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Glenn RA, Do SC, Guruvayurappan K, Corrigan EK, Santini L, Medina-Cano D, Singer S, Cho H, Liu J, Broman K, Czechanski A, Reinholdt L, Koche R, Furuta Y, Kunz M, Vierbuchen T. A PLURIPOTENT STEM CELL PLATFORM FOR IN VITRO SYSTEMS GENETICS STUDIES OF MOUSE DEVELOPMENT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597758. [PMID: 38895226 PMCID: PMC11185710 DOI: 10.1101/2024.06.06.597758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The directed differentiation of pluripotent stem cells (PSCs) from panels of genetically diverse individuals is emerging as a powerful experimental system for characterizing the impact of natural genetic variation on developing cell types and tissues. Here, we establish new PSC lines and experimental approaches for modeling embryonic development in a genetically diverse, outbred mouse stock (Diversity Outbred mice). We show that a range of inbred and outbred PSC lines can be stably maintained in the primed pluripotent state (epiblast stem cells -- EpiSCs) and establish the contribution of genetic variation to phenotypic differences in gene regulation and directed differentiation. Using pooled in vitro fertilization, we generate and characterize a genetic reference panel of Diversity Outbred PSCs (n = 230). Finally, we demonstrate the feasibility of pooled culture of Diversity Outbred EpiSCs as "cell villages", which can facilitate the differentiation of large numbers of EpiSC lines for forward genetic screens. These data can complement and inform similar efforts within the stem cell biology and human genetics communities to model the impact of natural genetic variation on phenotypic variation and disease-risk.
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Affiliation(s)
- Rachel A. Glenn
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Cell and Developmental Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Stephanie C. Do
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Emily K. Corrigan
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Present address: Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA and Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Laura Santini
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Medina-Cano
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah Singer
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyein Cho
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jing Liu
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karl Broman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI USA
| | | | | | - Richard Koche
- Center for Epigenetics Research, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasuhide Furuta
- Mouse Genetics Core Facility, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meik Kunz
- The Bioinformatics CRO, Sanford Florida, 32771 USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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2
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Larson DR, Kimber AJ, Meyer KJ, Anderson MG. Anterior chamber depth in mice is controlled by several quantitative trait loci. PLoS One 2023; 18:e0286897. [PMID: 37624784 PMCID: PMC10456175 DOI: 10.1371/journal.pone.0286897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Anterior chamber depth (ACD) is a quantitative trait associated with primary angle closure glaucoma (PACG). Although ACD is highly heritable, known genetic variations explain a small fraction of the phenotypic variability. The purpose of this study was to identify additional ACD-influencing loci using strains of mice. Cohorts of 86 N2 and 111 F2 mice were generated from crosses between recombinant inbred BXD24/TyJ and wild-derived CAST/EiJ mice. Using anterior chamber optical coherence tomography, mice were phenotyped at 10-12 weeks of age, genotyped based on 93 genome-wide SNPs, and subjected to quantitative trait locus (QTL) analysis. In an analysis of ACD among all mice, six loci passed the significance threshold of p = 0.05 and persisted after multiple regression analysis. These were on chromosomes 6, 7, 11, 12, 15 and 17 (named Acdq6, Acdq7, Acdq11, Acdq12, Acdq15, and Acdq17, respectively). Our findings demonstrate a quantitative multi-genic pattern of ACD inheritance in mice and identify six previously unrecognized ACD-influencing loci. We have taken a unique approach to studying the anterior chamber depth phenotype by using mice as genetic tool to examine this continuously distributed trait.
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Affiliation(s)
- Demelza R. Larson
- Department of Biology, College of Saint Benedict & Saint John’s University, Collegeville, Minnesota, United States of America
| | - Allysa J. Kimber
- Department of Biology, College of Saint Benedict & Saint John’s University, Collegeville, Minnesota, United States of America
| | - Kacie J. Meyer
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa, United States of America
| | - Michael G. Anderson
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, Iowa, United States of America
- Department of Ophthalmology and Visual Sciences, The University of Iowa, Iowa City, Iowa, United States of America
- Center for the Prevention and Treatment of Visual Loss, Iowa City VA Health Care System, Iowa City, Iowa, United States of America
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Seroussi E, Blum SE, Krifucks O, Shirak A, Jacoby S, Leitner G. Basal Levels of CD18 Antigen Presenting Cells in Cow Milk Associate with Copy Number Variation of Fc Gamma Receptors. Genes (Basel) 2020; 11:E952. [PMID: 32824852 PMCID: PMC7464846 DOI: 10.3390/genes11080952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
Differentiation of cells by flow cytometry provides informative somatic cell counts (SCCs) that allow analyzing leukocyte population patterns in udder infections of different etiologies. Postulating that this approach also enhances the statistical power to detect genetic variants linked to cell levels in milk of healthy mammary glands, we used monoclonal antibodies anti-CD18, anti-CD4, anti--CD14, and anti-PMN to count cells presenting these surface antigens, and performed a genome-wide association study of these counts in 125 Israeli Holsteins genotyped using SNP BeadChips. We identified an informative haplotype of 15 SNPs in the centromeric end of BTA3 that was strongly associated with CD18 cells (p < 2.3 × 10-9). Within this region, examination of the network of genes interacting with ITGB2 (CD18) indicated an Fc-γ-receptor gene cluster, including FCGR2A (CD32). Sanger-sequence analysis of FCGR2s-linked exon 3 variation to CD18 counts. Meta-analysis of RNA-Seq data revealed a significant negative correlation (R = -0.51) between expression of CD32 and CD18 in milk. Assembly of DNA-Seq reads uncovered FCGR copy-number variation and a variant, designated V7, was abundant in dairy cattle, probably reflecting adaptation to selection pressure for low SCC in Holstein milk.
