A Large-Scale Mutagenesis and Strain Characterization Project To Identify Genetic Variability in Mice: Resources Available from the Jackson Laboratory Program for Genomic Applications (JAX PGA).

Abstract Identifying the genes and gene products relevant to physiological systems and creating opportunities to elucidate their function are essential first steps in understanding the pathophysiology of disease. To dissect the genetic variation underlying hematopoietic, cardiovascular, lung, and sleep dysfunction, we established a Center for Mouse Models of Heart, Lung, Blood and Sleep (HLBS) Disorders at The Jackson Laboratory as part of the NHLBI Program for Genomic Applications (PGA). The major goal of the JAX PGA is to enable researchers to link both single-gene mutations and quantitative trait loci (QTL) to gene function and disease. To achieve this goal, we are generating new mutations in mice by chemical (ENU) mutagenesis, and characterizing the common inbred mouse strains to detect existing genetic variation. Here, we report an extensive body of hematologically relevant strain characterization data and the establishment of new animal models. All strain characterization data is deposited into the Mouse Phenome Database (MPD, http://www.jax.org/phenome), also accessible via the JAX PGA website (http://pga.jax.org). Data for up to 48 inbred strains are currently available and include complete blood counts and coagulation profiles (PT, aPTT, fibrinogen). These data allow investigators to identify the most appropriate strains for (a) physiological testing; (b) drug development; (c) progenitors in QTL crosses; (d) sensitized mutagenesis screens; and (e) direct hypothesis testing. For example, to maximize the potential for successful QTL identification, parental strains that differ substantially in the phenotype of interest, at least 2 standard deviations (SD), should be selected. We used our strain survey data to select parental strains for identification of QTL for baseline WBC count, an important risk factor for sickle cell disease severity. The strains C57BLKS/J and SM/J have WBC counts of 12.6 ± 1.6 and 3.3 ± 0.8 x 103/μL, respectively, a difference much greater the 2 SD, indicating a high statistical power. We identified a highly significant QTL (LOD = 7) on chromosome 1 in an initial genome wide scan of 279 F2 animals. Moreover, the availability of extensive phenotypic data across the inbred strains in conjunction with the availability of saturated sslp and SNP maps has allowed us to identify QTL in silico. As an example of the utility of the MPD in hypothesis testing, a modifier gene associated with decreased VWF levels is present in 5 of the 6 MPD strains showing the highest aPTT levels (see abstract by Johnsen et al). In total, 44 different phenotypic projects, each consisting of large datasets, can be freely accessed through the MPD. The JAX PGA mutagenesis effort in C57BL/6J mice has likewise yielded valuable resources. Nearly 100 new mutant strains are in various stages of development, including strains with phenotypes of interest to the hematology community (e. g., anemia, thrombocytopenia, leukopenia, leukocytosis). These animal models and all other JAX PGA resources (protocols, software, QTL locations) are freely available to the scientific community.

Download Full-text

Large-scale, high-throughput screening for coagulation and hematologic phenotypes in mice*

Physiological Genomics ◽

10.1152/physiolgenomics.00077.2002 ◽

2002 ◽

Vol 11 (3) ◽

pp. 185-193 ◽

Cited By ~ 52

Author(s):

Luanne L. Peters ◽

Eleanor M. Cheever ◽

Heather R. Ellis ◽

Phyllis A. Magnani ◽

Karen L. Svenson ◽

...

Keyword(s):

High Throughput ◽

High Throughput Screening ◽

Large Scale ◽

Inbred Mouse ◽

Inbred Strains ◽

Sample Volume ◽

Small Sample ◽

Mouse Strains ◽

Phenotypic Data ◽

Multiple Tests

The Mouse Phenome Project is an international effort to systematically gather phenotypic data for a defined set of inbred mouse strains. For such large-scale projects the development of high-throughput screening protocols that allow multiple tests to be performed on a single mouse is essential. Here we report hematologic and coagulation data for more than 30 inbred strains. Complete blood counts were performed using an Advia 120 analyzer. For coagulation testing, we successfully adapted the Dade Behring BCS automated coagulation analyzer for use in mice by lowering sample and reagent volume requirements. Seven automated assay procedures were developed. Small sample volume requirements make it possible to perform multiple tests on a single animal without euthanasia, while reductions in reagent volume requirements reduce costs. The data show that considerable variation in many basic hematological and coagulation parameters exists among the inbred strains. These data, freely available on the World Wide Web, allow investigators to knowledgeably select the most appropriate strain(s) to meet their individual study designs and goals.

