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Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice

https://doi.org/10.1038/ng.3609
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Permutation Testing in the Presence of Polygenic Variation
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Gene expression differences in mice divergently selected for methamphetamine sensitivity
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Fine-mapping alleles for body weight in LG/J × SM/J F2 and F34 advanced intercross lines
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The diversity outbred mouse population
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Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research
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Genome-Wide Association for Fear Conditioning in an Advanced Intercross Mouse Line
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Improved Heritability Estimation from Genome-wide SNPs
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Estimation of SNP Heritability from Dense Genotype Data
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Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
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Alternative mRNA transcription, processing, and translation: insights from RNA sequencing
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Genetic variance of laboratory outbred Swiss mice
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Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness
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Genetics of gene expression surveyed in maize, mouse and man
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Obesity-associated variants within FTO form long-range functional connections with IRX3
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CRISPR-Cas systems for editing, regulating and targeting genomes
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Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture
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Genome-wide efficient mixed-model analysis for association studies
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inferredcites →https://doi.org/10.1038/nmeth.1315openalex-snapshot
mRNA-Seq whole-transcriptome analysis of a single cell
inferredcites →https://doi.org/10.1038/nmeth.1359openalex-snapshot
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Improved linear mixed models for genome-wide association studies
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inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot
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inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot
RNA-Seq: a revolutionary tool for transcriptomics
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Pitfalls of predicting complex traits from SNPs
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inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
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Empirical threshold values for quantitative trait mapping.
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inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.113084.110openalex-snapshot
SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples
inferredcites →https://doi.org/10.1101/gr.117259.110openalex-snapshot
Low-coverage sequencing: Implications for design of complex trait association studies
inferredcites →https://doi.org/10.1111/gbb.12262openalex-snapshot
Integration of genome‐wide association and extant brain expression QTL identifies candidate genes influencing prepulse inhibition in inbred F1 mice
inferredcites →https://doi.org/10.1111/j.1601-183x.2010.00613.xopenalex-snapshot
Fine mapping of QTL for prepulse inhibition in LG/J and SM/J mice using F2 and advanced intercross lines
inferredcites →https://doi.org/10.1111/j.1601-183x.2011.00747.xopenalex-snapshot
Genome‐wide association for methamphetamine sensitivity in an advanced intercross mouse line
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Population genomic variation reveals roles of history, adaptation and ploidy in switchgrass
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Genetic heterogeneity in osteogenesis imperfecta.
inferredcites →https://doi.org/10.1146/annurev-genom-091212-153419openalex-snapshot
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inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1210/me.2010-0127openalex-snapshot
Regulation of Muscle Mass by Follistatin and Activins
inferredcites →https://doi.org/10.1371/journal.pgen.0020142openalex-snapshot
Allele Frequency Matching Between SNPs Reveals an Excess of Linkage Disequilibrium in Genic Regions of the Human Genome
inferredcites →https://doi.org/10.1371/journal.pgen.0030144openalex-snapshot
Linkage Disequilibrium in Wild Mice
