1
|
Allayee H, Farber CR, Seldin MM, Williams EG, James DE, Lusis AJ. Systems genetics approaches for understanding complex traits with relevance for human disease. eLife 2023; 12:e91004. [PMID: 37962168 PMCID: PMC10645424 DOI: 10.7554/elife.91004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative traits are often complex because of the contribution of many loci, with further complexity added by environmental factors. In medical research, systems genetics is a powerful approach for the study of complex traits, as it integrates intermediate phenotypes, such as RNA, protein, and metabolite levels, to understand molecular and physiological phenotypes linking discrete DNA sequence variation to complex clinical and physiological traits. The primary purpose of this review is to describe some of the resources and tools of systems genetics in humans and rodent models, so that researchers in many areas of biology and medicine can make use of the data.
Collapse
Affiliation(s)
- Hooman Allayee
- Departments of Population & Public Health Sciences, University of Southern CaliforniaLos AngelesUnited States
- Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Charles R Farber
- Center for Public Health Genomics, University of Virginia School of MedicineCharlottesvilleUnited States
- Departments of Biochemistry & Molecular Genetics, University of Virginia School of MedicineCharlottesvilleUnited States
- Public Health Sciences, University of Virginia School of MedicineCharlottesvilleUnited States
| | - Marcus M Seldin
- Department of Biological Chemistry, University of California, IrvineIrvineUnited States
| | - Evan Graehl Williams
- Luxembourg Centre for Systems Biomedicine, University of LuxembourgLuxembourgLuxembourg
| | - David E James
- School of Life and Environmental Sciences, University of SydneyCamperdownAustralia
- Faculty of Medicine and Health, University of SydneyCamperdownAustralia
- Charles Perkins Centre, University of SydneyCamperdownAustralia
| | - Aldons J Lusis
- Departments of Human Genetics, University of California, Los AngelesLos AngelesUnited States
- Medicine, University of California, Los AngelesLos AngelesUnited States
- Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLALos AngelesUnited States
| |
Collapse
|
2
|
Lusk R, Hoffman PL, Mahaffey S, Rosean S, Smith H, Silhavy J, Pravenec M, Tabakoff B, Saba LM. Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel. Front Genet 2022; 13:821026. [PMID: 35368676 PMCID: PMC8965255 DOI: 10.3389/fgene.2022.821026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/10/2022] [Indexed: 12/02/2022] Open
Abstract
Post transcriptional modifications of RNA are powerful mechanisms by which eukaryotes expand their genetic diversity. For instance, researchers estimate that most transcripts in humans undergo alternative splicing and alternative polyadenylation. These splicing events produce distinct RNA molecules, which in turn yield distinct protein isoforms and/or influence RNA stability, translation, nuclear export, and RNA/protein cellular localization. Due to their pervasiveness and impact, we hypothesized that alternative splicing and alternative polyadenylation in brain can contribute to a predisposition for voluntary alcohol consumption. Using the HXB/BXH recombinant inbred rat panel (a subset of the Hybrid Rat Diversity Panel), we generated over one terabyte of brain RNA sequencing data (total RNA) and identified novel splice variants (via StringTie) and alternative polyadenylation sites (via aptardi) to determine the transcriptional landscape in the brains of these animals. After establishing an analysis pipeline to ascertain high quality transcripts, we quantitated transcripts and integrated genotype data to identify candidate transcript coexpression networks and individual candidate transcripts associated with predisposition to voluntary alcohol consumption in the two-bottle choice paradigm. For genes that were previously associated with this trait (e.g., Lrap, Ift81, and P2rx4) (Saba et al., Febs. J., 282, 3556–3578, Saba et al., Genes. Brain. Behav., 20, e12698), we were able to distinguish between transcript variants to provide further information about the specific isoforms related to the trait. We also identified additional candidate transcripts associated with the trait of voluntary alcohol consumption (i.e., isoforms of Mapkapk5, Aldh1a7, and Map3k7). Consistent with our previous work, our results indicate that transcripts and networks related to inflammation and the immune system in brain can be linked to voluntary alcohol consumption. Overall, we have established a pipeline for including the quantitation of alternative splicing and alternative polyadenylation variants in the transcriptome in the analysis of the relationship between the transcriptome and complex traits.
