The DOI matches its Crossref record; 37 of the 37 references it cites were found in a registry or an index.
RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping
Open accessAbstract
Massively parallel sequencing has revolutionized many areas of biology, but sequencing large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many studies. Genomic complexity reduction techniques such as sequence capture and restriction enzyme-based methods enable the analysis of many more individuals per unit cost. Despite their utility, current complexity reduction methods have limitations, especially when large numbers of individuals are analyzed. Here we develop a much improved restriction site-associated DNA (RAD) sequencing protocol and a new method called Rapture (RAD capture). The new RAD protocol improves versatility by separating RAD tag isolation and sequencing library preparation into two distinct steps. This protocol also recovers more unique (nonclonal) RAD fragments, which improves both standard RAD and Rapture analysis. Rapture then uses an in-solution capture of chosen RAD tags to target sequencing reads to desired loci. Rapture combines the benefits of both RAD and sequence capture, i.e., very inexpensive and rapid library preparation for many individuals as well as high specificity in the number and location of genomic loci analyzed. Our results demonstrate that Rapture is a rapid and flexible technology capable of analyzing a very large number of individuals with minimal sequencing and library preparation cost. The methods presented here should improve the efficiency of genetic analysis for many aspects of agricultural, environmental, and biomedical science.
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Cites
The Sequence Alignment/Map format and SAMtools
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A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0019379 · Cited by 6,501
Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,486
Next-generation DNA sequencing
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509
Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
Baird, N. A., Etter, P. D., Atwood, T. S., Currey, M. C., Shiver, A. L., Lewis, Z. A., Selker, E. U., Cresko, W. A., & Johnson, E. A. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003376 · Cited by 3,356
ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982
Genome-wide genetic marker discovery and genotyping using next-generation sequencing
Davey, J. W., Hohenlohe, P. A., Etter, P. D., Boone, J. Q., Catchen, J. M., & Blaxter, M. L. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3012 · Cited by 2,481
Prescribing Personalized Nutrition for Cardiovascular Health: Are We Ready?
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How genomics can help biodiversity conservation
Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., Godoy, J. A., et al. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.01.005 · Cited by 401
Heritability of interpack aggression in a wild pedigreed population of North American grey wolves
vonHoldt, B. M., DeCandia, A. L., Heppenheimer, E., Janowitz‐Koch, I., Shi, R., Zhou, H., German, C. A., Brzeski, K. E., Cassidy, K. A., Stahler, D. R., et al. (2020) · Molecular Ecology · doi:10.1111/mec.15349 · Cited by 22
Mowry, C. B., Wilson, L. A., & vonHoldt, B. M. (2021) · Diversity · doi:10.3390/d13080372 · Cited by 5
Metadata
- Authors
- Ali, O. A., O’Rourke, S. M., Amish, S. J., Meek, M. H., Luikart, G., Jeffres, C., & Miller, M. R.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-12-29
- Volume
- 202
- Issue
- 2
- Pages
- 389-400
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2952033584
- Cited by
- 482
- References
- 37
- FWCI
- 10.68
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Ali, O. A., O’Rourke, S. M., Amish, S. J., Meek, M. H., Luikart, G., Jeffres, C., & Miller, M. R. (2016). RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping. Genetics. https://doi.org/10.1534/genetics.115.183665
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