Computational challenges in the analysis of ancient DNA

High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identi...

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Autores principales: Prüfer, Kay, Stenzel, Udo, Hofreiter, Michael, Pääbo, Svante, Kelso, Janet, Green, Richard E
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898072/
https://www.ncbi.nlm.nih.gov/pubmed/20441577
http://dx.doi.org/10.1186/gb-2010-11-5-r47
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author Prüfer, Kay
Stenzel, Udo
Hofreiter, Michael
Pääbo, Svante
Kelso, Janet
Green, Richard E
author_facet Prüfer, Kay
Stenzel, Udo
Hofreiter, Michael
Pääbo, Svante
Kelso, Janet
Green, Richard E
author_sort Prüfer, Kay
collection PubMed
description High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering.
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spelling pubmed-28980722010-07-07 Computational challenges in the analysis of ancient DNA Prüfer, Kay Stenzel, Udo Hofreiter, Michael Pääbo, Svante Kelso, Janet Green, Richard E Genome Biol Method High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering. BioMed Central 2010 2010-05-06 /pmc/articles/PMC2898072/ /pubmed/20441577 http://dx.doi.org/10.1186/gb-2010-11-5-r47 Text en Copyright ©2010 Prüfer et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Prüfer, Kay
Stenzel, Udo
Hofreiter, Michael
Pääbo, Svante
Kelso, Janet
Green, Richard E
Computational challenges in the analysis of ancient DNA
title Computational challenges in the analysis of ancient DNA
title_full Computational challenges in the analysis of ancient DNA
title_fullStr Computational challenges in the analysis of ancient DNA
title_full_unstemmed Computational challenges in the analysis of ancient DNA
title_short Computational challenges in the analysis of ancient DNA
title_sort computational challenges in the analysis of ancient dna
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898072/
https://www.ncbi.nlm.nih.gov/pubmed/20441577
http://dx.doi.org/10.1186/gb-2010-11-5-r47
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