The DOI matches its Crossref record; 89 of the 89 references it cites were found in a registry or an index.
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
Open accessAbstract
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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Self-citationFrom telomere to telomere: The transcriptional and epigenetic state of human repeat elements
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The population genetics of structural variants in grapevine domestication
Zhou, Y., Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., & Gaut, B. S. (2019) · Nature Plants · doi:10.1038/s41477-019-0507-8 · Cited by 339
Metadata
- Authors
- Gardner, E. J., Lam, V. K., Harris, D. N., Chuang, N. T., Scott, E. C., Pittard, W. S., Mills, R. E., The 1000 Genomes Project Consortium, & Devine, S. E.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2017-08-30
- Volume
- 27
- Issue
- 11
- Pages
- 1916-1929
- ISSN
- 1088-9051 (ISSN-L)
- 1549-5469
- OpenAlex
- W2750782486
- Cited by
- 367
- References
- 89
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Gardner, E. J., Lam, V. K., Harris, D. N., Chuang, N. T., Scott, E. C., Pittard, W. S., Mills, R. E., The 1000 Genomes Project Consortium, & Devine, S. E. (2017). The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Research. https://doi.org/10.1101/gr.218032.116
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