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Affiliation(s)
- Eyal Seroussi
- Institute of Animal Science, ARO, Volcani Center, HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, Israel; (A.S.); (S.J.)
| | - Shlomo E. Blum
- National Mastitis Reference Center, Kimron Veterinary Institute, P.O. Box 12, Bet Dagan 50250, Israel; (S.E.B.); (O.K.); (G.L.)
| | - Oleg Krifucks
- National Mastitis Reference Center, Kimron Veterinary Institute, P.O. Box 12, Bet Dagan 50250, Israel; (S.E.B.); (O.K.); (G.L.)
| | - Andrey Shirak
- Institute of Animal Science, ARO, Volcani Center, HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, Israel; (A.S.); (S.J.)
| | - Shamay Jacoby
- Institute of Animal Science, ARO, Volcani Center, HaMaccabim Road, P.O. Box 15159, Rishon LeTsiyon 7528809, Israel; (A.S.); (S.J.)
| | - Gabriel Leitner
- National Mastitis Reference Center, Kimron Veterinary Institute, P.O. Box 12, Bet Dagan 50250, Israel; (S.E.B.); (O.K.); (G.L.)
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Facilitating Complex Trait Analysis via Reduced Complexity Crosses. Trends Genet 2020; 36:549-562. [PMID: 32482413 DOI: 10.1016/j.tig.2020.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 01/02/2023]
Abstract
Genetically diverse inbred strains are frequently used in quantitative trait mapping to identify sequence variants underlying trait variation. Poor locus resolution and high genetic complexity impede variant discovery. As a solution, we explore reduced complexity crosses (RCCs) between phenotypically divergent, yet genetically similar, rodent substrains. RCCs accelerate functional variant discovery via decreasing the number of segregating variants by orders of magnitude. The simplified genetic architecture of RCCs often permit immediate identification of causal variants or rapid fine-mapping of broad loci to smaller intervals. Whole-genome sequences of substrains make RCCs possible by supporting the development of array- and targeted sequencing-based genotyping platforms, coupled with rapid genome editing for variant validation. In summary, RCCs enhance discovery-based genetics of complex traits.
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Edmondson EF, Gatti DM, Ray FA, Garcia EL, Fallgren CM, Kamstock DA, Weil MM. Genomic mapping in outbred mice reveals overlap in genetic susceptibility for HZE ion- and γ-ray-induced tumors. SCIENCE ADVANCES 2020; 6:eaax5940. [PMID: 32494593 PMCID: PMC7159905 DOI: 10.1126/sciadv.aax5940] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 01/14/2020] [Indexed: 05/02/2023]
Abstract
Cancer risk from galactic cosmic radiation exposure is considered a potential "showstopper" for a manned mission to Mars. Calculating the actual risks confronted by spaceflight crews is complicated by our limited understanding of the carcinogenic effects of high-charge, high-energy (HZE) ions, a radiation type for which no human exposure data exist. Using a mouse model of genetic diversity, we find that the histotype spectrum of HZE ion-induced tumors is similar to the spectra of spontaneous and γ-ray-induced tumors and that the genomic loci controlling susceptibilities overlap between groups for some tumor types. Where it occurs, this overlap indicates shared tumorigenesis mechanisms regardless of the type of radiation exposure and supports the use of human epidemiological data from γ-ray exposures to predict cancer risks from galactic cosmic rays.
