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Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo-Manuel de Villena F. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet 2015; 47:353-60. [PMID: 25730764 PMCID: PMC4380817 DOI: 10.1038/ng.3222] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/26/2015] [Indexed: 12/15/2022]
Abstract
Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Since regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in this process. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. These effects influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a novel, global allelic imbalance in favor of the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.
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Affiliation(s)
- James J Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vasyl Zhabotynsky
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wei Sun
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shunping Huang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Isa Kemal Pakatci
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yunjung Kim
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy R Wang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Andrew P Morgan
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John D Calaway
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David L Aylor
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zaining Yun
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy A Bell
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ryan J Buus
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark E Calaway
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John P Didion
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Terry J Gooch
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephanie D Hansen
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nashiya N Robinson
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ginger D Shaw
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason S Spence
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corey R Quackenbush
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cordelia J Barrick
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Randal J Nonneman
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyungsu Kim
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James Xenakis
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yuying Xie
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - William Valdar
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Alan B Lenarcic
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wei Wang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine E Welsh
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Chen-Ping Fu
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zhaojun Zhang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James Holt
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zhishan Guo
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas, USA
| | - Lisa M Tarantino
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Darla R Miller
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Patrick F Sullivan
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [4] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Fernando Pardo-Manuel de Villena
- 1] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. [3] Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Crowley JJ, Kim Y, Lenarcic AB, Quackenbush CR, Barrick CJ, Adkins DE, Shaw GS, Miller DR, de Villena FPM, Sullivan PF, Valdar W. Genetics of adverse reactions to haloperidol in a mouse diallel: a drug-placebo experiment and Bayesian causal analysis. Genetics 2014; 196:321-47. [PMID: 24240528 PMCID: PMC3872195 DOI: 10.1534/genetics.113.156901] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/14/2013] [Indexed: 12/21/2022] Open
Abstract
Haloperidol is an efficacious antipsychotic drug that has serious, unpredictable motor side effects that limit its utility and cause noncompliance in many patients. Using a drug-placebo diallel of the eight founder strains of the Collaborative Cross and their F1 hybrids, we characterized aggregate effects of genetics, sex, parent of origin, and their combinations on haloperidol response. Treating matched pairs of both sexes with drug or placebo, we measured changes in the following: open field activity, inclined screen rigidity, orofacial movements, prepulse inhibition of the acoustic startle response, plasma and brain drug level measurements, and body weight. To understand the genetic architecture of haloperidol response we introduce new statistical methodology linking heritable variation with causal effect of drug treatment. Our new estimators, "difference of models" and "multiple-impute matched pairs", are motivated by the Neyman-Rubin potential outcomes framework and extend our existing Bayesian hierarchical model for the diallel (Lenarcic et al. 2012). Drug-induced rigidity after chronic treatment was affected by mainly additive genetics and parent-of-origin effects (accounting for 28% and 14.8% of the variance), with NZO/HILtJ and 129S1/SvlmJ contributions tending to increase this side effect. Locomotor activity after acute treatment, by contrast, was more affected by strain-specific inbreeding (12.8%). In addition to drug response phenotypes, we examined diallel effects on behavior before treatment and found not only effects of additive genetics (10.2-53.2%) but also strong effects of epistasis (10.64-25.2%). In particular: prepulse inhibition showed additivity and epistasis in about equal proportions (26.1% and 23.7%); there was evidence of nonreciprocal epistasis in pretreatment activity and rigidity; and we estimated a range of effects on body weight that replicate those found in our previous work. Our results provide the first quantitative description of the genetic architecture of haloperidol response in mice and indicate that additive, dominance-like inbreeding and parent-of-origin effects contribute strongly to treatment effect heterogeneity for this drug.
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Affiliation(s)
- James J. Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - Yunjung Kim
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - Alan B. Lenarcic
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - Corey R. Quackenbush
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - Cordelia J. Barrick
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - Daniel E. Adkins
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Ginger S. Shaw
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - Darla R. Miller
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | | | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
| | - William Valdar
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599-7264
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Phillippi J, Xie Y, Miller DR, Bell TA, Zhang Z, Lenarcic AB, Aylor DL, Krovi SH, Threadgill DW, de Villena FPM, Wang W, Valdar W, Frelinger JA. Using the emerging Collaborative Cross to probe the immune system. Genes Immun 2013; 15:38-46. [PMID: 24195963 PMCID: PMC4004367 DOI: 10.1038/gene.2013.59] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 12/21/2022]
Abstract
The Collaborative Cross (CC) is an emerging panel of recombinant inbred (RI) mouse strains. Each strain is genetically distinct but all descended from the same eight inbred founders. In 66 strains from incipient lines of the CC (pre-CC), as well as the 8 CC founders and some of their F1 offspring, we examined subsets of lymphocytes and antigen-presenting cells. We found significant variation among the founders, with even greater diversity in the pre-CC. Genome-wide association using inferred haplotypes detected highly significant loci controlling B-to-T cell ratio, CD8 T-cell numbers, CD11c and CD23 expression. Comparison of overall strain effects in the CC founders with strain effects at QTL in the pre-CC revealed sharp contrasts in the genetic architecture of two traits with significant loci: variation in CD23 can be explained largely by additive genetics at one locus, whereas variation in B-to-T ratio has a more complex etiology. For CD23, we found a strong QTL whose confidence interval contained the CD23 structural gene Fcer2a. Our data on the pre-CC demonstrate the utility of the CC for studying immunophenotypes and the value of integrating founder, CC and F1 data. The extreme immunophenotypes observed could have pleiotropic effects in other CC experiments.
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Affiliation(s)
- J Phillippi
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Y Xie
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - D R Miller
- 1] Department of Genetics, University of North Carolina, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - T A Bell
- 1] Department of Genetics, University of North Carolina, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Z Zhang
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - A B Lenarcic
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - D L Aylor
- 1] Department of Genetics, University of North Carolina, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - S H Krovi
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - D W Threadgill
- Department of Genetics, North Carolina State University, Raleigh, NC, USA
| | - F Pardo-Manuel de Villena
- 1] Department of Genetics, University of North Carolina, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - W Wang
- Department of Computer Science, and the Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | - W Valdar
- 1] Department of Genetics, University of North Carolina, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - J A Frelinger
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
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