| SNP discovery and genotyping for evolutionary genetics using RAD sequencing. | |
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MedLine Citation:
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PMID: 22065437 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Next-generation sequencing technologies are revolutionizing the field of evolutionary biology, opening the possibility for genetic analysis at scales not previously possible. Research in population genetics, quantitative trait mapping, comparative genomics, and phylogeography that was unthinkable even a few years ago is now possible. More importantly, these next-generation sequencing studies can be performed in organisms for which few genomic resources presently exist. To speed this revolution in evolutionary genetics, we have developed Restriction site Associated DNA (RAD) genotyping, a method that uses Illumina next-generation sequencing to simultaneously discover and score tens to hundreds of thousands of single-nucleotide polymorphism (SNP) markers in hundreds of individuals for minimal investment of resources. In this chapter, we describe the core RAD-seq protocol, which can be modified to suit a diversity of evolutionary genetic questions. In addition, we discuss bioinformatic considerations that arise from unique aspects of next-generation sequencing data as compared to traditional marker-based approaches, and we outline some general analytical approaches for RAD-seq and similar data. Despite considerable progress, the development of analytical tools remains in its infancy, and further work is needed to fully quantify sampling variance and biases in these data types. |
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Authors:
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Paul D Etter; Susan Bassham; Paul A Hohenlohe; Eric A Johnson; William A Cresko |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S. |
Journal Detail:
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Title: Methods in molecular biology (Clifton, N.J.) Volume: 772 ISSN: 1940-6029 ISO Abbreviation: Methods Mol. Biol. Publication Date: 2011 |
Date Detail:
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Created Date: 2011-11-08 Completed Date: 2012-02-22 Revised Date: 2012-06-29 |
Medline Journal Info:
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Nlm Unique ID: 9214969 Medline TA: Methods Mol Biol Country: United States |
Other Details:
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Languages: eng Pagination: 157-78 Citation Subset: IM |
Affiliation:
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Institute of Molecular Biology, University of Oregon, Eugene, OR, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Base Sequence DNA / isolation & purification DNA Restriction Enzymes / metabolism Electrophoresis, Agar Gel Evolution, Molecular* Gene Library Genetics, Population Genome / genetics Genotyping Techniques / methods* Humans Molecular Sequence Data Polymerase Chain Reaction Polymorphism, Single Nucleotide / genetics* Restriction Mapping / methods* Ribonucleases / metabolism Sequence Alignment Sequence Analysis, DNA / methods* |
| Grant Support | |
ID/Acronym/Agency:
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1R24GM079486-01A1/GM/NIGMS NIH HHS; F32 GM078949/GM/NIGMS NIH HHS; R24 GM079486/GM/NIGMS NIH HHS; R24 OD011199/OD/NIH HHS; R24 RR032670/RR/NCRR NIH HHS |
| Chemical | |
Reg. No./Substance:
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9007-49-2/DNA; EC 3.1.-/Ribonucleases; EC 3.1.21.-/DNA Restriction Enzymes |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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