Genetic Analysis Resources

Neurogenetics and Behavior Center

Research Emphasis/Objectives

This center provides routine behavioral/cognitive testing of mice with phenotypes that are expressed as a consequence of alterations at the level of gene function, and that are relevant to basic neuroscience and to animal models of neurological and psychiatric disorders.

Current Research

Behavioral testing within the center involves a collaborative component in which mice provided by users are assessed for behavioral/cognitive functions. All research includes behavioral assessment of a variety of genetically altered mice provided by users.

Services Provided

The objective of the center is to provide a link between genetic and molecular analyses of neural function and the study of integrative systems and clinical conditions through behavioral assessment of animal models, and mouse behavioral phenotypes generated by genetic modification.

Contact Information

Johns Hopkins University
3400 North Charles Street
101 Ames Hall
Baltimore, MD 21218

Grant No.: P40 RR017688

Web site: http://nbc.jhu.edu/

Principal Investigator
Michela Gallagher, Ph.D.
410-516-0167; Fax: 410-516-0494
E-mail: michela@jhu.edu

Additional Contact
Dani Smith
410-516-0429; 410-516-0494
E-mail: daniro@jhu.edu

Referral Center for Animal Models of Human Genetics Disease

Research Emphasis/Objectives

A major objective is the identification of animal homologs of human disease not previously recognized. After initial ascertainment, potential models are characterized at the clinical, pathologic, and biochemical levels and their homology with the human disorder is assessed. Models in which there is strong evidence of homology and that offer opportunities for investigation of pathogenesis and therapy not currently feasible in humans and not available in other species are further pursued.

Current Research

Current projects involved in the characterization of animal models with inherited metabolic diseases that are potential targets for research on gene therapy include: Alpha mannosidase deficiency (alpha-mannosidosis); erythrocyte pyruvate kinase deficient hemolytic anemia; branching enzyme deficiency (glycogen storage disease IV); mannose-6-phosphorylase deficiency (I-cell disease) in the cat; beta-glucuronidase deficiency (mucopolysaccharidosis VII) in the dog and cat; cystinuria in the dog (renal basic amino acid transport, rBAT gene); X-linked severe combined immunodeficiency (common gamma chain mutation); myotonic myopathy (chloride channel mutation); X-linked anhydrotic ectodermal dysplasia; and phosphofructokinase deficiency in the dog. The species-specific genes for these disorders have been cloned or are in the process of cloning and characterization by the center, in collaboration with other investigators. Small nuclear animal colonies of these models are maintained for study. The center is collaborating with investigators at Jefferson Medical College to manage a colony of dogs with galactocerebrosidase deficiency (globoid leukodystrophy, Krabbe's disease) for studies of gene therapy of this disorder. The canine gene was previously cloned and characterized in Dr. Wenger's laboratory. The center is also characterizing a number of other promising models for the study of genetic disease pathogenesis and gene therapy that have not yet reached the level of molecular genetic characterization. These include recessive osteogenesis imperfecta, juvenile dilated cardiomyopathy, and tricuspid valve dysplasia.

Cloning and Characterization of Animal Model Disease Genes

This function is limited by resources to genes for diseases in which the studies can lead to further understanding of pathogenesis in ways not possible in human patients, or that are reasonable candidates for gene therapy studies. Contact Paula Henthorn, Ph.D., 215-898-9061; Fax: 215-573-2162; email: henthorn@vet.upenn.edu.

Gene Therapy

Potential models for research on gene therapy are evaluated in the context of the present status of the field and the availability of other animal models through contacts with other investigators. Contact Dr. Mark Haskins, 215-898-4852; e-mail: mhaskins@vet.upenn.edu.

Services Provided

Consultation and Diagnostic Services

The center provides consultation, certain diagnostic services, and preliminary genetic studies to facilitate the discovery and preservation of new and potentially useful animal models. Emphasis is primarily on, but not limited to, models that occur in domesticated species. Services depend on preliminary consultation and evaluation of the potential model by scientists at the referral center. These general classes of genetic diseases are emphasized:

Hereditary Metabolic Diseases

Includes inborn errors of amino acid, organic acid, carbohydrate, and glycosaminoglycan metabolism; enzyme, receptor, and transporter defects. Contact Dr. Urs Giger, 215-898-8830; e-mail: giger@vet.upenn.edu.

Hereditary Defects in Sexual Development

Includes male and female pseudohermaphroditism, sex reversal, and true hermaphroditism. Contact Dr. Mark Haskins, 215-898-4852; e-mail: mhaskins@vet.upenn.edu.