inferredcites →https://doi.org/10.1371/journal.pgen.1000006openalex-snapshot
Differential Allelic Expression in the Human Genome: A Robust Approach To Identify Genetic and Epigenetic Cis-Acting Mechanisms Regulating Gene Expression
inferredcites →https://doi.org/10.1371/journal.pgen.1000149openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pgen.1000529openalex-snapshot
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1001085openalex-snapshot
Commercially Available Outbred Mice for Genome-Wide Association Studies
inferredcites →https://doi.org/10.1371/journal.pgen.1002038openalex-snapshot
Mouse Genome-Wide Association and Systems Genetics Identify Asxl2 As a Regulator of Bone Mineral Density and Osteoclastogenesis
inferredcites →https://doi.org/10.1371/journal.pgen.1002967openalex-snapshot
Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
inferredcites →https://doi.org/10.1371/journal.pgen.1003150openalex-snapshot
Systems Genetic Analysis of Osteoblast-Lineage Cells
inferredcites →https://doi.org/10.1371/journal.pgen.1003264openalex-snapshot
Polygenic Modeling with Bayesian Sparse Linear Mixed Models
inferredcites →https://doi.org/10.1371/journal.pgen.1003486openalex-snapshot
A Statistical Framework for Joint eQTL Analysis in Multiple Tissues
inferredcites →https://doi.org/10.1371/journal.pone.0000789openalex-snapshot
Quadrupling Muscle Mass in Mice by Targeting TGF-ß Signaling Pathways
inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot
A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
inferredcites →https://doi.org/10.1534/g3.114.013748openalex-snapshot
Quantitative Trait Locus Mapping Methods for Diversity Outbred Mice
inferredcites →https://doi.org/10.1534/g3.115.022087openalex-snapshot
The Mouse Universal Genotyping Array: From Substrains to Subspecies
inferredcites →https://doi.org/10.1534/genetics.110.116863openalex-snapshot
Genome-Wide Association Studies and the Problem of Relatedness Among Advanced Intercross Lines and Other Highly Recombinant Populations
inferredcites →https://doi.org/10.1534/genetics.111.132597openalex-snapshot
High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population
inferredcites →https://doi.org/10.1534/genetics.111.132639openalex-snapshot
The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population
inferredcites →https://doi.org/10.1534/genetics.112.146332openalex-snapshot
A Simulation Study of Permutation, Bootstrap, and Gene Dropping for Assessing Statistical Significance in the Case of Unequal Relatedness
inferredcites →https://doi.org/10.1534/genetics.114.167056openalex-snapshot
High-Resolution Genetic Mapping of Complex Traits from a Combined Analysis of F2 and Advanced Intercross Mice
inferredcites →https://doi.org/10.3389/fgene.2011.00032openalex-snapshot
Dark Matter: Are Mice the Solution to Missing Heritability?

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Physiological Trait And Genotype Data For 1,038 Outbred Cfw Mice
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Ultimate (Re)Thinking for Behavioural Biology
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Genes and Behaviour
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HAB / LAB Mice and Rats: Approaching the Genetics and Epigenetics of Trait Anxiety
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Genome‐Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose
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Genetic Factors in Cannabinoid Use and Dependence
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Genome-wide barebones regression scan for mixed-model association analysis
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Canonical transformation for multivariate mixed model association analyses
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Genome-wide association for testis weight in the diversity outbred mouse population
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Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses
inferred← citeshttps://doi.org/10.1007/s10162-025-00994-1openalex-snapshot
Genome-Wide Association Study of Age-Related Hearing Loss in CFW Mice Identifies Multiple Genes and Loci, Including Prkag2
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Quantile generalized measures of correlation
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Inbred Mouse Strains in the Study of Bone Disease
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Reduced Complexity Cross Design for Behavioral Genetics
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Studying the Genetics of Behavior in the Genomics Era
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Molecular genetic approaches to dissect complex behaviors in zebrafish
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Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2