Collapse
Affiliation(s)
- Ryan Lusk
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Paula L. Hoffman
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Samuel Rosean
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Harry Smith
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jan Silhavy
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czechia
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laura M. Saba
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- *Correspondence: Laura M. Saba,
| |
Collapse
|
3
|
Sharp BM, Fan X, Redei EE, Mulligan MK, Chen H. Sex and heredity are determinants of drug intake in a novel model of rat oral oxycodone self-administration. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12770. [PMID: 34459088 PMCID: PMC8815756 DOI: 10.1111/gbb.12770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 11/26/2022]
Abstract
The steady rise in prescription opioids such as oxycodone has led to a virulent epidemic of widespread abuse and deaths in the United States; approximately 80% of affected individuals initiate the habitual use of oxycodone by using prescription oral oxycodone. Given the importance of drug pharmacokinetics in determining abuse potential, we designed an oral operant oxycodone self-administration (SA) procedure in rats to model drug intake by most human users/abusers of oxycodone. Key aspects of the model include limited initial drug intake followed by increasing drug concentrations during extended 4-h sessions on alternating days. Sex and genetic predisposition are major determinants of human opiate abuse. Therefore, we studied females in seven inbred strains (WLI, WMI, LEW, DSS, F344, BN and SHR) and both sexes in three of these strains. All strains increased intake across serially increasing doses (0.025-0.2 mg/ml; p < 0.001): the range of intakes at the final concentration of oxycodone was 0.72 ± 0.17-4.84 ± 1.42 mg/kg (mean ± SEM) - a 6.7-fold difference across strains. In LEW, WLI and WMI strains, oxycodone intake increased significantly across all sessions in both sexes. However, in LEW and WMI male rats but not WLI, daily oxycodone intake was significantly lower across all 4-h sessions than females (p < 0.005). The estimated heritability in oxycodone intake was in the range of 0.21-0.41. In summary, our novel operant oral oxycodone SA model captures the strong abuse potential of oral oxycodone and shows dose, sex and strain-specific drug intake that is significantly dependent on heredity.
Collapse
Affiliation(s)
- Burt M Sharp
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Xinyu Fan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Eva E Redei
- Department of Psychiatry and Behavioral Sciences, and Physiology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Megan K Mulligan
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Mandt BH, Larson C, Fay T, Bludeau P, Allen RM, Deitrich RA, Radcliffe RA. Quantitative trait loci for sensitivity to acute ethanol and ethanol consummatory behaviors in rats. Alcohol 2018; 66:55-67. [PMID: 29182922 DOI: 10.1016/j.alcohol.2017.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 08/04/2017] [Accepted: 08/05/2017] [Indexed: 12/13/2022]
Abstract
Individuals with a low initial response to alcohol (i.e., ethanol) are at greater risk of developing alcohol abuse or dependence later in life. Similar to humans, individual differences in ethanol sensitivity also can be seen in rats, and several laboratories have used these individual differences to generate selectively bred rats that differ in acute ethanol sensitivity. We have worked with two sets of such rats (Inbred High or Low Alcohol Sensitivity strains, IHAS or ILAS, respectively; Inbred Alcohol Tolerant or Non-Tolerant strains, IAT and IANT, respectively) and have confirmed previously mapped quantitative trait loci (QTL) for these acute differences with the use of recombinant congenic lines; however, the relationship between acute sensitivity and ethanol drinking in these rats has yet to be determined. Thus, here we tested the hypothesis that QTLs underlying variation in initial low sensitivity to ethanol also will modulate variation in ethanol drinking behaviors. Separate groups of selectively inbred parent and congenic rats were tested for the loss of righting response (LORR) and also assessed for ethanol consummatory behavior using either operant self-administration or an intermittent-access two-bottle choice procedure. LORR testing confirmed the presence of a LORR duration QTL in all of the congenics; however, the lack of a corresponding difference in blood ethanol concentration at the regaining of the righting response suggests that these QTLs may be mediating a difference in ethanol metabolism rather than in neuronal sensitivity. IHAS/ILAS-derived congenic rats did not differ from parent rats at any point during operant self-administration. IAT/IANT-derived congenic rats showed small, but significant, increases in ethanol consumption relative to the parent strains only during the initial stages of operant self-administration. In contrast to operant testing, IHAS/ILAS-derived congenic rats showed significantly greater ethanol consumption and preference than parent rats during intermittent-access testing. There were not differences, however, between IAT/IANT congenic and parent rats during intermittent access. These data support the hypothesis that there is a genetic relationship between initial ethanol sensitivity and ethanol consumption, at least for the IHAS/ILAS-derived congenic rats. Our current studies, however, cannot eliminate pharmacokinetic or taste preference factors as contributing to the rats' responses, nor can we eliminate the possibility of a linkage effect because of the fairly large size of the QTL intervals; i.e., distinct genes may be mediating the acute sensitivity and drinking responses.
