Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Jul 1;29(13):1682-4.
doi: 10.1093/bioinformatics/btt193. Epub 2013 Apr 23.

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Hákon Jónsson  1 , Aurélien Ginolhac, Mikkel Schubert, Philip L F Johnson, Ludovic Orlando
Affiliations

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

Hákon Jónsson et al. Bioinformatics. .

Abstract

Motivation: Ancient DNA (aDNA) molecules in fossilized bones and teeth, coprolites, sediments, mummified specimens and museum collections represent fantastic sources of information for evolutionary biologists, revealing the agents of past epidemics and the dynamics of past populations. However, the analysis of aDNA generally faces two major issues. Firstly, sequences consist of a mixture of endogenous and various exogenous backgrounds, mostly microbial. Secondly, high nucleotide misincorporation rates can be observed as a result of severe post-mortem DNA damage. Such misincorporation patterns are instrumental to authenticate ancient sequences versus modern contaminants. We recently developed the user-friendly mapDamage package that identifies such patterns from next-generation sequencing (NGS) sequence datasets. The absence of formal statistical modeling of the DNA damage process, however, precluded rigorous quantitative comparisons across samples.

Results: Here, we describe mapDamage 2.0 that extends the original features of mapDamage by incorporating a statistical model of DNA damage. Assuming that damage events depend only on sequencing position and post-mortem deamination, our Bayesian statistical framework provides estimates of four key features of aDNA molecules: the average length of overhangs (λ), nick frequency (ν) and cytosine deamination rates in both double-stranded regions ( ) and overhangs ( ). Our model enables rescaling base quality scores according to their probability of being damaged. mapDamage 2.0 handles NGS datasets with ease and is compatible with a wide range of DNA library protocols.

Availability: mapDamage 2.0 is available at ginolhac.github.io/mapDamage/ as a Python package and documentation is maintained at the Centre for GeoGenetics Web site (geogenetics.ku.dk/publications/mapdamage2.0/).

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
A schematic view describing the DNA damage Markov chain, which extends the DNA substitution model. The states formula image and formula image correspond to the final nucleotides in the sequences
See this image and copyright information in PMC

References

    1. Briggs AW, et al. Patterns of damage in genomic DNA sequences from a Neandertal. Proc. Natl Acad. Sci. USA. 2007;104:14616–14621. - PMC - PubMed
    1. Ginolhac A, et al. mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics. 2011;27:2153–2155. - PubMed
    1. Hasegawa M, et al. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 1985;22:160–174. - PubMed
    1. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993;362:709–715. - PubMed
    1. Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010;2010 pdb.prot5448. - PubMed

Publication types

LinkOut - more resources