Faculty Collaboration Database

High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Genome Res 2004 Apr;14(4):750-7

Date

04/03/2004

Pubmed ID

15060019

Pubmed Central ID

PMC383322

DOI

10.1101/gr.1968704

Scopus ID

2-s2.0-1842667858 (requires institutional sign-in at Scopus site)   32 Citations

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.

Author List

Kwitek AE, Gullings-Handley J, Yu J, Carlos DC, Orlebeke K, Nie J, Eckert J, Lemke A, Andrae JW, Bromberg S, Pasko D, Chen D, Scheetz TE, Casavant TL, Soares MB, Sheffield VC, Tonellato PJ, Jacob HJ

Author

Anne E. Kwitek PhD Professor in the Physiology department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Animals
Chromosome Mapping
Chromosomes
Crosses, Genetic
Databases, Genetic
Expressed Sequence Tags
Genes
Genetic Markers
Genome
Lod Score
Polymorphism, Genetic
Radiation Hybrid Mapping
Rats
Rats, Inbred ACI
Rats, Inbred BN
Rats, Inbred OLETF
Rats, Inbred SHR
Repetitive Sequences, Nucleic Acid
Sequence Tagged Sites