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Affiliation(s)
- E. F. Edmondson
- Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Colorado State University, Fort Collins, CO 80523, USA
| | - D. M. Gatti
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - F. A. Ray
- Colorado State University, Fort Collins, CO 80523, USA
| | - E. L. Garcia
- Colorado State University, Fort Collins, CO 80523, USA
| | | | | | - M. M. Weil
- Colorado State University, Fort Collins, CO 80523, USA
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6
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Legoff L, D’Cruz SC, Tevosian S, Primig M, Smagulova F. Transgenerational Inheritance of Environmentally Induced Epigenetic Alterations during Mammalian Development. Cells 2019; 8:cells8121559. [PMID: 31816913 PMCID: PMC6953051 DOI: 10.3390/cells8121559] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 12/11/2022] Open
Abstract
Genetic studies traditionally focus on DNA as the molecule that passes information on from parents to their offspring. Changes in the DNA code alter heritable information and can more or less severely affect the progeny's phenotype. While the idea that information can be inherited between generations independently of the DNA's nucleotide sequence is not new, the outcome of recent studies provides a mechanistic foundation for the concept. In this review, we attempt to summarize our current knowledge about the transgenerational inheritance of environmentally induced epigenetic changes. We focus primarily on studies using mice but refer to other species to illustrate salient points. Some studies support the notion that there is a somatic component within the phenomenon of epigenetic inheritance. However, here, we will mostly focus on gamete-based processes and the primary molecular mechanisms that are thought to contribute to epigenetic inheritance: DNA methylation, histone modifications, and non-coding RNAs. Most of the rodent studies published in the literature suggest that transgenerational epigenetic inheritance through gametes can be modulated by environmental factors. Modification and redistribution of chromatin proteins in gametes is one of the major routes for transmitting epigenetic information from parents to the offspring. Our recent studies provide additional specific cues for this concept and help better understand environmental exposure influences fitness and fidelity in the germline. In summary, environmental cues can induce parental alterations and affect the phenotypes of offspring through gametic epigenetic inheritance. Consequently, epigenetic factors and their heritability should be considered during disease risk assessment.
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Affiliation(s)
- Louis Legoff
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
| | - Shereen Cynthia D’Cruz
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
| | - Sergei Tevosian
- University of Florida, Department of Physiological Sciences Box 100144, 1333 Center Drive, Gainesville, FL 32610, USA;
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
| | - Fatima Smagulova
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)—UMR_S 1085, F-35000 Rennes, France; (L.L.); (S.C.D.); (M.P.)
- Correspondence:
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Abstract
In this chapter we will review both the rationale and experimental design for using Heterogeneous Stock (HS) populations for fine-mapping of complex traits in mice and rats. We define an HS as an outbred population derived from an intercross between two or more inbred strains. HS have been used to perform genome-wide association studies (GWAS) for multiple behavioral, physiological, and gene expression traits. GWAS using HS require four key steps, which we review: selection of an appropriate HS population, phenotyping, genotyping, and statistical analysis. We provide advice on the selection of an HS, comment on key issues related to phenotyping, discuss genotyping methods relevant to these populations, and describe statistical genetic analyses that are applicable to genetic analyses that use HS.
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Poltorak A, Apalko S, Sherbak S. Wild-derived mice: from genetic diversity to variation in immune responses. Mamm Genome 2018; 29:577-584. [PMID: 30056578 DOI: 10.1007/s00335-018-9766-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/23/2018] [Indexed: 10/28/2022]
Abstract
Classical inbred mouse strains have historically been instrumental in mapping immunological traits. However, most of the classical strains originate from a relatively limited number of founder animals, largely within the Mus musculus domesticus subspecies. Therefore, their genetic diversity is ultimately limited. For this reason, it is not feasible to use these mice for exhaustive interrogation of immune signaling pathways. In order to investigate networks through forward genetic analysis, larger genetic diversity is required than is introduced under laboratory conditions. Recently, inbred strains from other mouse subspecies were established such as Mus musculus castaneus and Mus musculus musculus, which diverged from a shared common ancestor with Mus musculus domesticus more than one million years ago. A direct genomic comparison clearly demonstrates the evolutionary divergence that has occurred between wild-derived mice and the classical inbred strains. When compared to classical inbred strains, wild-derived mice exhibit polymorphisms every 100-200 base pairs. Studying the molecular basis of these traits provides us with insight into how the immune system can evolve regulatory features to accommodate environment-specific constraints. Because most wild-derived strains are able to breed with classical inbred mice, they represent a rich source of evolutionarily significant diversity for forward genetic studies. These organisms are an emerging, though still largely unexplored, model for the identification and study of novel immunological genes.
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Affiliation(s)
- Alexander Poltorak
- Department of Immunology, Tufts University, Boston, MA, 02111, USA. .,Petrozavodsk State University, Karelia, Russian Federation.
| | | | - Sergei Sherbak
- City Hospital, 40, St. Petersburg, Russian Federation.,St. Petersburg State University, St. Petersburg, Russian Federation
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Abstract
Heterogeneous Stock (HS) populations allow for fine-resolution genetic mapping of a variety of complex traits. HS mice and rats were created from breeding together eight inbred strains, followed by maintaining the colony in a manner that minimizes inbreeding. After 50 or more generations of breeding, the resulting animals' chromosomes represent a genetic mosaic of the founders' haplotypes, with the average distance between recombination events in the centiMorgan range. This allows for genetic mapping to only a few Mb, a much smaller region than what can be identified using traditional F2 intercross or backcross mapping strategies. HS animals have been used to fine-map a variety of complex traits including anxiety and fear behaviors, diabetes, asthma, and heart disease, among others. Once a quantitative trait locus (QTL) has been identified, founder sequence and expression analysis can be used to identify underlying causal genes. In the following review, we provide an overview of how HS rats and mice have been used to identify genetic loci, and in some cases the causal genes, underlying complex traits. We discuss the creation and breeding strategies for both HS rats and mice. We then discuss the statistical analyses used to identify genetic loci, as well as strategies to identify causal genes underlying these loci. We end the chapter by discussing limitations faced when using HS populations, including several statistical challenges that have not been fully resolved.
