High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence

Anne E Kwitek; Jo Gullings-Handley; Jiaming Yu; Danilo C Carlos; Kimberly Orlebeke; Jeff Nie; Jeffrey Eckert; Angela Lemke; Jaime Wendt Andrae; Susan Bromberg; Dean Pasko; Dan Chen; Todd E Scheetz; Thomas L Casavant; M Bento Soares; Val C Sheffield; Peter J Tonellato; Howard J Jacob

doi:10.1101/gr.1968704

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High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence

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High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence

Anne E Kwitek, Jo Gullings-Handley, Jiaming Yu, Danilo C Carlos, Kimberly Orlebeke, Jeff Nie, Jeffrey Eckert, Angela Lemke, Jaime Wendt Andrae, Susan Bromberg, …

Genome research, Vol.14(4), pp.750-757

04/2004

DOI: 10.1101/gr.1968704

PMCID: PMC383322

PMID: 15060019

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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.

Rats, Inbred SHR

Databases, Genetic

Genes - genetics

Rats

Lod Score

Rats, Inbred ACI

Rats, Inbred BN

Rats, Inbred OLETF

Animals

Chromosomes - genetics

Chromosome Mapping - methods

Genetic Markers - genetics

Repetitive Sequences, Nucleic Acid

Polymorphism, Genetic - genetics

Radiation Hybrid Mapping - methods

Genetic Markers - physiology

Genome

Sequence Tagged Sites

Crosses, Genetic

Expressed Sequence Tags

Details

Title: Subtitle: High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence
Creators: Anne E Kwitek - Human & Molecular Genetics Center and Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA. akwitek@mcw.edu
Jo Gullings-Handley
Jiaming Yu
Danilo C Carlos
Kimberly Orlebeke
Jeff Nie
Jeffrey Eckert
Angela Lemke
Jaime Wendt Andrae
Susan Bromberg
Dean Pasko
Dan Chen
Todd E Scheetz
Thomas L Casavant
M Bento Soares
Val C Sheffield
Peter J Tonellato
Howard J Jacob
Resource Type: Journal article
Publication Details: Genome research, Vol.14(4), pp.750-757
DOI: 10.1101/gr.1968704
PMID: 15060019
PMCID: PMC383322
NLM abbreviation: Genome Res
ISSN: 1088-9051
eISSN: 1549-5469
Publisher: United States
Grant note: R01 HL64541 / NHLBI NIH HHS R01 HL064541 / NHLBI NIH HHS R01 HL59789 / NHLBI NIH HHS R01 HL59826 / NHLBI NIH HHS
Language: English
Date published: 04/2004
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Medical Genetics and Genomics; Ophthalmology and Visual Sciences
Record Identifier: 9983979991702771

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