Download Full-text

Large Scale Evaluation of Genetic Variation and the Risk of Multiple Myeloma.

Blood ◽

10.1182/blood.v112.11.1679.1679 ◽

2008 ◽

Vol 112 (11) ◽

pp. 1679-1679

Author(s):

Sonja I Berndt ◽

David C Johnson ◽

John Crowley ◽

Brian G Durie ◽

Robert Hoover ◽

...

Keyword(s):

Multiple Myeloma ◽

Dna Damage ◽

Genetic Variation ◽

Statistical Power ◽

Large Scale ◽

Cell Cycle Checkpoint ◽

Health Study ◽

Candidate Gene Approach ◽

Ovarian Cancer Screening ◽

Increased Risk

Abstract Genetic factors are thought to influence susceptibility to multiple myeloma, but most published studies to date have been small and limited in scope. To identify genetic polymorphisms associated with myeloma risk, we conducted a case-control study of 976 Caucasian myeloma cases enrolled from clinical trials as part of the International Myeloma Foundation’s Bank On A Cure® initiative and 3692 Caucasian controls from the three cohorts [Nurses’ Health Study (NHS), Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO), and 1958 British Birth Cohort (BC58)] with genome-wide scan data. A candidate gene approach was taken with a preference given to single nucleotide polymorphisms (SNPs) in coding or regulatory regions. A total of 1097 SNPs with a minor allele frequency ≥1% were genotyped in the cases and at least one control population. In order to increase our statistical power, SNPs not genotyped in NHS and PLCO were imputed from the genome scan with MACH using the HapMap CEU population as a referent and included in the analysis if the quality control r2 was high (r2 ≥0.9). Logistic regression was used to estimate the odds ratios (ORs) and 95% confidence intervals (95% CIs) adjusting for age, sex, and country as appropriate. We found 26 loci to be associated with myeloma risk with P < 0.01. Of particular interest, we observed an increased risk of myeloma with variants in two genes involved in the metabolism of pyrimidines, DPYD and MTHFR. An increased risk of myeloma was found with two independent SNPs, rs1023244 and rs1399291, in DPYD (ORperGallele = 1.43, 95% CI: 1.16–1.76, P = 0.0008 and ORperTallele = 1.18, 95% CI: 1.06–1.31, P = 0.003, respectively) and with the MTHFR high activity 677C allele (rs1801133, ORperC allele = 1.18, 95% CI: 1.05–1.33, P = 0.006). We also observed significant associations for nonsynonymous SNPs in genes involved in cell cycle checkpoint regulation (ATR, P = 0.009; ZAK, P = 0.007) and the DNA damage bypass pathway (REV3L, P = 0.008), suggesting that alterations in DNA damage mediation may modulate myeloma susceptibility. In conclusion, this large study found SNPs in several pathways, including pyrimidine metabolism and DNA damage mediation, to be associated with myeloma risk. Additional studies are needed to replicate these findings and to further explore genetic variation in these regions.

Download Full-text

Genetics of metabolic syndrome: potential clues from wild-derived inbred mouse strains

Physiological Genomics ◽

10.1152/physiolgenomics.00059.2017 ◽

2018 ◽

Vol 50 (1) ◽

pp. 35-51 ◽

Cited By ~ 5

Author(s):

Subashini Karunakaran ◽

Susanne M. Clee

Keyword(s):

Metabolic Syndrome ◽

Genetic Variation ◽

Inbred Mouse ◽

Inbred Strains ◽

Human Studies ◽

Mouse Strains ◽

Great Promise ◽

Abnormal Glucose Metabolism ◽

The Metabolic Syndrome ◽

Underlying Basis

The metabolic syndrome (MetS) is a complex constellation of metabolic abnormalities including obesity, abnormal glucose metabolism, dyslipidemia, and elevated blood pressure that together substantially increase risk for cardiovascular disease and Type 2 diabetes. Both genetic and environmental factors contribute to the development of MetS, but this process is still far from understood. Human studies have revealed only part of the underlying basis. Studies in mice offer many strengths that can complement human studies to help elucidate the etiology and pathophysiology of MetS. Here we review the ways mice can contribute to MetS research. In particular, we focus on the information that can be obtained from studies of the inbred strains, with specific focus on the phenotypes of the wild-derived inbred strains. These are newly derived inbred strains that were created from wild-caught mice. They contain substantial genetic variation that is not present in the classical inbred strains, have phenotypes of relevance for MetS, and various mouse strain resources have been created to facilitate the mining of this new genetic variation. Thus studies using wild-derived inbred strains hold great promise for increasing our understanding of MetS.