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Affiliation(s)
- Leah C Solberg Woods
- Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53130, USA.
| | - Richard Mott
- UCL Genetics Institute, University College London, Gower St., London, WC1E 6BT, UK
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The role of genetic background in susceptibility to chemical warfare nerve agents across rodent and non-human primate models. Toxicology 2017; 393:51-61. [PMID: 29113833 DOI: 10.1016/j.tox.2017.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/13/2017] [Accepted: 11/02/2017] [Indexed: 11/22/2022]
Abstract
Genetics likely play a role in various responses to nerve agent exposure, as genetic background plays an important role in behavioral, neurological, and physiological responses to environmental stimuli. Mouse strains or selected lines can be used to identify susceptibility based on background genetic features to nerve agent exposure. Additional genetic techniques can then be used to identify mechanisms underlying resistance and sensitivity, with the ultimate goal of developing more effective and targeted therapies. Here, we discuss the available literature on strain and selected line differences in cholinesterase activity levels and response to nerve agent-induced toxicity and seizures. We also discuss the available cholinesterase and toxicity literature across different non-human primate species. The available data suggest that robust genetic differences exist in cholinesterase activity, nerve agent-induced toxicity, and chemical-induced seizures. Available cholinesterase data suggest that acetylcholinesterase activity differs across strains, but are limited by the paucity of carboxylesterase data in strains and selected lines. Toxicity and seizures, two outcomes of nerve agent exposure, have not been fully evaluated for genetic differences, and thus further studies are required to understand baseline strain and selected line differences.
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11
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Sequence analysis of chromosome 1 revealed different selection patterns between Chinese wild mice and laboratory strains. Mol Genet Genomics 2017. [PMID: 28631230 DOI: 10.1007/s00438-017-1335-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Both natural and artificial selection play a critical role in animals' adaptation to the environment. Detection of the signature of selection in genomic regions can provide insights for understanding the function of specific phenotypes. It is generally assumed that laboratory mice may experience intense artificial selection while wild mice more natural selection. However, the differences of selection signature in the mouse genome and underlying genes between wild and laboratory mice remain unclear. In this study, we used two mouse populations: chromosome 1 (Chr 1) substitution lines (C1SLs) derived from Chinese wild mice and mouse genome project (MGP) sequenced inbred strains and two selection detection statistics: Fst and Tajima's D to identify the signature of selection footprint on Chr 1. For the differentiation between the C1SLs and MGP, 110 candidate selection regions containing 47 protein coding genes were detected. A total of 149 selection regions which encompass 7.215 Mb were identified in the C1SLs by Tajima's D approach. While for the MGP, we identified nearly twice selection regions (243) compared with the C1SLs which accounted for 13.27 Mb Chr 1 sequence. Through functional annotation, we identified several biological processes with significant enrichment including seven genes in the olfactory transduction pathway. In addition, we searched the phenotypes associated with the 47 candidate selection genes identified by Fst. These genes were involved in behavior, growth or body weight, mortality or aging, and immune systems which align well with the phenotypic differences between wild and laboratory mice. Therefore, the findings would be helpful for our understanding of the phenotypic differences between wild and laboratory mice and applications for using this new mouse resource (C1SLs) for further genetics studies.
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12
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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.
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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
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13
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Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E, Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Nat Genet 2016; 48:919-26. [PMID: 27376237 PMCID: PMC4963286 DOI: 10.1038/ng.3609] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/08/2016] [Indexed: 12/15/2022]
Abstract
Although mice are the most widely used mammalian model organism, genetic studies have suffered from limited mapping resolution due to extensive linkage disequilibrium (LD) that is characteristic of crosses among inbred strains. Carworth Farms White (CFW) mice are a commercially available outbred mouse population that exhibit rapid LD decay in comparison to other available mouse populations. We performed a genome-wide association study (GWAS) of behavioral, physiological and gene expression phenotypes using 1,200 male CFW mice. We used genotyping by sequencing (GBS) to obtain genotypes at 92,734 SNPs. We also measured gene expression using RNA sequencing in three brain regions. Our study identified numerous behavioral, physiological and expression quantitative trait loci (QTLs). We integrated the behavioral QTL and eQTL results to implicate specific genes, including Azi2 in sensitivity to methamphetamine and Zmynd11 in anxiety-like behavior. The combination of CFW mice, GBS and RNA sequencing constitutes a powerful approach to GWAS in mice.
