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  The Mobile Element Locator Tool (MELT): Population-scale mobile element discovery and biology

Gardner, E. J., Lam, V. K., Harris, D. N., Chuang, N. T., Scott, E. C., Pittard, W. S., et al. (2017). The Mobile Element Locator Tool (MELT): Population-scale mobile element discovery and biology. Genome Research, 27(11), 1916-1929. doi:10.1101/gr.218032.116.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0000-C7E3-F Version Permalink: http://hdl.handle.net/21.11116/0000-0000-C7E4-E
Genre: Journal Article

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 Creators:
Gardner, Eugene J. , Author
Lam, Vincent K. , Author
Harris, Daniel N. , Author
Chuang, Nelson T. , Author
Scott, Emma C. , Author
Pittard, W. Stephen , Author
Mills, Ryan E. , Author
1000 Genomes Project, Consortium, Author
Timmermann, Bernd1, 2, Author              
Devine, Scott E. , Author
Affiliations:
1Sequencing (Head: Bernd Timmermann), Scientific Service (Head: Christoph Krukenkamp), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479670              
21000 Genomes Project Consortium, ou_persistent22              

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 Abstract: Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale. Using both Illumina WGS data and simulations, we demonstrate that MELT outperforms existing MEI discovery tools in terms of speed, scalability, specificity, and sensitivity, while also detecting a broader spectrum of MEI-associated features. Several run modes were developed to perform MEI discovery on local and cloud systems. In addition to using MELT to discover MEIs in modern humans as part of the 1000 Genomes Project, we also used it to discover MEIs in chimpanzees and ancient (Neanderthal and Denisovan) hominids. We detected diverse patterns of MEI stratification across these populations that likely were caused by (1) diverse rates of MEI production from source elements, (2) diverse patterns of MEI inheritance, and (3) the introgression of ancient MEIs into modern human genomes. Overall, our study provides the most comprehensive map of MEIs to date spanning chimpanzees, ancient hominids, and modern humans and reveals new aspects of MEI biology in these lineages. We also demonstrate that MELT is a robust platform for MEI discovery and analysis in a variety of experimental settings.

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Language(s): eng - English
 Dates: 2017-08-302017-11
 Publication Status: Published in print
 Pages: 14
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1101/gr.218032.116
PMC: PMC5668948
 Degree: -

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Title: Genome Research
Source Genre: Journal
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Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 27 (11) Sequence Number: - Start / End Page: 1916 - 1929 Identifier: ISSN: 1088-9051
CoNE: /journals/resource/954926997202