Download Full-text

Modeling diseases in multiple mouse strains for precision medicine studies

Physiological Genomics ◽

10.1152/physiolgenomics.00123.2016 ◽

2017 ◽

Vol 49 (3) ◽

pp. 177-179 ◽

Cited By ~ 3

Author(s):

Andrés D. Klein

Keyword(s):

Statistical Power ◽

Association Studies ◽

Phenotypic Variability ◽

Inbred Strains ◽

Mouse Strains ◽

Genome Wide Association Studies ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Genome Wide ◽

Number Of Patients

The genetic basis of the phenotypic variability observed in patients can be studied in mice by generating disease models through genetic or chemical interventions in many genetic backgrounds where the clinical phenotypes can be assessed and used for genome-wide association studies (GWAS). This is particularly relevant for rare disorders, where patients sharing identical mutations can present with a wide variety of symptoms, but there are not enough number of patients to ensure statistical power of GWAS. Inbred strains are homozygous for each loci, and their single nucleotide polymorphisms catalogs are known and freely available, facilitating the bioinformatics and reducing the costs of the study, since it is not required to genotype every mouse. This kind of approach can be applied to pharmacogenomics studies as well.

Download Full-text

Integrative Analyses Reveal Tstd1 as a Potential Modulator of HDL Cholesterol and Mitochondrial Function in Mice

Cells ◽

10.3390/cells10112976 ◽

2021 ◽

Vol 10 (11) ◽

pp. 2976

Author(s):

Adi Zheng ◽

Hao Li ◽

Zhihui Feng ◽

Jiankang Liu

Keyword(s):

Correlation Analysis ◽

Mitochondrial Function ◽

Complex Traits ◽

Large Scale ◽

Molecular Mechanisms ◽

Density Lipoprotein ◽

Hdl Cholesterol ◽

Chromosome 1 ◽

Mouse Strains ◽

Gene Sets

High-density lipoprotein (HDL) cholesterol levels are closely associated with human health and diseases. To identify genes modulating plasma HDL levels, we integrated HDL measurements and multi-omics data collected from diverse mouse cohorts and combined a list of systems genetics methods, including quantitative trait loci (QTL) mapping analysis, mediation analysis, transcriptome-wide association analysis (TWAS), and correlation analysis. We confirmed a significant and conserved QTL for plasma HDL on chromosome 1 and identified that Tstd1 liver transcript correlates with plasma HDL in several independent mouse cohorts, suggesting Tstd1 may be a potential modulator of plasma HDL levels. Correlation analysis using over 70 transcriptomics datasets in humans and mice revealed consistent correlations between Tstd1 and genes known to be involved in cholesterol and HDL regulation. Consistent with strong enrichment in gene sets related to cholesterol and lipoproteins in the liver, mouse strains with high Tstd1 exhibited higher plasma levels of HDL, total cholesterol and other lipid markers. GeneBridge using large-scale expression datasets identified conserved and positive associations between TSTD1/Tstd1 and mitochondrial pathways, as well as cholesterol and lipid pathways in human, mouse and rat. In summary, we identified Tstd1 as a new modulator of plasma HDL and mitochondrial function through integrative systems analyses, and proposed a new mechanism of HDL modulation and a potential therapeutic target for relevant diseases. This study highlights the value of such integrative approaches in revealing molecular mechanisms of complex traits or diseases.

Download Full-text

Mouse models of ocular diseases

Visual Neuroscience ◽

10.1017/s0952523805225075 ◽

2005 ◽

Vol 22 (5) ◽

pp. 587-593 ◽

Cited By ~ 52

Author(s):

B. CHANG ◽

N.L. HAWES ◽

R.E. HURD ◽

J. WANG ◽

D. HOWELL ◽

...