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Affiliation(s)
- Clarissa C. Parker
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Department of Psychology, Middlebury College, Middlebury, VT 05753, USA
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753, USA
| | - Shyam Gopalakrishnan
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Museum of Natural History, Copenhagen University, Copenhagen, Denmark
| | - Peter Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- AncestryDNA, San Francisco, CA 94105, USA
| | | | - Emily Leung
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Yeonhee J Park
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Emmanuel Aryee
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Joe Davis
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - David A. Blizard
- Department of Biobehavioral Health, Pennsylvania State University, University Park, PA 16802, USA
| | - Cheryl L. Ackert-Bicknell
- Center for Musculoskeletal Research, University of Rochester, Rochester, NY 14624, USA
- Department of Orthopaedics and Rehabilitation, University of Rochester, Rochester, NY 14624, USA
| | - Arimantas Lionikas
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill Aberdeen, Scotland UK
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA 94305, USA
| | - Abraham A. Palmer
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92103, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92103, USA
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14
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Navarro N, Maga AM. Does 3D Phenotyping Yield Substantial Insights in the Genetics of the Mouse Mandible Shape? G3 (BETHESDA, MD.) 2016; 6:1153-63. [PMID: 26921296 PMCID: PMC4856069 DOI: 10.1534/g3.115.024372] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/16/2016] [Indexed: 02/07/2023]
Abstract
We describe the application of high-resolution 3D microcomputed tomography, together with 3D landmarks and geometric morphometrics, to validate and further improve previous quantitative genetic studies that reported QTL responsible for variation in the mandible shape of laboratory mice using a new backcross between C57BL/6J and A/J inbred strains. Despite the increasing availability of 3D imaging techniques, artificial flattening of the mandible by 2D imaging techniques seems at first an acceptable compromise for large-scale phenotyping protocols, thanks to an abundance of low-cost digital imaging systems such as microscopes or digital cameras. We evaluated the gain of information from considering explicitly this additional third dimension, and also from capturing variation on the bone surface where no precise anatomical landmark can be marked. Multivariate QTL mapping conducted with different landmark configurations (2D vs. 3D; manual vs. semilandmarks) broadly agreed with the findings of previous studies. Significantly more QTL (23) were identified and more precisely mapped when the mandible shape was captured with a large set of semilandmarks coupled with manual landmarks. It appears that finer phenotypic characterization of the mandibular shape with 3D landmarks, along with higher density genotyping, yields better insights into the genetic architecture of mandibular development. Most of the main variation is, nonetheless, preferentially embedded in the natural 2D plane of the hemi-mandible, reinforcing the results of earlier influential investigations.
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Affiliation(s)
- Nicolas Navarro
- Biogéosciences, UMR CNRS 6282, Univ Bourgogne Franche-Comté, EPHE, PSL Research University, F-21000 Dijon, France
| | - A Murat Maga
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98105 Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington 98101
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15
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Sittig LJ, Carbonetto P, Engel KA, Krauss KS, Palmer AA. Integration of genome-wide association and extant brain expression QTL identifies candidate genes influencing prepulse inhibition in inbred F1 mice. GENES BRAIN AND BEHAVIOR 2016; 15:260-70. [PMID: 26482417 DOI: 10.1111/gbb.12262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 12/12/2022]
Abstract
Genetic association mapping in structured populations of model organisms can offer a fruitful complement to human genetic studies by generating new biological hypotheses about complex traits. Here we investigated prepulse inhibition (PPI), a measure of sensorimotor gating that is disrupted in a number of psychiatric disorders. To identify genes that influence PPI, we constructed a panel of half-sibs by crossing 30 females from common inbred mouse strains with inbred C57BL/6J males to create male and female F1 offspring. We used publicly available single nucleotide polymorphism (SNP) genotype data from these inbred strains to perform a genome-wide association scan using a dense panel of over 150,000 SNPs in a combined sample of 604 mice representing 30 distinct F1 genotypes. We identified two independent PPI-associated loci on Chromosomes 2 and 7, each of which explained 12-14% of the variance in PPI. Searches of available databases did not identify any plausible causative coding polymorphisms within these loci. However, previously collected expression quantitative trait locus (eQTL) data from hippocampus and striatum indicated that the SNPs on Chromosomes 2 and 7 that showed the strongest association with PPI were also strongly associated with expression of several transcripts, some of which have been implicated in human psychiatric disorders. This integrative approach successfully identified a focused set of genes which can be prioritized for follow-up studies. More broadly, our results show that F1 crosses among common inbred strains can be used in combination with other informatics and expression datasets to identify candidate genes for complex behavioral traits.
