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Computational challenges in the analysis of ancient DNA.

ABSTRACT: 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.

SUBMITTER: Prufer K

PROVIDER: S-EPMC2898072 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Computational challenges in the analysis of ancient DNA.

Prüfer Kay K Stenzel Udo U Hofreiter Michael M Pääbo Svante S Kelso Janet J Green Richard E RE

Genome biology 20100506 5

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 appro ...[more]

PMID: 20441577

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