International Mammalian Genome Society

logo18th International Mouse Genome Conference

17-22 October 2004, Seattle, USA


POSTER 105 - INTEGRATING MOUSE SNPS INTO MGI: PLANS, PROGRESS, AND PROTOTYPES

Richardson JE, Blake JA, Bult CJ, Eppig JT, Kadin JA, King BL, Ringwald M

The Jackson Laboratory, Bar Harbor, United States

Strain polymorphisms have always been an important resource for biological analysis. Until recently, polymorphisms, e.g. RFLPs and SSLPs, have been used primarily as mapping landmarks. New technology for large-scale detection of single nucleotide, multiple nucleotide, and deletion/insertion polymorphisms (SNPs, MNPs, and DIPs, respectively) offers the potential to correlate phenotypic differences directly to base-changes in the DNA. Large data sets offering dense coverage across the genome are already available, as are public repositories of these data, e.g., dbSNP.

MGI (http://www.informatics.jax.org/ ) adds value to data by integration, both within and across data domains, and by offering the integrated resource for query, display, and download. The database has always included polymorphism data, e.g. RFLPs and SSLPs. We now plan to integrate mouse SNP data and to provide interfaces that exploit this integration. For example, a user will be able to query for SNPs mapping (within a specified bp range) near genes (mapped to the genome assembly sequence) known to be involved in DNA repair (via GO annotations), where those genes occur within any QTL region for radiation induced apoptosis (e.g., Rapop1, et.al.,  based on the MGD genetic map).

We will describe our plans for integrating SNP data into MGI, including planned data and initial data sets, integration strategy, and Web interface mockups, including query forms, result summary pages, SNP data pages, and other related pages, such as gene details. We will also describe an operational prototype tool, PLAD ( http://proto.informatics.jax.org/prototypes/plad/), which demonstrates the kind of positional candidate analysis expressed by the above example query.

MGI is supported by NIH Grants HG00330,  HD33745, and HG002273.

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