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Expression of Cntn1 is regulated by stress and associated with anxiety and depression phenotypes
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A Thalamic Orphan Receptor Drives Variability in Short-Term Memory
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Large-scale phenotyping and characterization of age-related hearing loss in outbred CFW mice
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Plant pan-genomics: recent advances, new challenges, and roads ahead
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Decreased myelin-related gene expression in the nucleus accumbens during spontaneous neonatal opioid withdrawal in the absence of long-term behavioral effects in adult outbred CFW mice
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Mouse Systems Genetics as a Prelude to Precision Medicine
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Hidden variables in stress neurobiology research
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Parker et al. GWAS approach in mice investigates genetic basis of complex traits
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Identification of a novel gene regulating amygdala-mediated fear extinction
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Negr1 controls adult hippocampal neurogenesis and affective behaviors
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Genome-wide association study reveals multiple loci for nociception and opioid consumption behaviors associated with heroin vulnerability in outbred rats
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Epistasis regulates the developmental stability of the mouse craniofacial shape
inferred← citeshttps://doi.org/10.1038/s41467-018-07642-8openalex-snapshot
Genome wide association analysis in a mouse advanced intercross line
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HyperTRIBE uncovers increased MUSASHI-2 RNA binding activity and differential regulation in leukemic stem cells
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Genomic prediction for growth using a low-density SNP panel in dromedary camels
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Systems genetics applications in metabolism research
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Genetic polymorphisms and their association with brain and behavioural measures in heterogeneous stock mice
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Genetic mapping of species differences via in vitro crosses in mouse embryonic stem cells
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R package for analysis of data with mixed measurement error and misclassification in covariates: augSIMEX
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A Regression-Based Approach to Robust Estimation and Inference for Genetic Covariance
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Heritable natural variation of light/dark preference in an outbred zebrafish population
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Improving multi-population genomic prediction accuracy using multi-trait GBLUP models which incorporate global or local genetic correlation information
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A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data
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Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility
inferred← citeshttps://doi.org/10.1093/g3journal/jkac114openalex-snapshot
Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegans
inferred← citeshttps://doi.org/10.1093/g3journal/jkad055openalex-snapshot
Whole-exome sequencing prioritizes candidate genes for hereditary cataract in the Emory mouse mutant
inferred← citeshttps://doi.org/10.1093/g3journal/jkae046openalex-snapshot
Validation of positional candidates Rps6ka6 and Pou3f4 for a locus associated with skeletal muscle mass variability
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A cost-effective, high-throughput, highly accurate genotyping method for outbred populations
inferred← citeshttps://doi.org/10.1093/genetics/iyab157openalex-snapshot
Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice
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GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition
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An expectation and maximization algorithm for multivariate genome-wide association studies (EMmvGWAS)
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The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats
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Multi-omics reveals the genetic regulation and functions of long non-coding RNAs in tomato
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DeepArk: modeling cis -regulatory codes of model species with deep learning
inferred← citeshttps://doi.org/10.1101/2020.08.22.262709openalex-snapshot
