Comparative Mouse Genomics Centers Consortium: The Mouse Genotype Database

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Abstract

The Comparative Mouse Genomics Centers Consortium (CMGCC) is a branch of the Environmental Genome Project sponsored by the National Institute of Environmental Health Sciences (NIEHS) focusing upon the identification of human single nucleotide polymorphisms (SNPs) that may confer disease susceptibility within the human population. The goal of the CMGCC (http://www.niehs.nih.gov/cmgcc/) is to make genetic mouse models for human SNPs within cell cycle control, DNA replication and DNA repair genes that may be associated with human pathologies. In order to facilitate information sharing and analysis within the consortium a set of informatics resources have been generated to support the mouse model development efforts. The primary entry point for information about the mouse models developed by the consortium is through the CMGCC Genotype Database (http://mrages.niehs.nih.gov/genotype/), which maintains both a consortium specific and public access display of the available and developing mouse models.

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Background

The completion of the human genome project has ushered in the next era of genetic exploration—the role of variability in genetics within the human population. The primary form of genetic variation between individuals is single base changes in the DNA, known as single nucleotide polymorphisms (SNPs). SNPs may account for up to 90% of the genetic variability observed between individuals [1], and are linked with heritable forms of disease prevalence ranging from cancer to Alzheimer's disease [2].

Overview

The CMGCC Genotype Database has two levels of access: secure (for consortium members and affiliates) and open (intended for public browsing). The secure and open views of the database both maintain web-based front-ends. The secure version of the database is intended for collecting and sharing data between groups that intend to work with the specific mouse models. Consequently, the secure front-end to the database allows workflow based storage of information intended to track and share

Discussion and utility

The goal of the CGD is to provide an information conduit for the scientific community about the mouse models developed by the CMGCC, and to facilitate data storage and sharing within the consortium. One aspect of the information sharing promoted by the CGD is the integration of biological data from both CMGCC informatics teams and other public bioinformatics resources. The unified CMGCC informatics tools are referred to as the Mouse Federated Database (MFD) system. The MFD is a

Conclusions

The goal of the CMGCC is to develop mouse models based on human genetic variation which will spark future research within the broader scientific community. Hopefully, the CGD will contribute to communication and collaborations between consortium and non-consortium scientists interested in the role of SNPs within CMGCC target genes. As part of the EGP, the CMGCC is particularly interested in the role that polymorphic variants of human genes may play in the biological response to sensitive

Acknowledgements

Many thanks to members of the CMGCC supported by U01ES11045 (Ladiges, PI) for their thoughtful input into the CGD. Brent Calder and John David Garza at UTHSCSA were of invaluable assistance in the development of this resource. Jerry Niehls, Larry Hall and F.O. Finch within the infrastructure support team at NIEHS were also invaluable in implementing this work. Further, the input of Jan Vijg and Bruce Aronow were extremely helpful at various points during the CGD development.

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