomics}},
  title        = {{Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets}},
  url          = {{http://dx.doi.org/10.1186/s12864-020-07229-y}},
  doi          = {{10.1186/s12864-020-07229-y}},
  volume       = {{21}},
  year         = {{2020}},
}