Functional validation of a finding from a mouse genome-wide association study demonstrates that a mutant allele of Azi2 alters sensitivity to methamphetamine
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Genotype-free individual genome reconstruction of Multiparental Population Models by RNA sequencing data
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Polygenic Prediction of Complex Traits with Iterative Screen Regression Models
inferred← citeshttps://doi.org/10.1101/2021.02.05.429998openalex-snapshot
Analysis of independent cohorts of outbred CFW mice reveals novel loci for behavioral and physiological traits and identifies factors determining reproducibility
inferred← citeshttps://doi.org/10.1101/2021.03.10.434745openalex-snapshot
Efficient Genomic Control for Mixed Model Associations in Large-scale Population
inferred← citeshttps://doi.org/10.1101/2022.11.11.516099openalex-snapshot
Non-parametric GWAS: Another View on Genome-wide Association Study
inferred← citeshttps://doi.org/10.1101/2023.09.06.556529openalex-snapshot
Causal Genetic Loci for a Motivated Behavior Spectrum Harbor Psychiatric Risk Genes
inferred← citeshttps://doi.org/10.1101/2023.09.19.558496openalex-snapshot
Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and AHR , ATF3 , GATA3 , HNF1B , POU2F2 , and TFCP2 transcription factors as potential candidates to explain incomplete penetrance
inferred← citeshttps://doi.org/10.1101/2023.10.23.563569openalex-snapshot
Systems genetics identifies the association between Enc1 and cognitive function in the hippocampus
inferred← citeshttps://doi.org/10.1101/2024.06.10.598304openalex-snapshot
Genome-wide association study for age-related hearing loss in CFW mice
inferred← citeshttps://doi.org/10.1101/370312openalex-snapshot
Genome-wide associations reveal human-mouse genetic convergence and modifiers of myogenesis, CPNE1 and STC2
inferred← citeshttps://doi.org/10.1101/412924openalex-snapshot
Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies
inferred← citeshttps://doi.org/10.1101/gr.266171.120openalex-snapshot
Modeling transcriptional regulation of model species with deep learning
inferred← citeshttps://doi.org/10.1111/biom.13623openalex-snapshot
Generalized Network Structured Models with Mixed Responses Subject to Measurement Error and Misclassification
inferred← citeshttps://doi.org/10.1111/cge.14023openalex-snapshot
ZMYND11 variants are a novel cause of centrotemporal and generalised epilepsies with neurodevelopmental disorder
inferred← citeshttps://doi.org/10.1111/ejn.14171openalex-snapshot
Neurogenetic determinants and mechanisms of addiction to nicotine and smoked tobacco
inferred← citeshttps://doi.org/10.1111/gbb.12441openalex-snapshot
Post‐genomic behavioral genetics: From revolution to routine
inferred← citeshttps://doi.org/10.1111/gbb.12511openalex-snapshot
Decoding the transcriptional programs activated by psychotropic drugs in the brain
inferred← citeshttps://doi.org/10.1111/gbb.12583openalex-snapshot
Novel biomarkers to assess in utero effects of maternal opioid use: First steps toward understanding short‐ and long‐term neurodevelopmental sequelae
inferred← citeshttps://doi.org/10.1111/gbb.12730openalex-snapshot
Anxiety‐related defensive behavioral responses in mice selectively bred for High and Low Activity
inferred← citeshttps://doi.org/10.1111/gbb.12760openalex-snapshot
Functional validation of a finding from a mouse genome‐wide association study shows that Azi2 influences the acute locomotor stimulant response to methamphetamine
inferred← citeshttps://doi.org/10.1111/gbb.12769openalex-snapshot
Quantitative trait locus mapping identifies a locus linked to striatal dopamine and points to collagen IV alpha‐6 chain as a novel regulator of striatal axonal branching in mice
inferred← citeshttps://doi.org/10.1111/gbb.12774openalex-snapshot
A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity
inferred← citeshttps://doi.org/10.1111/gbb.12832openalex-snapshot
Hippocampal RNA sequencing in mice selectively bred for high and low activity
inferred← citeshttps://doi.org/10.1111/gbb.12851openalex-snapshot
Testing associations between human anxiety and genes previously implicated by mouse anxiety models
inferred← citeshttps://doi.org/10.1111/gbb.70018openalex-snapshot
Genetic Loci Influencing Cue‐Reactivity in Heterogeneous Stock Rats
inferred← citeshttps://doi.org/10.1111/mec.16076openalex-snapshot
Expression of Concern: Natural copy number variation of tandemly repeated regulatory SNORD RNAs leads to individual phenotypic differences in mice
inferred← citeshttps://doi.org/10.1111/sjos.70009openalex-snapshot
Inference on data with both multiplicative and additive measurement errors
inferred← citeshttps://doi.org/10.1163/22134468-bja10052openalex-snapshot
Not All Mice Are Created Equal: Interval Timing Accuracy and Scalar Timing in 129, Swiss-Webster, and C57BL/6 Mice
inferred← citeshttps://doi.org/10.1177/0962280220983587openalex-snapshot