Hereditary Congenital Malformations

Includes congenital heart disease and anomalies of other organ systems. Particular emphasis given to isolated malformations or malformation syndromes that may be due to chromosomal anomalies or defects in single major genes. Contact Dr. Mark Haskins, 215-898-4852; e-mail: mhaskins@vet.upenn.edu.

Hereditary Hematologic Diseases

Includes defects in erythrocytes, leukocytes, and hemostasis (bleeding disorders). Contact Dr. Urs Giger, 215-898-8830; e-mail: giger@vet.upenn.edu.

Hereditary Diseases of Immune Function

Includes immunodeficiencies and autoimmune disorders. Contact Dr. Urs Giger, 215-898-8830; e-mail: giger@vet.upenn.edu or Dr. Peter Felsburg, 215-898-6678; e-mail: felsburg@vet.upenn.edu.

Services Provided

If an affected animal is believed to represent a potentially new and useful model after the initial consultation, the following services are available:

Clinical Examination

Arrangements for transporting the affected animal to the center are usually the responsibility of the veterinarian or other investigator who makes the referral. If an animal shows sufficient promise as a disease model, the center pays shipping charges. Physical examinations and routine diagnostic tests are performed. If the animal is owned by the client and the examination is primarily in the owner's interest, a reduced fee for clinical services is charged to the owner.

Postmortem/Biopsy Examinations

If biopsy specimens are to be sent after initial consultation, the center provides instructions for tissue fixation and may provide fixatives where needed. Complete postmortem examinations include gross and microscopic studies of organs and tissues, electron microscopy, and special histochemical stains. Some tissues may be stored or cells cultured and stored for metabolic studies, and DNA may be prepared for other tests.

Metabolic Disease Screening

This consists of a series of chromatographic and spot tests designed to detect abnormalities in the types or concentrations of metabolites in body fluids. Urine and serum are usually submitted for initial studies. If screening reveals evidence of a metabolic defect, the abnormal metabolites are further evaluated, as appropriate, by gas/liquid chromatography, amino acid analysis, mass spectrometry, enzyme assay, or other laboratory methods.

Hematologic Evaluation

If the initial evaluation suggests an inherited hematologic defect, appropriate erythrocyte, platelet, leukocyte, and macrophage function tests are performed.

Other Biochemical Studies

Results of histologic studies and/or metabolic screening determine the additional studies required. Such examinations include studies of the concentrations of specific substrates in tissues and body fluids by gas/liquid chromatography and mass spectrometry, as well as assays of specific enzymes, receptors, and transporters.

Cytogenetic Studies

Currently these studies are confined to the dog and cat and include standard and Giemsa-banded karyotyping and fluorescence in situ hybridization (FISH). These studies are available only on a limited basis and are conducted when preliminary studies yield sufficient evidence to suspect a chromosomal anomaly or when the physical location of the disease gene locus is to be mapped.

Pedigree Analysis

When family data are available or family studies are possible, the center classifies the phenotype of family members and examines pedigree patterns for consistency with various modes of inheritance.

Breeding Studies

The center maintains an animal colony facility that can house a limited number of affected animals and their close relatives for breeding experiments designed to verify whether a defect is inheritable and to determine the mode of inheritance. These studies depend on whether affected animals and their relatives can be obtained as donations or purchased.

Fees for Diagnostic Services

There is no charge for initial consultation with veterinarians or other investigators in the center. Subsequent studies also are free of charge if considered appropriate by investigators at the center. When clinical and postmortem examinations are primarily in the interest of an animal's owner, the owner is charged, usually at a reduced rate.

Availability of Models to Investigators

Another objective of the center is to establish a small breeding colony for each promising model, but the center usually does not serve as a source of animals to be used directly in studies by outside investigators because of limited financial and physical resources. However, once initial characterization of the model is completed, with sufficient lead time breeding stock or semen can be made available to those who wish to start their own breeding colonies. Breeding stock or semen currently is available for various models.

Contact Information

University of Pennsylvania
School of Veterinary Medicine
3800 Spruce Street
Philadelphia, PA 19104-6051

Grant No.: P40 RR002512

Principal Investigator and Contact
Mark E. Haskins, V.M.D., Ph.D.
215-898-4852; Fax: 215-898-0719
E-mail: mhaskins@vet.upenn.edu

Resources for Complex Trait Analysis: Chromosome Substitution Strains

Research Emphasis/Objectives

Chromosome Substitution Strains (CSSs) are genetically engineered inbred strains with single chromosome substitutions. Not only are they identical to the host strain, except for the single chromosome being substituted in a homosomic state on an inbred genetic background, they are also uniquely made by transferring each chromosome from a donor strain to a host strain. For laboratory mice, the CSS panel consists of 22 strains: one for each of the 19 autosomes, one each for the X and Y chromosomes, and one for the mitochrondria.

