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

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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.; Pecnerová, Patrícia; Dehasque, Marianne; Ureña, Irene; Ersmark, Erik; Lagerholm, Vendela Kempe; Krzewinska, Maja; Rodríguez-Varela, Ricardo; Götherström, Anders; Dalén, Love; Díez-del-Molino, David.

In: BMC Genomics, Vol. 21, 844, 2020.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Feuerborn, TR, Palkopoulou, E, van der Valk, T, von Seth, J, Munters, AR, Pecnerová, P, Dehasque, M, Ureña, I, Ersmark, E, Lagerholm, VK, Krzewinska, M, Rodríguez-Varela, R, Götherström, A, Dalén, L & Díez-del-Molino, D 2020, 'Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets', BMC Genomics, vol. 21, 844. https://doi.org/10.1186/s12864-020-07229-y

APA

Feuerborn, T. R., Palkopoulou, E., van der Valk, T., von Seth, J., Munters, A. R., Pecnerová, P., Dehasque, M., Ureña, I., Ersmark, E., Lagerholm, V. K., Krzewinska, M., Rodríguez-Varela, R., Götherström, A., Dalén, L., & Díez-del-Molino, D. (2020). Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets. BMC Genomics, 21, [844]. https://doi.org/10.1186/s12864-020-07229-y

Vancouver

Feuerborn TR, Palkopoulou E, van der Valk T, von Seth J, Munters AR, Pecnerová P et al. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets. BMC Genomics. 2020;21. 844. https://doi.org/10.1186/s12864-020-07229-y

Author

Feuerborn, Tatiana R. ; Palkopoulou, Eleftheria ; van der Valk, Tom ; von Seth, Johanna ; Munters, Arielle R. ; Pecnerová, Patrícia ; Dehasque, Marianne ; Ureña, Irene ; Ersmark, Erik ; Lagerholm, Vendela Kempe ; Krzewinska, Maja ; Rodríguez-Varela, Ricardo ; Götherström, Anders ; Dalén, Love ; Díez-del-Molino, David. / Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets. In: BMC Genomics. 2020 ; Vol. 21.

Bibtex

@article{b5568a3628014cf0a17fcc55aca852ec,

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

abstract = "BackgroundAfter 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.ResultsHere 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.ConclusionsWe 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.",

keywords = "Ancient DNA, DNA contamination removal, Palaeogenomics, Competitive mapping, SEQUENCE, PATTERNS, DECAY, AGE, EXTRACTION, DAMAGE, BONES",

author = "Feuerborn, {Tatiana R.} and Eleftheria Palkopoulou and {van der Valk}, Tom and {von Seth}, Johanna and Munters, {Arielle R.} and Patr{\'i}cia Pecnerov{\'a} and Marianne Dehasque and Irene Ure{\~n}a and Erik Ersmark and Lagerholm, {Vendela Kempe} and Maja Krzewinska and Ricardo Rodr{\'i}guez-Varela and Anders G{\"o}therstr{\"o}m and Love Dal{\'e}n and David D{\'i}ez-del-Molino",

year = "2020",

doi = "10.1186/s12864-020-07229-y",

language = "English",

volume = "21",

journal = "BMC Genomics",

issn = "1471-2164",

publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets

AU - Feuerborn, Tatiana R.

AU - Palkopoulou, Eleftheria

AU - van der Valk, Tom

AU - von Seth, Johanna

AU - Munters, Arielle R.

AU - Pecnerová, Patrícia

AU - Dehasque, Marianne

AU - Ureña, Irene

AU - Ersmark, Erik

AU - Lagerholm, Vendela Kempe

AU - Krzewinska, Maja

AU - Rodríguez-Varela, Ricardo

AU - Götherström, Anders

AU - Dalén, Love

AU - Díez-del-Molino, David

PY - 2020

Y1 - 2020

N2 - BackgroundAfter 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.ResultsHere 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.ConclusionsWe 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.

AB - BackgroundAfter 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.ResultsHere 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.ConclusionsWe 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.

KW - Ancient DNA

KW - DNA contamination removal

KW - Palaeogenomics

KW - Competitive mapping

KW - SEQUENCE

KW - PATTERNS

KW - DECAY

KW - AGE

KW - EXTRACTION

KW - DAMAGE

KW - BONES

U2 - 10.1186/s12864-020-07229-y

DO - 10.1186/s12864-020-07229-y

M3 - Journal article

C2 - 33256612

VL - 21

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

M1 - 844

ER -

ID: 254663327