Overview

We have developed several tools for the analysis of mouse genetics and genomics datasets. Thee tools and the webservers which display the results of analysis with these tools are available to the scientific community.

Mouse Resources:

• EMMA Efficient Mixed Model Association. Software package for mouse association studies which corrects for population structure.
• EMMA Server Efficient Mixed Model Association Webserver. Webserver for analysis of mouse association studies using EMMA software. Users can upload their phenotype data and the server will perform whole genome association using the phenotypes.
• EMMA Study Design Model Organism Association Study Design. Software package for calculating power of model organism association study designs.
• EMMA Study Design Server Mouse Association Study Design Webserver. Webserver for calculating power of mouse association study designs. Users can upload the study designes and the server will perform simulations to compute statistical power and significance thresholds of a proposed study.
• Mouse Phenome Association Database Database containing results of genome wide association studies using publicly available data from the JAX Mouse Phenome Project.
• Mouse HapMap Genetic maps for 94 inbred strains of mouse and imputed genotypes using the NIEHS/Perlegen resequencing resource.
• Mouse Ancestry Browser A visualization of Mouse Ancestry Assignment using NIEHS/Perlegen resequencing resource.
• Mouse Haplotype Block Viewer A visualization of Mouse Haplotype Blocks using the NIEHS/Perlegen resequencing resource.
• Mouse Genome-wide Association Mapping Server A webserver for performing genome wide association from submitted phenotypes.

About the Mouse HapMap

The Mouse HapMap aims to create a genome-wide haplotype map in all commonly used inbred lab strains of mice in order to enable efficient positional cloning and genotype-phenotype correlation studies. Recent data has established that the genomes of commonly used inbred lab mice, the primary mammalian model system, are simple mosaics of long segments from a limited number of distinct subspecies of Mus musculus. By providing a more complete catalog of variation patterns in each modern strain and their origins, the map will allow the use of QTL mapping data from many crosses simultaneously, as well as strain phenotype data, to accelerate the fine mapping and identification of genes responsible for medically relevant phenotypes.

About the NIEHS/Perlegen Mouse Resequencing Data

The National Institute of Environmental Health Sciences (NIEHS) contracted with Perlegen Sciences, Inc. to identify DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice (N01-ES-45530). Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2).