Collapse
Affiliation(s)
- Bruce H Mandt
- Department of Psychology, University of Colorado Denver, Denver, CO 80217, USA
| | - Colin Larson
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tina Fay
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Pequita Bludeau
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Richard M Allen
- Department of Psychology, University of Colorado Denver, Denver, CO 80217, USA
| | - Richard A Deitrich
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Richard A Radcliffe
- Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| |
Collapse
|
6
|
Saba L, Hoffman P, Tabakoff B. Using Baseline Transcriptional Connectomes in Rat to Identify Genetic Pathways Associated with Predisposition to Complex Traits. Methods Mol Biol 2018; 1488:299-317. [PMID: 27933531 DOI: 10.1007/978-1-4939-6427-7_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although rat is a critical model organism in preclinical medications development, its use in systems genetics studies remains sparse. The PhenoGen database and website contain detailed information on the qualitative and quantitative aspects of the rat brain, liver, heart, and brown adipose transcriptome. This database has been generated using the HXB/BXH recombinant inbred panel and is being expanded to a hybrid rat diversity panel that includes many common inbred strains as well. By using such a panel, the PhenoGen project has created a renewable and cumulative resource for the rat genomics community. The database has been used to reconstruct the brain transcriptome identifying both annotated and unannotated transcribed elements that range in size from 20 nucleotides to over 30,000 nucleotides and elements that have a wide variety of roles in the cell including generation of proteins and regulation of the transcription and translation processes. In all 4 tissues, baseline transcriptional connectomes have been generated to model the relationships among transcripts. These connectomes can be used to identify genetic pathways associated with complex traits and to gain insight into biological function of individual transcripts. The PhenoGen website contains tools that allow the user to explore qualitative features of individual genes and to see how the gene relates to other genes within a tissue. The PhenoGen database and website continue to grow and to make use of the latest statistical methods for systems genetics creating a national resource for the rat genomics community.
Collapse
Affiliation(s)
- Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Aurora, CO, 80045, USA.
| | - Paula Hoffman
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 E. Montview Blvd., Aurora, CO, 80045, USA
| |
Collapse
|
7
|
Harrill AH, McAllister KA. New Rodent Population Models May Inform Human Health Risk Assessment and Identification of Genetic Susceptibility to Environmental Exposures. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:086002. [PMID: 28886592 PMCID: PMC5783628 DOI: 10.1289/ehp1274] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND This paper provides an introduction for environmental health scientists to emerging population-based rodent resources. Mouse reference populations provide an opportunity to model environmental exposures and gene-environment interactions in human disease and to inform human health risk assessment. OBJECTIVES This review will describe several mouse populations for toxicity assessment, including older models such as the Mouse Diversity Panel (MDP), and newer models that include the Collaborative Cross (CC) and Diversity Outbred (DO) models. METHODS This review will outline the features of the MDP, CC, and DO mouse models and will discuss published case studies investigating the use of these mouse population resources in each step of the risk assessment paradigm. DISCUSSION These unique resources have the potential to be powerful tools for generating hypotheses related to gene-environment interplay in human disease, performing controlled exposure studies to understand the differential responses in humans for susceptibility or resistance to environmental exposures, and identifying gene variants that influence sensitivity to toxicity and disease states. CONCLUSIONS These new resources offer substantial advances to classical toxicity testing paradigms by including genetically sensitive individuals that may inform toxicity risks for sensitive subpopulations. Both in vivo and complementary in vitro resources provide platforms with which to reduce uncertainty by providing population-level data around biological variability. https://doi.org/10.1289/EHP1274.
