Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis

Abstract In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of e...

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Autores principales: Anja Furtwängler, Ella Reiter, Gunnar U. Neumann, Inga Siebke, Noah Steuri, Albert Hafner, Sandra Lösch, Nils Anthes, Verena J. Schuenemann, Johannes Krause
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Publicado: Nature Portfolio 2018
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Acceso en línea:https://doaj.org/article/58dee04bd36044d0971ec0b630335110
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spelling oai:doaj.org-article:58dee04bd36044d0971ec0b6303351102021-12-02T15:08:24ZRatio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis10.1038/s41598-018-32083-02045-2322https://doaj.org/article/58dee04bd36044d0971ec0b6303351102018-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-32083-0https://doaj.org/toc/2045-2322Abstract In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.Anja FurtwänglerElla ReiterGunnar U. NeumannInga SiebkeNoah SteuriAlbert HafnerSandra LöschNils AnthesVerena J. SchuenemannJohannes KrauseNature PortfolioarticleContamination EstimatesPetrous BoneSkeletal ElementsmtDNA ContaminationMapping StringenciesMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-8 (2018)
institution DOAJ
collection DOAJ
language EN
topic Contamination Estimates
Petrous Bone
Skeletal Elements
mtDNA Contamination
Mapping Stringencies
Medicine
R
Science
Q
spellingShingle Contamination Estimates
Petrous Bone
Skeletal Elements
mtDNA Contamination
Mapping Stringencies
Medicine
R
Science
Q
Anja Furtwängler
Ella Reiter
Gunnar U. Neumann
Inga Siebke
Noah Steuri
Albert Hafner
Sandra Lösch
Nils Anthes
Verena J. Schuenemann
Johannes Krause
Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
description Abstract In the last decade, ancient DNA research has grown rapidly and started to overcome several of its earlier limitations through Next-Generation-Sequencing (NGS). Among other advances, NGS allows direct estimation of sample contamination from modern DNA sources. First NGS-based approaches of estimating contamination measured heterozygosity. These measurements, however, could only be performed on haploid genomic regions, i.e. the mitochondrial genome or male X chromosomes, but provided no measures of contamination in the nuclear genome of females with their two X chromosomes. Instead, female nuclear contamination is routinely extrapolated from mitochondrial contamination estimates, but it remains unclear if this extrapolation is reliable and to what degree variation in mitochondrial to nuclear DNA ratios affects this extrapolation. We therefore analyzed ancient DNA from 317 samples of different skeletal elements from multiple sites, spanning a temporal range from 7,000 BP to 386 AD. We found that the mitochondrial to nuclear DNA (mt/nc) ratio negatively correlates with an increase in endogenous DNA content and strongly influenced mitochondrial and nuclear contamination estimates in males. The ratio of mt to nc contamination estimates remained stable for overall mt/nc ratios below 200, as found particularly often in petrous bones but less in other skeletal elements and became more variable above that ratio.
format article
author Anja Furtwängler
Ella Reiter
Gunnar U. Neumann
Inga Siebke
Noah Steuri
Albert Hafner
Sandra Lösch
Nils Anthes
Verena J. Schuenemann
Johannes Krause
author_facet Anja Furtwängler
Ella Reiter
Gunnar U. Neumann
Inga Siebke
Noah Steuri
Albert Hafner
Sandra Lösch
Nils Anthes
Verena J. Schuenemann
Johannes Krause
author_sort Anja Furtwängler
title Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
title_short Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
title_full Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
title_fullStr Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
title_full_unstemmed Ratio of mitochondrial to nuclear DNA affects contamination estimates in ancient DNA analysis
title_sort ratio of mitochondrial to nuclear dna affects contamination estimates in ancient dna analysis
publisher Nature Portfolio
publishDate 2018
url https://doaj.org/article/58dee04bd36044d0971ec0b630335110
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