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bioRxiv · 10.1101/2023.11.06.565746

Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage

Zhao, L.·Henriksen, R. A.·Ramsoe, A. D.·Nielsen, R.·Korneliussen, T. S.
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Abstract

MotivationOne essential initial step in the analysis of ancient DNA is to authenticate its ancientness to ensure reliable conclusions. That is, meticulously assessing whether next-generation sequencing reads exhibit ancient characteristics, with a particular focus on the postmortem damage (PMD) signal induced by cytosine deamination in the fragments termini. We present a novel statistical method implementation in a fast multithreaded program ngsBriggs that enables the rapid quantification of PMD by calculation of the Briggs ancient damage model parameters (Briggs parameters). ResultsUsing a fast multinomial regression approach, ngsBriggs accurately models the Briggs parameters, quantifying the PMD signal from single and double-stranded DNA regions. We revisit and extend the original Briggs model, with ngsBriggs modeling PMD signals for contemporary sequencing platforms. Furthermore, ngsBriggs asserts itself as a reliable and consistent tool, by accurately estimating the Briggs parameters across a variety of contamination levels. The classification accuracy of ngsBriggs significantly exceeds the current tool available when discerning ancient-from modern sequencing reads to decontaminate samples. Our novel method and implementation ngsBriggs outperforms existing tools regarding computational speed and accuracy, establishing its practicality and usability. Our tool, ngsBriggs offers a practical and accurate toolset for researchers seeking to authenticate ancient DNA and improve the quality of their data. Availabilityhttps://github.com/lz398/metadamage_briggs

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Zhao, L., Henriksen, R. A., Ramsoe, A. D., Nielsen, R., Korneliussen, T. S.. 2023-11-06. Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage. https://doi.org/10.1101/2023.11.06.565746

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