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  Present-Day DNA Contamination in Ancient DNA Datasets

Peyrégne, S., & Prüfer, K. (2020). Present-Day DNA Contamination in Ancient DNA Datasets. Bioessays, n/a(n/a): 2000081. doi:10.1002/bies.202000081.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-BBDC-0 Version Permalink: http://hdl.handle.net/21.11116/0000-0006-BBDD-F
Genre: Journal Article

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 Creators:
Peyrégne, Stéphane, Author              
Prüfer, Kay1, Author              
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

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Free keywords: ancient DNA, contamination, paleogenomics
 Abstract: Abstract Present-day contamination can lead to false conclusions in ancient DNA studies. A number of methods are available to estimate contamination, which use a variety of signals and are appropriate for different types of data. Here an overview of currently available methods highlighting their strengths and weaknesses is provided, and a classification based on the signals used to estimate contamination is proposed. This overview aims at enabling researchers to choose the most appropriate methods for their dataset. Based on this classification, potential avenues for the further development of methods are discussed.

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Language(s): eng - English
 Dates: 2020-07-10
 Publication Status: Published online
 Pages: 11
 Publishing info: -
 Table of Contents: 1. Introduction

2. Classification of Signals Used to Estimate Contamination
2.1. Differences in the DNA Sequence
2.2. Deviation from the Expected Ploidy
2.3. Ancient DNA Degradation Patterns

3. Methods to Estimate Contamination
3.1. Mitochondrial DNA
3.1.1. Methods Based on Differences in the DNA Sequence
3.1.2. Methods Based on Deviations from the Expected Ploidy
3.2. Sex Chromosomes
3.2.1. Methods Based on Differences in the DNA Sequence
3.2.2. Methods Based on Deviations from the Expected Ploidy
3.3. Autosomal DNA
3.3.1. Methods Based on Differences in the DNA Sequence
3.3.2. Methods Based on Deviations from the Expected Ploidy
3.3.3. Methods Based on Patterns of Ancient DNA Damage

4. Perspectives
4.1. Methods Based on Differences in the DNA Sequence
4.2. Methods Based on Deviations from the Expected Ploidy
4.3. Methods Based on Characteristics of Ancient DNA

5. Conclusion
 Rev. Type: Peer
 Identifiers: DOI: 10.1002/bies.202000081
Other: shh2660
 Degree: -

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Title: Bioessays
  Other : Bioessays
Source Genre: Journal
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Publ. Info: Cambridge, UK : Co. of Biologists
Pages: - Volume / Issue: n/a (n/a) Sequence Number: 2000081 Start / End Page: - Identifier: ISSN: 0265-9247
CoNE: https://pure.mpg.de/cone/journals/resource/954925499109