Collapse
Affiliation(s)
- Alison H Harrill
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , Research Triangle Park, North Carolina, USA
| | - Kimberly A McAllister
- Genes, Environment, and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services , Research Triangle Park, North Carolina, USA
| |
Collapse
|
8
|
Abstract
Identifying genes and pathways that contribute to differences in neurobehavioural traits is a key goal in psychiatric research. Despite considerable success in identifying quantitative trait loci (QTLs) associated with behaviour in laboratory rodents, pinpointing the causal variants and genes is more challenging. For a long time, the main obstacle was the size of QTLs, which could encompass tens if not hundreds of genes. However, recent studies have exploited mouse and rat resources that allow mapping of phenotypes to narrow intervals, encompassing only a few genes. Here, we review these studies, showcase the rodent resources they have used and highlight the insights into neurobehavioural traits provided to date. We discuss what we see as the biggest challenge in the field - translating QTLs into biological knowledge by experimentally validating and functionally characterizing candidate genes - and propose that the CRISPR/Cas genome-editing system holds the key to overcoming this obstacle. Finally, we challenge traditional views on inbred versus outbred resources in the light of recent resource and technology developments.
Collapse
Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095-1761, USA
| |
Collapse
|
9
|
Uncovering the liver's role in immunity through RNA co-expression networks. Mamm Genome 2016; 27:469-84. [PMID: 27401171 PMCID: PMC5002042 DOI: 10.1007/s00335-016-9656-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/27/2016] [Indexed: 01/16/2023]
Abstract
Gene co-expression analysis has proven to be a powerful tool for ascertaining the organization of gene products into networks that are important for organ function. An organ, such as the liver, engages in a multitude of functions important for the survival of humans, rats, and other animals; these liver functions include energy metabolism, metabolism of xenobiotics, immune system function, and hormonal homeostasis. With the availability of organ-specific transcriptomes, we can now examine the role of RNA transcripts (both protein-coding and non-coding) in these functions. A systems genetic approach for identifying and characterizing liver gene networks within a recombinant inbred panel of rats was used to identify genetically regulated transcriptional networks (modules). For these modules, biological consensus was found between functional enrichment analysis and publicly available phenotypic quantitative trait loci (QTL). In particular, the biological function of two liver modules could be linked to immune response. The eigengene QTLs for these co-expression modules were located at genomic regions coincident with highly significant phenotypic QTLs; these phenotypes were related to rheumatoid arthritis, food preference, and basal corticosterone levels in rats. Our analysis illustrates that genetically and biologically driven RNA-based networks, such as the ones identified as part of this research, provide insight into the genetic influences on organ functions. These networks can pinpoint phenotypes that manifest through the interaction of many organs/tissues and can identify unannotated or under-annotated RNA transcripts that play a role in these phenotypes.
Collapse
|
10
|
Saba LM, Flink SC, Vanderlinden LA, Israel Y, Tampier L, Colombo G, Kiianmaa K, Bell RL, Printz MP, Flodman P, Koob G, Richardson HN, Lombardo J, Hoffman PL, Tabakoff B. The sequenced rat brain transcriptome--its use in identifying networks predisposing alcohol consumption. FEBS J 2015; 282:3556-78. [PMID: 26183165 DOI: 10.1111/febs.13358] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/10/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023]
Abstract
UNLABELLED A quantitative genetic approach, which involves correlation of transcriptional networks with the phenotype in a recombinant inbred (RI) population and in selectively bred lines of rats, and determination of coinciding quantitative trait loci for gene expression and the trait of interest, has been applied in the present study. In this analysis, a novel approach was used that combined DNA-Seq data, data from brain exon array analysis of HXB/BXH RI rat strains and six pairs of rat lines selectively bred for high and low alcohol preference, and RNA-Seq data (including rat brain transcriptome reconstruction) to quantify transcript expression levels, generate co-expression modules and identify biological functions that contribute to the predisposition of consuming varying amounts of alcohol. A gene co-expression module was identified in the RI rat strains that contained both annotated and unannotated transcripts expressed in the brain, and was associated with alcohol consumption in the RI panel. This module was found to be enriched with differentially expressed genes from the selected lines of rats. The candidate genes within the module and differentially expressed genes between high and low drinking selected lines were associated with glia (microglia and astrocytes) and could be categorized as being related to immune function, energy metabolism and calcium homeostasis, as well as glial-neuronal communication. The results of the present study show that there are multiple combinations of genetic factors that can produce the same phenotypic outcome. Although no single gene accounts for predisposition to a particular level of alcohol consumption in every animal model, coordinated differential expression of subsets of genes in the identified pathways produce similar phenotypic outcomes. DATABASE The datasets supporting the results of the present study are available at http://phenogen.ucdenver.edu.
