High-Density Rat Radiation Hybrid Maps Containing Over 24,000 SSLPs, Genes, and ESTs Provide a Direct Link to the Rat Genome Sequence
Open Access
- 1 April 2004
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in Genome Research
- Vol. 14 (4) , 750-757
- https://doi.org/10.1101/gr.1968704
Abstract
The laboratory rat is a major model organism for systems biology. To complement the cornucopia of physiological and pharmacological data generated in the rat, a large genomic toolset has been developed, culminating in the release of the rat draft genome sequence. The rat draft sequence used a variety of assembly packages, as well as data from the Radiation Hybrid (RH) map of the rat as part of their validation. As part of the Rat Genome Project, we have been building a high-density RH map to facilitate data integration from multiple maps and now to help validate the genome assembly. By incorporating vectors from our lab and several other labs, we have doubled the number of simple sequence length polymorphisms (SSLPs), genes, expressed sequence tags (ESTs), and sequence-tagged sites (STSs) compared to any other genome-wide rat map, a total of 24,437 elements. During the process, we also identified a novel approach for integrating the RH placement results from multiple maps. This new integrated RH map contains approximately 10 RH-mapped elements per Mb on the genome assembly, enabling the RH maps to serve as a scaffold for a variety of data visualization tools.Keywords
This publication has 22 references indexed in Scilit:
- Integrative Genomics: In Silico Coupling of Rat Physiology and Complex Traits With Mouse and Human DataGenome Research, 2004
- Genome sequence of the Brown Norway rat yields insights into mammalian evolutionNature, 2004
- Localization of the Mutation Responsible for Osteopetrosis in the op Rat to a 1.5-cM Genetic Interval on Rat Chromosome 10: Identification of Positional Candidate Genes by Radiation Hybrid MappingJournal of Bone and Mineral Research, 2002
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- Rat genetics: attachign physiology and pharmacology to the genomeNature Reviews Genetics, 2002
- A High-Resolution Consensus Linkage Map of the Rat, Integrating Radiation Hybrid and Genetic MapsGenomics, 2001
- High-Throughput Scanning of the Rat Genome Using Interspersed Repetitive Sequence-PCR MarkersGenomics, 2000
- Radiation Hybrid Mapping: A Somatic Cell Genetic Method for Constructing High-Resolution Maps of Mammalian ChromosomesScience, 1990
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990
- Basic local alignment search toolJournal of Molecular Biology, 1990