Keyword(s):

Genetic Analysis ◽

Mouse Models ◽

Inbred Strains ◽

Fundus Photography ◽

Gene Identification ◽

Mouse Strains ◽

Ocular Diseases ◽

Jackson Laboratory ◽

Mammalian Genomes ◽

Genetically Determined

The Jackson Laboratory, having the world's largest collection of mouse mutant stocks and genetically diverse inbred strains, is an ideal place to discover genetically determined eye variations and disorders. In this paper, we list and describe mouse models for ocular research available from Mouse Eye Mutant Resource at The Jackson Laboratory. While screening mouse strains and stocks at The Jackson Laboratory (TJL) for genetic mouse models of human ocular disorders, we have identified numerous spontaneous or naturally occurring mutants. We characterized these mutants using serial indirect ophthalmoscopy, fundus photography, electroretinography (ERG) and histology, and performed genetic analysis including linkage studies and gene identification. Utilizing ophthalmoscopy, electroretinography, and histology, to date we have discovered 109 new disorders affecting all aspects of the eye including the lid, cornea, iris, lens, and retina, resulting in corneal disorders, glaucoma, cataracts, and retinal degenerations. The number of known serious or disabling eye diseases in humans is large and affects millions of people each year. Yet research on these diseases frequently is limited by the obvious restrictions on studying pathophysiologic processes in the human eye. Likewise, many human ocular diseases are genetic in origin, but appropriate families often are not readily available for genetic studies. Mouse models of inherited ocular disease provide powerful tools for rapid genetic analysis, characterization, and gene identification. Because of the great similarity among mammalian genomes, these findings in mice have direct relevance to the homologous human conditions.

Download Full-text

Selecting Clustering Algorithms for IBD Mapping

10.1101/2021.08.11.456036 ◽

2021 ◽

Author(s):

Ruhollah Shemirani ◽

Gillian M Belbin ◽

Keith Burghardt ◽

Kristina Lerman ◽

Christy L Avery ◽

...

Keyword(s):

Statistical Power ◽

Large Scale ◽

Clustering Algorithms ◽

False Negative ◽

Chromosome 1 ◽

Detection Methods ◽

Scalable Clustering ◽

Markov Clustering ◽

Cluster Properties ◽

Greedy Methods

Background: Groups of distantly related individuals who share a short segment of their genome identical-by-descent (IBD) can provide insights about rare traits and diseases in massive biobanks via a process called IBD mapping. Clustering algorithms play an important role in finding these groups. We set out to analyze the fitness of commonly used, fast and scalable clustering algorithms for IBD mapping applications. We designed a realistic benchmark for local IBD graphs and utilized it to compare clustering algorithms in terms of statistical power. We also investigated the effectiveness of common clustering metrics as replacements for statistical power. Results: We simulated 3.4 million clusters across 850 experiments with varying cluster counts, false-positive, and false-negative rates. Infomap and Markov Clustering (MCL) community detection methods have high statistical power in most of the graphs, compared to greedy methods such as Louvain and Leiden. We demonstrate that standard clustering metrics, such as modularity, cannot predict statistical power of algorithms in IBD mapping applications, though they can help with simulating realistic benchmarks. We extend our findings to real datasets by analyzing 3 populations in the Population Architecture using Genomics and Epidemiology (PAGE) Study with ~51,000 members and 2 million shared segments on Chromosome 1, resulting in the extraction of ~39 million local IBD clusters across three different populations in PAGE. We used cluster properties derived in PAGE to increase the accuracy of our simulations and comparison. Conclusions: Markov Clustering produces a 30% increase in statistical power compared to the current state-of-art approach, while reducing runtime by 3 orders of magnitude; making it computationally tractable in modern large-scale genetic datasets. We provide an efficient implementation to enable clustering at scale for IBD mapping and poplation-based linkage for various populations and scenarios.

Download Full-text

Skin Grafting and The Homogeneity of Inbred Mouse Strains

Laboratory Animals ◽

10.1258/002367767781035585 ◽

1967 ◽

Vol 1 (2) ◽

pp. 81-90 ◽

Cited By ~ 2

Author(s):

Annie M. Brown ◽

Marjorie Dinsley

Keyword(s):

Breeding System ◽

Large Scale ◽

Common Ancestor ◽

Inbred Mouse ◽

Skin Grafting ◽

Inbred Strains ◽

Mouse Strains ◽

Inbred Mouse Strains ◽

Two Generations ◽

Line Breeding

Summary The results of the routine skin grafting on mice from fifteen inbred strains have been collated and examined. It has been shown that when strains are maintained on a modification of the single line breeding system there is an overall frequency of only two per cent of graft rejections with at least six generations between donor and recipient mice. Successful grafts are usually obtained even when donor and recipient mice are separated by as many as fourteen generations. It is suggested that mice not more than two generations from their common ancestor should be used for large scale skin grafting experiments because of the unsuccessful skin transfer between some mice more distantly related. With some mouse strains difficulty of graft healing is apparent, and it has been shown that these results point to a valid difference between the C57 and A strains.

Download Full-text