Completion of the C57BL/6J-Chr#A/J (or B6-Chr#A/J) panel was reported by Singer et al. The parental strains, B6 (host) and A/J (donor) differ in a remarkable variety of traits (see the Phenome Project at www.jax.org). These CSSs are made available at the Jackson Laboratory or from program staff at CWRU.

These strains have many applications: 1) Genetic dissection of complex traits. The CSS panel can be surveyed to identify chromosomes that have at least one gene affecting the trait of interest. Crosses between a CSS and the host strain can be used to determine the number and location of genes on the substituted chromosome. Congenic strains derived from a CSS, which can be made in fewer generations than conventional methods, can also be used to establish gene number and location. Because of their unique nature, namely single chromosome substitutions on an inbred genetic background, more genes with weaker effects can be detected in fewer mice than is possible with any other method. 2) Gene discovery. In combination with congenic strains and crosses derived from the CSSs, together with other mouse genetic resources and the nearly complete genome sequences of the host and donor strains, CSSs are a powerful enabling resource to identify the genes that control complex traits. 3) Phenotype engineering. Complex traits are composed of various genetically controlled traits, each of which contributes to the overall phenotype. With CSSs, sub-phenotypes can be readily made into separate CSSs and congenic strains derived from CSSs for functional analysis. Inbred, genetically, and uniform strains are valuable for characterizing functional properties, pathogenic mechanisms, and treatment responses.

Contact Information

Department of Genetics
Case Western Reserve University
School of Medicine
10900 Euclid Avenue
Cleveland, OH 44106

Grant No.: P40 RR012305

Principal Investigator
Joseph H. Nadeau, Ph.D.
216-368-0581; Fax: 216-368-3832
E-mail: jhn4@case.edu

Co-investigator
Eric S. Lander, Ph.D.
617-252-1900; Fax: 617-252-1933
E-mail: lander@broad.wi.mit.edu

Additional Contact
Annie E. Hill
216-368-0626; Fax: 216-368-3432
E-mail: aeh2@pop.cwru.edu

Sea Urchin Genome Resource

Research Emphasis/Objectives

The Sea Urchin Genome Resource prepares and distributes high-density arrayed filters (macroarrays) containing large genomic and cDNA libraries from the sea urchin (Strongylocentrotus purpuratus) and comparable species. The cDNA libraries represent every stage of embryogenesis, several individual cell types, and various adult tissues. The genomic DNA in bacterial artificial chromosomes includes a range of species covering divergence times from 20 million to 540 million years. The resource also grows and ships individual library clones as identified and requested by users. The resource has developed robust protocols for hybridization on the macroarrays and analysis of the results. The majority of this information is posted on the Sea Urchin Genome Project Web site. The resource serves as part of a distributed system whose individual efforts make up a highly connected, useable whole genome resource. The resource acts as a portal to bring the accumulated experience of experimental developmental biology to bioinformaticists and to present the bioinformatics tools and databases of genomic sequence collections to the experimentalist.

Current Research

This resource is the sole provider of genomic materials for the whole genome sequencing effort, in addition to its service to the cell and developmental research community. The resource also will provide cDNA libraries to inform the annotation of the genome. The resource continues the development of algorithms and programs to analyze cis-regulatory sequences in the genome.

Services Provided

The collection of materials in the resource now includes more than 25 cDNA and genomic libraries. The cDNA libraries are all approximately 100,000 clones in size. They are stored in 384-well plates and double-spotted to facilitate identification of positive clones against hybridization background. Requests for macroarray filter sets can be submitted by e-mail to acameron@caltech.edu. Questions concerning use of the resource can also be directed to this address. The Cartwheel Web site provides entry and a suite of analysis program and the extensive computing resources behind them.

Contact Information

The California Institute of Technology
Division of Biology 156-29
1200 East California Boulevard
Pasadena, CA 91125 Web site: http://sugp.caltech.edu

Grant No.: P40 RR15044

Principal Investigator
Eric H. Davidson, Ph.D.
626-395-4937; Fax: 626-793-3047
E-mail: davidson@caltech.edu

Co-investigator and Contact
R. Andrew Cameron, Ph.D.
626-95-8421; Fax: 626-795-3382
E-mail: acameron@caltech.edu