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Genetic variation in coding regions between and within commonly used inbred rat strains
Bart M G Smits1, Bert F M van Zutphen, Ronald H A Plasterk
1Hubrecht Laboratory, The Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
Genome Research
|July 3, 2004
Summary
Researchers identified novel genetic variations called single nucleotide polymorphisms (SNPs) in commonly used rat strains. These SNPs can help understand disease links and genetic mapping in mammals.
Area of Science:
- Genetics
- Genomics
- Molecular Biology
Background:
- Single nucleotide polymorphisms (SNPs) represent the most prevalent form of genetic variation in mammalian populations.
- SNPs hold significant potential for understanding common diseases and for applications in genetic association and mapping studies.
Purpose of the Study:
- To investigate the genetic variation among commonly used inbred rat strains.
- To discover and genotype novel single nucleotide polymorphisms (SNPs) in genes relevant to human diseases.
Main Methods:
- Utilized an efficient SNP discovery and typing assay based on enzyme-based (CEL I) heteroduplex cleavage.
- Screened 96 rat (sub-)strains across 100 genomic loci in 55 genes, including homologs of human disease genes (neurological disorder, cancer, schizophrenia, obesity).
Main Results:
- Identified 103 novel polymorphisms, including 17 non-synonymous SNPs with potential effects on protein function.
- Observed significant genetic variation between colonies of the same inbred strain housed in different locations.
- Estimated genetic variation both between and within commonly used rat inbred strains.
Conclusions:
- The study highlights substantial genetic diversity within and between laboratory rat strains, including variations within supposedly identical strains.
- Identified non-synonymous SNPs offer potential explanations for phenotypic differences observed in laboratory rat strains.
- The findings provide valuable genetic resources for future research in areas such as disease modeling and genetic association studies in mammals.