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Affiliation(s)
- L J Sittig
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - P Carbonetto
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - K A Engel
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - K S Krauss
- Department of Human Genetics, University of Chicago, Chicago, IL
| | - A A Palmer
- Department of Human Genetics, University of Chicago, Chicago, IL.,Department of Psychiatry, University of California San Diego, San Diego, CA, USA
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16
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Koehn DR, Meyer KJ, Anderson MG. Genetic Evidence for Differential Regulation of Corneal Epithelial and Stromal Thickness. Invest Ophthalmol Vis Sci 2015; 56:5599-607. [PMID: 26305532 DOI: 10.1167/iovs.15-17179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Central corneal thickness (CCT) is a quantitative trait associated with keratoconus and primary open-angle glaucoma. Although CCT is highly heritable, known genetic variations explain only a fraction of the phenotypic variability. The purpose of this study was to identify additional CCT-influencing loci using inbred strains of mice. METHODS Cohorts of 82 backcrossed (N2) and 99 intercrossed (F2) mice were generated from crosses between recombinant inbred BXD24/TyJ and wild-derived CAST/EiJ mice. Using anterior chamber optical coherence tomography, mice were phenotyped at 10 to 12 weeks of age, genotyped based on 96 genome-wide single nucleotide polymorphisms (SNPs), and subjected to quantitative trait locus (QTL) analysis. RESULTS In an analysis of total CCT among all mice, two loci passed the significance threshold of P = 0.05. These were on Chr 3 and Chr 11 (Cctq4 and Cctq5, respectively). A third locus of interest was identified in a two-dimensional pairwise analysis; this locus on Chr 14 (Cctq6) exhibited a significant additive effect with Cctq5. Independent analyses of the dataset for epithelial and stromal thickness revealed that Cctq4 is specific to the epithelial layer and that Cctq5 and Cctq6 are specific to the stromal layer. CONCLUSIONS Our findings demonstrate a quantitative multigenic pattern of CCT inheritance in mice and identify three previously unrecognized CCT-influencing loci: Cctq4, Cctq5, and Cctq6. This is the first demonstration that distinct layers of the cornea are under differential genetic control and highlights the need to refine the design of future genome-wide association studies of CCT.
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Affiliation(s)
- Demelza R Koehn
- Department of Molecular Physiology and Biophysics University of Iowa, Iowa City, Iowa, United States
| | - Kacie J Meyer
- Department of Molecular Physiology and Biophysics University of Iowa, Iowa City, Iowa, United States
| | - Michael G Anderson
- Department of Molecular Physiology and Biophysics University of Iowa, Iowa City, Iowa, United States 2Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States 3Center for the Prevention and Treatment of Visual Lo
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The Founder Strains of the Collaborative Cross Express a Complex Combination of Advantageous and Deleterious Traits for Male Reproduction. G3-GENES GENOMES GENETICS 2015; 5:2671-83. [PMID: 26483008 PMCID: PMC4683640 DOI: 10.1534/g3.115.020172] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Surveys of inbred strains of mice are standard approaches to determine the heritability and range of phenotypic variation for biomedical traits. In addition, they may lead to the identification of novel phenotypes and models of human disease. Surprisingly, male reproductive phenotypes are among the least-represented traits in the Mouse Phenome Database. Here we report the results of a broad survey of the eight founder inbred strains of both the Collaborative Cross (CC) and the Diversity Outbred populations, two new mouse resources that are being used as platforms for systems genetics and sources of mouse models of human diseases. Our survey includes representatives of the three main subspecies of the house mice and a mix of classical and wild-derived inbred strains. In addition to standard staples of male reproductive phenotyping such as reproductive organ weights, sperm counts, and sperm morphology, our survey includes sperm motility and the first detailed survey of testis histology. As expected for such a broad survey, heritability varies widely among traits. We conclude that although all eight inbred strains are fertile, most display a mix of advantageous and deleterious male reproductive traits. The CAST/EiJ strain is an outlier, with an unusual combination of deleterious male reproductive traits including low sperm counts, high levels of morphologically abnormal sperm, and poor motility. In contrast, sperm from the PWK/PhJ and WSB/EiJ strains had the greatest percentages of normal morphology and vigorous motility. Finally, we report an abnormal testis phenotype that is highly heritable and restricted to the WSB/EiJ strain. This phenotype is characterized by the presence of a large, but variable, number of vacuoles in at least 10% of the seminiferous tubules. The onset of the phenotype between 2 and 3 wk of age is temporally correlated with the formation of the blood-testis barrier. We speculate that this phenotype may play a role in high rates of extinction in the CC project and in the phenotypes associated with speciation in genetic crosses that use the WSB/EiJ strain as representative of the Mus muculus domesticus subspecies.
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The Genetic Architecture of Hearing Impairment in Mice: Evidence for Frequency-Specific Genetic Determinants. G3-GENES GENOMES GENETICS 2015; 5:2329-39. [PMID: 26342000 PMCID: PMC4632053 DOI: 10.1534/g3.115.021592] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies (GWAS) have been successfully applied in humans for the study of many complex phenotypes. However, identification of the genetic determinants of hearing in adults has been hampered, in part, by the relative inability to control for environmental factors that might affect hearing throughout the lifetime, as well as a large degree of phenotypic heterogeneity. These and other factors have limited the number of large-scale studies performed in humans that have identified candidate genes that contribute to the etiology of this complex trait. To address these limitations, we performed a GWAS analysis using a set of inbred mouse strains from the Hybrid Mouse Diversity Panel. Among 99 strains characterized, we observed approximately two-fold to five-fold variation in hearing at six different frequencies, which are differentiated biologically from each other by the location in the cochlea where each frequency is registered. Among all frequencies tested, we identified a total of nine significant loci, several of which contained promising candidate genes for follow-up study. Taken together, our results indicate the existence of both genes that affect global cochlear function, as well as anatomical- and frequency-specific genes, and further demonstrate the complex nature of mammalian hearing variation.
