International Mammalian Genome Society

17th International Mouse Genome Conference

9-12 November 2003, Braunschweig, Germany


ORAL PRESENTATION

MONDAY 10 NOVEMBER
09:45 – 10:00 HRS

TOWARDS A SNP-BASED MOUSE HAPLOTYPE MAP

Pletcher M T
The Genomics Institute of the Novartis Research Foundation

Co-Authors: Batalov S, McClurg P, Barnes S W, Wiltshire T
Institutions: The Genomics Institute of the Novartis Research Foundation

Haplotype analysis, or determination of ancestral inheritance in chromosome evolution, has the potential to increase the speed and efficiency in which phenotypic traits are mapped in both humans and model organisms. A high-resolution haplotype map will allow for genome-wide in silico QTL analysis in mice. To this end, we have previously assembled a haplotype map of 6 common inbred strains of mice based on sample sequencing of loci relatively evenly spaced across the genome. This type of map produced haplotype blocks with a resolution of approximately + 2 Megabases. To increase the scope and precision of this map, we are currently genotyping the 48 designated mouse strains of the JAX Phenome Project with 10,000 SNP-based markers. Currently, we have 5000+ markers typed for these DNAs, giving a dense set of markers for any strain-pair mapping combinations. Despite the limitations of the biallelic nature of the SNP markers, this preliminary data has provided insights into the breeding lineage of these mice as well as indicating that the sources of genetic diversity seen in these mice is somewhat different than commonly assumed. A complete haplotype map will require a higher density of markers but this set will provide sufficient data to identify some associations with small physical map regions for many of the Phenome Project phenotypes as well as suggest the best mapping pairs to use for further refining these loci. Algorithms are currently being developed in association with this effort to be able to identify this genotype – phenotype interactions.


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