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
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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