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Kamberov YG, Karlsson EK, Kamberova GL, Lieberman DE, Sabeti PC, Morgan BA, Tabin CJ. A genetic basis of variation in eccrine sweat gland and hair follicle density. Proc Natl Acad Sci U S A 2015; 112:9932-7. [PMID: 26195765 PMCID: PMC4538659 DOI: 10.1073/pnas.1511680112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Among the unique features of humans, one of the most salient is the ability to effectively cool the body during extreme prolonged activity through the evapotranspiration of water on the skin's surface. The evolution of this novel physiological ability required a dramatic increase in the density and distribution of eccrine sweat glands relative to other mammals and a concomitant reduction of body hair cover. Elucidation of the genetic underpinnings for these adaptive changes is confounded by a lack of knowledge about how eccrine gland fate and density are specified during development. Moreover, although reciprocal changes in hair cover and eccrine gland density are required for efficient thermoregulation, it is unclear if these changes are linked by a common genetic regulation. To identify pathways controlling the relative patterning of eccrine glands and hair follicles, we exploited natural variation in the density of these organs between different strains of mice. Quantitative trait locus mapping identified a large region on mouse Chromosome 1 that controls both hair and eccrine gland densities. Differential and allelic expression analysis of the genes within this interval coupled with subsequent functional studies demonstrated that the level of En1 activity directs the relative numbers of eccrine glands and hair follicles. These findings implicate En1 as a newly identified and reciprocal determinant of hair follicle and eccrine gland density and identify a pathway that could have contributed to the evolution of the unique features of human skin.
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Affiliation(s)
- Yana G Kamberov
- Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Dermatology, Harvard Medical School and Cutaneous Biology Research Center, Mass General Hospital, Charlestown, MA 02129; The Broad Institute of MIT and Harvard, Cambridge, MA 02142; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138; Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Elinor K Karlsson
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142; Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Gerda L Kamberova
- Department of Computer Science, Hofstra University, Hempstead, NY 11549
| | - Daniel E Lieberman
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Pardis C Sabeti
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142; Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - Bruce A Morgan
- Department of Dermatology, Harvard Medical School and Cutaneous Biology Research Center, Mass General Hospital, Charlestown, MA 02129;
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, Boston, MA 02115;
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20
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The genetic and epigenetic landscape for CNS drug discovery targeting cross-diagnostic behavioral domains. Eur J Pharmacol 2015; 753:135-9. [DOI: 10.1016/j.ejphar.2014.07.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 05/28/2014] [Accepted: 07/24/2014] [Indexed: 12/23/2022]
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Hoffmann A, Griffin P, Dillon S, Catullo R, Rane R, Byrne M, Jordan R, Oakeshott J, Weeks A, Joseph L, Lockhart P, Borevitz J, Sgrò C. A framework for incorporating evolutionary genomics into biodiversity conservation and management. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40665-014-0009-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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22
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Kebede MA, Attie AD. Insights into obesity and diabetes at the intersection of mouse and human genetics. Trends Endocrinol Metab 2014; 25:493-501. [PMID: 25034129 PMCID: PMC4177963 DOI: 10.1016/j.tem.2014.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/06/2014] [Accepted: 06/06/2014] [Indexed: 11/25/2022]
Abstract
Many of our insights into obesity and diabetes come from studies in mice carrying natural or induced mutations. In parallel, genome-wide association studies (GWAS) in humans have identified numerous genes that are causally associated with obesity and diabetes, but discovering the underlying mechanisms required in-depth studies in mice. We discuss the advantages of studying natural variation in mice and summarize several examples where the combination of human and mouse genetics opened windows into fundamental physiological pathways. A noteworthy example is the melanocortin-4 receptor (MC4R) and its role in energy balance. The pathway was delineated by discovering the gene responsible for the Agouti mutation in mice. With more targeted phenotyping, we predict that additional pathways relevant to human pathophysiology will be discovered.
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Affiliation(s)
- Melkam A Kebede
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Chalfin L, Dayan M, Levy DR, Austad SN, Miller RA, Iraqi FA, Dulac C, Kimchi T. Mapping ecologically relevant social behaviours by gene knockout in wild mice. Nat Commun 2014; 5:4569. [DOI: 10.1038/ncomms5569] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 07/01/2014] [Indexed: 11/10/2022] Open
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Carbonetto P, Cheng R, Gyekis JP, Parker CC, Blizard DA, Palmer AA, Lionikas A. Discovery and refinement of muscle weight QTLs in B6 × D2 advanced intercross mice. Physiol Genomics 2014; 46:571-82. [PMID: 24963006 DOI: 10.1152/physiolgenomics.00055.2014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The genes underlying variation in skeletal muscle mass are poorly understood. Although many quantitative trait loci (QTLs) have been mapped in crosses of mouse strains, the limited resolution inherent in these conventional studies has made it difficult to reliably pinpoint the causal genetic variants. The accumulated recombination events in an advanced intercross line (AIL), in which mice from two inbred strains are mated at random for several generations, can improve mapping resolution. We demonstrate these advancements in mapping QTLs for hindlimb muscle weights in an AIL (n = 832) of the C57BL/6J (B6) and DBA/2J (D2) strains, generations F8-F13. We mapped muscle weight QTLs using the high-density MegaMUGA SNP panel. The QTLs highlight the shared genetic architecture of four hindlimb muscles and suggest that the genetic contributions to muscle variation are substantially different in males and females, at least in the B6D2 lineage. Out of the 15 muscle weight QTLs identified in the AIL, nine overlapped the genomic regions discovered in an earlier B6D2 F2 intercross. Mapping resolution, however, was substantially improved in our study to a median QTL interval of 12.5 Mb. Subsequent sequence analysis of the QTL regions revealed 20 genes with nonsense or potentially damaging missense mutations. Further refinement of the muscle weight QTLs using additional functional information, such as gene expression differences between alleles, will be important for discerning the causal genes.
