Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse

Lindblad-Toh, K., Winchester, E., Daly, M. J., Wang, D. G., Hirschhorn, J. N., Laviolette, J. P., Ardlie, K., Reich, D. E., Robinson, E., Sklar, P., Shah, N., Thomas, D., Fan, J. B., Gingeras, T. R., Warrington, J., Patil, N., Hudson, T. J., Lander, E. S. (2000) Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse. Nature Genetics, 24 (4). pp. 381-386. ISSN 10614036 (ISSN)

DOI: 10.1038/74215


Single-nucleotide polymorphisms (SNPs) have been the focus of much attention in human genetics because they are extremely abundant and well- suited for automated large-scale genotyping. Human SNPs, however, are less informative than other types of genetic markers (such as simple-sequence length polymorphisms or microsatellites) and thus more loci are required for mapping traits. SNPs offer similar advantages for experimental genetic organisms such as the mouse, but they entail no loss of informativeness because bi-allelic markers are fully informative in analysing crosses between inbred strains. Here we report a large-scale analysis of SNPs in the mouse genome. We characterized the rate of nucleotide polymorphism in eight mouse strains and identified a collection of 2,848 SNPs located in 1,755 sequence- tagged sites (STSs) using high-density oligonucleotide arrays. Three-quarters of these SNPs have been mapped on the mouse genome, providing a first- generation SNP map of the mouse. We have also developed a multiplex genotyping procedure by which a genome scan can be performed with only six genotyping reactions per animal.

Item Type: Paper
Uncontrolled Keywords: DNA microarray gene locus gene mapping gene mutation genetic screening genome genotype mouse nonhuman priority journal single nucleotide polymorphism Animals CpG Islands Gene Frequency Mice Mice Inbred Strains Oligonucleotide Array Sequence Analysis Phylogeny Physical Chromosome Mapping Point Mutation Polymorphism Genetic Sequence Tagged Sites Animalia Rodentia
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > SNP
CSHL Authors:
Communities: CSHL labs > Gingeras lab
Depositing User: CSHL Librarian
Date: 2000
Date Deposited: 13 Mar 2012 14:58
Last Modified: 27 Mar 2014 20:27
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