Marginal analysis of bivariate mixed responses with measurement error and misclassification
inferred← citeshttps://doi.org/10.1186/s12864-025-11416-0openalex-snapshot
Integrative genomic analysis reveals shared loci for reproduction and production traits in Yorkshire pigs
inferred← citeshttps://doi.org/10.1186/s12888-018-1753-4openalex-snapshot
Collective interaction effects associated with mammalian behavioral traits reveal genetic factors connecting fear and hemostasis
inferred← citeshttps://doi.org/10.1186/s13020-025-01320-wopenalex-snapshot
Optimization of potential targets for antidepressant Chinese medicines: AI and multi-omics methods
inferred← citeshttps://doi.org/10.1186/s13059-021-02415-xopenalex-snapshot
Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.1242/dmm.027789openalex-snapshot
Identifying genes for neurobehavioural traits in rodents: progress and pitfalls
inferred← citeshttps://doi.org/10.12688/f1000research.9762.1openalex-snapshot
Viewing RNA-seq data on the entire human genome
inferred← citeshttps://doi.org/10.1371/journal.pgen.1010234openalex-snapshot
Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies
inferred← citeshttps://doi.org/10.1371/journal.pgen.1011583openalex-snapshot
RatXcan: A framework for cross-species integration of genome-wide association and gene expression data
inferred← citeshttps://doi.org/10.14814/phy2.13561openalex-snapshot
Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines
inferred← citeshttps://doi.org/10.1523/eneuro.0143-21.2021openalex-snapshot
Sex Differences in Behavioral and Brainstem Transcriptomic Neuroadaptations following Neonatal Opioid Exposure in Outbred Mice
inferred← citeshttps://doi.org/10.1523/jneurosci.0252-24.2024openalex-snapshot
Systems Genetics Analyses Reveals Key Genes Related to Behavioral Traits in the Striatum of CFW Mice
inferred← citeshttps://doi.org/10.1534/g3.119.400763openalex-snapshot
Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity
inferred← citeshttps://doi.org/10.1534/g3.120.401325openalex-snapshot
Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats
inferred← citeshttps://doi.org/10.1534/genetics.120.303668openalex-snapshot
Genetic Basis of Aerobically Supported Voluntary Exercise: Results from a Selection Experiment with House Mice
inferred← citeshttps://doi.org/10.3168/jds.2023-24614openalex-snapshot
Genome-wide copy number variant analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis)
inferred← citeshttps://doi.org/10.3389/fgene.2020.00894openalex-snapshot
Genetic Dissection of Growth Traits in a Unique Chicken Advanced Intercross Line
inferred← citeshttps://doi.org/10.3389/fgene.2020.00901openalex-snapshot
Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)
inferred← citeshttps://doi.org/10.3389/fncel.2023.1256619openalex-snapshot
Cochlear transcriptome analysis of an outbred mouse population (CFW)
inferred← citeshttps://doi.org/10.3390/ani10010096openalex-snapshot
A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus
inferred← citeshttps://doi.org/10.3390/ani11082226openalex-snapshot
In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data
inferred← citeshttps://doi.org/10.3390/brainsci10100725openalex-snapshot
Alcohol Sensitivity as an Endophenotype of Alcohol Use Disorder: Exploring Its Translational Utility between Rodents and Humans
inferred← citeshttps://doi.org/10.3390/d12120483openalex-snapshot
Development of Novel SNP Assays for Genetic Analysis of Rare Minnow (Gobiocypris rarus) in a Successive Generation Closed Colony
inferred← citeshttps://doi.org/10.3390/ijms26136397openalex-snapshot
Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges
inferred← citeshttps://doi.org/10.47248/hpgg2303040007openalex-snapshot
The quantitative genetics of human disease: 1. Foundations
inferred← citeshttps://doi.org/10.5705/ss.202023.0088openalex-snapshot
Statistical Inference for High Dimensional Regression with Proxy Data
inferred← citeshttps://doi.org/10.6084/m9.figshare.15058257openalex-snapshot
Additional file 1 of Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.6084/m9.figshare.15058260openalex-snapshot
Additional file 2 of Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.6084/m9.figshare.15058263openalex-snapshot
Additional file 3 of Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.6084/m9.figshare.15058266openalex-snapshot
Additional file 4 of Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.6084/m9.figshare.15058272openalex-snapshot
Additional file 5 of Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.6084/m9.figshare.15058275openalex-snapshot
Additional file 6 of Dissecting indirect genetic effects from peers in laboratory mice
inferred← citeshttps://doi.org/10.7554/elife.64329openalex-snapshot
Age and diet shape the genetic architecture of body weight in diversity outbred mice
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