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Affiliation(s)
| | - R Cheng
- Australian National University, Canberra, Australia
| | - J P Gyekis
- Pennsylvania State University, State College, Pennsylvania; and
| | | | - D A Blizard
- Pennsylvania State University, State College, Pennsylvania; and
| | - A A Palmer
- University of Chicago, Chicago, Illinois
| | - A Lionikas
- University of Aberdeen, Aberdeen, United Kingdom;
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Snoek LB, Joeri van der Velde K, Li Y, Jansen RC, Swertz MA, Kammenga JE. Worm variation made accessible: Take your shopping cart to store, link, and investigate! WORM 2014; 3:e28357. [PMID: 24843834 PMCID: PMC4024057 DOI: 10.4161/worm.28357] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/17/2014] [Accepted: 02/25/2014] [Indexed: 11/20/2022]
Abstract
In Caenorhabditis elegans, the recent advances in high-throughput quantitative analyses of natural genetic and phenotypic variation have led to a wealth of data on genotype phenotype relations. This data has resulted in the discovery of genes with major allelic effects and insights in the effect of natural genetic variation on a whole range of complex traits as well as how this variation is distributed across the genome. Regardless of the advances presented in specific studies, the majority of the data generated in these studies had yet to be made easily accessible, allowing for meta-analysis. Not only data in figures or tables but meta-data should be accessible for further investigation and comparison between studies. A platform was created where all the data, phenotypic measurements, genotypes, and mappings can be stored, compared, and new linkages within and between published studies can be discovered. WormQTL focuses on quantitative genetics in Caenorhabditis and other nematode species, whereas WormQTLHD quantitatively links gene expression quantitative trait loci (eQTL) in C. elegans to gene–disease associations in humans.
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Affiliation(s)
- L Basten Snoek
- Laboratory of Nematology; Wageningen University; The Netherlands
| | - K Joeri van der Velde
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands ; Department of Genetics; University of Groningen; University Medical Center Groningen; The Netherlands
| | - Yang Li
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands
| | - Ritsert C Jansen
- Groningen Bioinformatics Center; University of Groningen; The Netherlands
| | - Morris A Swertz
- Genomics Coordination Center; University of Groningen; University Medical Center Groningen; The Netherlands ; Groningen Bioinformatics Center; University of Groningen; The Netherlands ; Department of Genetics; University of Groningen; University Medical Center Groningen; The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology; Wageningen University; The Netherlands
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Genome-wide association study for age-related hearing loss (AHL) in the mouse: a meta-analysis. J Assoc Res Otolaryngol 2014; 15:335-52. [PMID: 24570207 DOI: 10.1007/s10162-014-0443-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 01/13/2014] [Indexed: 01/04/2023] Open
Abstract
Age-related hearing loss (AHL) is characterized by a symmetric sensorineural hearing loss primarily in high frequencies and individuals have different levels of susceptibility to AHL. Heritability studies have shown that the sources of this variance are both genetic and environmental, with approximately half of the variance attributable to hereditary factors as reported by Huag and Tang (Eur Arch Otorhinolaryngol 267(8):1179-1191, 2010). Only a limited number of large-scale association studies for AHL have been undertaken in humans, to date. An alternate and complementary approach to these human studies is through the use of mouse models. Advantages of mouse models include that the environment can be more carefully controlled, measurements can be replicated in genetically identical animals, and the proportion of the variability explained by genetic variation is increased. Complex traits in mouse strains have been shown to have higher heritability and genetic loci often have stronger effects on the trait compared to humans. Motivated by these advantages, we have performed the first genome-wide association study of its kind in the mouse by combining several data sets in a meta-analysis to identify loci associated with age-related hearing loss. We identified five genome-wide significant loci (<10(-6)). One of these loci confirmed a previously identified locus (ahl8) on distal chromosome 11 and greatly narrowed the candidate region. Specifically, the most significant associated SNP is located 450 kb upstream of Fscn2. These data confirm the utility of this approach and provide new high-resolution mapping information about variation within the mouse genome associated with hearing loss.
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