Collapse
Affiliation(s)
- Laura M Saba
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Stephen C Flink
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Lauren A Vanderlinden
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA
| | - Yedy Israel
- Laboratory of Pharmacogenetics of Alcoholism, Molecular & Clinical Pharmacology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Lutske Tampier
- Laboratory of Pharmacogenetics of Alcoholism, Molecular & Clinical Pharmacology Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Giancarlo Colombo
- Neuroscience Institute, National Research Council of Italy, Section of Cagliari, Monserrato, Italy
| | - Kalervo Kiianmaa
- Department of Alcohol, Drugs and Addiction, National Institute for Health and Welfare, Helsinki, Finland
| | - Richard L Bell
- Department of Psychiatry, Institute of Psychiatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Morton P Printz
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Pamela Flodman
- Department of Pediatrics, University of California, Irvine, Irvine, CA, USA
| | - George Koob
- Committee on the Neurobiology of Addiction Disorders, The Scripps Research Institute, La Jolla, CA, USA
| | - Heather N Richardson
- Committee on the Neurobiology of Addiction Disorders, The Scripps Research Institute, La Jolla, CA, USA
| | - Joseph Lombardo
- National Supercomputing Center for Energy and Environment, University of Nevada, Las Vegas, Nevada, USA
| | - Paula L Hoffman
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Denver, Aurora, CO, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, CO, USA.,Department of Pharmacology, University of Colorado Denver, Aurora, CO, USA
| |
Collapse
|
11
|
Genomic landscape of rat strain and substrain variation. BMC Genomics 2015; 16:357. [PMID: 25943489 PMCID: PMC4422378 DOI: 10.1186/s12864-015-1594-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 04/28/2015] [Indexed: 01/08/2023] Open
Abstract
Background Since the completion of the rat reference genome in 2003, whole-genome sequencing data from more than 40 rat strains have become available. These data represent the broad range of strains that are used in rat research including commonly used substrains. Currently, this wealth of information cannot be used to its full extent, because the variety of different variant calling algorithms employed by different groups impairs comparison between strains. In addition, all rat whole genome sequencing studies to date used an outdated reference genome for analysis (RGSC3.4 released in 2004). Results Here we present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains. We reanalyzed all primary data using a recent version of the rat reference assembly (RGSC5.0 released in 2012) and identified over 12 million genomic variants (SNVs, indels and structural variants) among the 40 strains. 28,318 SNVs are specific to individual substrains, which may be explained by introgression from other unsequenced strains and ongoing evolution by genetic drift. Substrain SNVs may have a larger predicted functional impact compared to older shared SNVs. Conclusions In summary we present a comprehensive catalog of uniformly analyzed genetic variants among 40 widely used rat inbred strains based on the RGSC5.0 assembly. This represents a valuable resource, which will facilitate rat functional genomic research. In line with previous observations, our genome-wide analyses do not show evidence for contribution of multiple ancestral founder rat subspecies to the currently used rat inbred strains, as is the case for mouse. In addition, we find that the degree of substrain variation is highly variable between strains, which is of importance for the correct interpretation of experimental data from different labs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1594-1) contains supplementary material, which is available to authorized users.
Collapse
|