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  Modelling segmental duplications in the human genome

Abdullaev, E., Umarova, I. R., & Arndt, P. F. (2021). Modelling segmental duplications in the human genome. BMC Genomics, 22: 496. doi:10.1186/s12864-021-07789-7.

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 Creators:
Abdullaev, Eldar1, Author              
Umarova, Iren R.2, Author
Arndt, Peter F.1, Author              
Affiliations:
1Evolutionary Genomics (Peter Arndt), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479638              
2Faculty of Computational Mathematics and Cybernetics, Moscow State University, Leninskiye Gory 1-52, Moscow, 119991, Russia, ou_persistent22              

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Free keywords: Segmental duplications, SDs, Complex networks
 Abstract: Background: Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copies in a genome. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, however, we do not have a full understanding of the dynamic properties of the duplication process. Results: We study segmental duplications through a graph representation where nodes represent genomic regions and edges represent duplications between them. The resulting network (the SD network) is quite complex and has distinct features which allow us to make inference on the evolution of segmantal duplications. We come up with the network growth model that explains features of the SD network thus giving us insights on dynamics of segmental duplications in the human genome. Based on our analysis of genomes of other species the network growth model seems to be applicable for multiple mammalian genomes. Conclusions: Our analysis suggests that duplication rates of genomic loci grow linearly with the number of copies of a duplicated region. Several scenarios explaining such a preferential duplication rates were suggested.

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Language(s): eng - English
 Dates: 2021-06-102021-07-02
 Publication Status: Published online
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: DOI: 10.1186/s12864-021-07789-7
 Degree: -

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Title: BMC Genomics
Source Genre: Journal
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Publ. Info: BioMed Central
Pages: - Volume / Issue: 22 Sequence Number: 496 Start / End Page: - Identifier: ISSN: 1471-2164
CoNE: https://pure.mpg.de/cone/journals/resource/111000136905010