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Networking in Biology: The Hybrid Rat Diversity Panel

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Rat Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2018))

Abstract

One of the most fruitful resources for systems genetic studies of nonhuman mammals is a panel of inbred strains that exhibits significant genetic diversity between strains but genetic stability (isogenicity) within strains. These characteristics allow for fine mapping of complex phenotypes (QTLs) and provide statistical power to identify loci which contribute nominally to the phenotype. This type of resource also allows the planning and performance of investigations using the same genetic backgrounds over several generations of the test animals. Often, rats are preferred over mice for physiologic and behavioral studies because of their larger size and more distinguishable anatomy (particularly for their central nervous system). The Hybrid Rat Diversity Panel (HRDP) is a panel of inbred rat strains, which combines two recombinant inbred panels (the HXB/BXH, 30 strains; the LEXF/FXLE, 34 strains and 35 more strains of inbred rats which were selected for genetic diversity, based on their fully sequenced genomes and/or thorough genotyping). The genetic diversity and statistical power of this panel for mapping studies rivals or surpasses currently available panels in mouse. The genetic stability of this panel makes it particularly suitable for collection of high-throughput omics data as relevant technology becomes available for engaging in truly integrative systems biology. The PhenoGen website (http://phenogen.org) is the repository for the initial transcriptome data, making the raw data, the processed data, and the analysis results, e.g., organ-specific protein coding and noncoding transcripts, isoform analysis, expression quantitative trait loci, and co-expression networks, available to the research public. The data sets and tools being developed will complement current efforts to analyze the human transcriptome and its genetic controls (the Genotype-Tissue Expression Project (GTEx)) and allow for dissection of genetic networks that predispose to particular phenotypes and gene-by-environment interactions that are difficult or even impossible to study in humans. The HRDP is an essential population for exploring truly integrative systems genetics.

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Acknowledgments

This work is supported by NIH/NIAAA (R24 AA013162), NIH/NIDA (P30 DA044223), and the Banbury Fund.

Author information

Authors and Affiliations

  1. Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, USA

    Boris Tabakoff, Paula L. Hoffman & Laura M. Saba

  2. Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA

    Harry Smith & Lauren A. Vanderlinden

  3. Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA

    Paula L. Hoffman

Authors
  1. Boris Tabakoff
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  2. Harry Smith
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  3. Lauren A. Vanderlinden
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  4. Paula L. Hoffman
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  5. Laura M. Saba
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Corresponding author

Correspondence to Laura M. Saba .

Editor information

Editors and Affiliations

  1. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    G. Thomas Hayman

  2. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    Jennifer R. Smith

  3. Department of Physiology, Rat Genome Database, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA

    Melinda R. Dwinell

  4. Department of Biomedical Engineering, Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA

    Mary Shimoyama

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Tabakoff, B., Smith, H., Vanderlinden, L.A., Hoffman, P.L., Saba, L.M. (2019). Networking in Biology: The Hybrid Rat Diversity Panel. In: Hayman, G., Smith, J., Dwinell, M., Shimoyama, M. (eds) Rat Genomics. Methods in Molecular Biology, vol 2018. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9581-3_10

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  • DOI: https://doi.org/10.1007/978-1-4939-9581-3_10

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9580-6

  • Online ISBN: 978-1-4939-9581-3

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