Distortion of Population Statistics due to the Use of Different Methodological Approaches to the Construction of Genomic DNA Libraries.

Autor:	Sharko FS; Laboratory of vertebrate genomics and epigenomics, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, 119071 Russian Federation., Zhur KV; Laboratory of vertebrate genomics and epigenomics, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, 119071 Russian Federation., Trifonov VA; Laboratory of vertebrate genomics and epigenomics, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, 119071 Russian Federation.; Institute for the History of Material Culture of the Russian Academy of Sciences, Saint Petersburg, 191186 Russian Federation., Prokhortchouk EB; Laboratory of vertebrate genomics and epigenomics, Federal Research Centre 'Fundamentals of Biotechnology' of the Russian Academy of Sciences, Moscow, 119071 Russian Federation.
Jazyk:	angličtina
Zdroj:	Acta naturae [Acta Naturae] 2023 Jan-Mar; Vol. 15 (1), pp. 87-96.
DOI:	10.32607/actanaturae.11898
Abstrakt:	Several different methods of DNA library preparation for paleogenetic studies are now available. However, the chemical reactions underlying each of them can affect the primary sequence of ancient DNA (aDNA) in the libraries and taint the results of a statistical analysis. In this paper, we compare the results of a sequencing of the aDNA libraries of a Bronze Age sample from burials of the Caucasian burial ground Klady, prepared using three different approaches: (1) shotgun sequencing, (2) strategies for selecting target genomic regions, and (3) strategies for selecting target genomic regions, including DNA pre-treatment with a mixture of uracil-DNA glycosylase (UDG) and endonuclease VIII. The impact of the studied approaches to genomic library preparation on the results of a secondary analysis of the statistical data, namely F4 statistics, ADMIXTURE, and principal component analysis (PCA), was analyzed. It was shown that preparation of genomic libraries without the use of UDG can result in distorted statistical data due to postmortem chemical modifications of the aDNA. This distortion can be alleviated by analyzing only the single nucleotide polymorphisms caused by transversions in the genome. (Copyright ® 2023 National Research University Higher School of Economics.)
Databáze:	MEDLINE
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