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Comparative Study
. 2004 Apr;14(4):750-7.
doi: 10.1101/gr.1968704.

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  1 , 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
Affiliations
Comparative Study

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 et al. Genome Res. 2004 Apr.

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.

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Figures

Figure 1
Figure 1
Placement map integration algorithm. Placement maps resulting from incremental LOD thresholds between 8 and 15 were aligned. The framework bins for all maps were normalized to that of the LOD 15 map so that the bin sizes were identical across maps (left panel). The position of markers placed within the bins on all maps were accordingly adjusted to be proportional to the normalized bin size (middle panel). The normalized position from the map with the highest LOD threshold for each marker was added to the integrated map, with markers placing upstream of the first framework designated as a negative distance from that framework marker (middle panel, integrated). Finally, the absolute positions of the markers were determined with the first placed marker at 0 cR (right panel, final integrated).
Figure 2
Figure 2
Screenshot from VCMapView (http://rgd.mcw.edu/VCMAP/mapview.shtml) showing visual alignment between genetic maps (SHRSP × BN), RH map (Version 3.4), and rat genome assembly (Release 3.1) for RNO17. Lines between the maps indicate common STSs between the maps. Please see Twigger et al. 2004, for details on the VCMapView visualization.
See this image and copyright information in PMC

References

    1. Altschul, S., Gish, W., Miller, W., Myers, E., and Lipman, D. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410. - PubMed
    1. Bihoreau, M., Sebag-Montefiore, L., Godfrey, R., Wallis, R., Brown, J., Danoy, P., Collins, S., Rouhard, M., Kaisaki, P., Lathrop, M., et al. 2001. A high-resolution consensus linkage map of the rat, integrating radiation hybrid and genetic maps. Genomics 75: 57-69. - PubMed
    1. Chowdhary, B., Raudsepp, T., Kata, S., Goh, G., Millon, L., Allan, V., Piumi, F., Guerin, G., Swinburne, J., Binns, M., et al. 2003. The first-generation whole-genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Res. 13: 742-751. - PMC - PubMed
    1. Cox, D.R., Burmeister, M., Priece, E.R., Kim, S., and Myers, R.M. 1990. Radiation hybrid mapping: A somatic cell genetic method for constructing high-resolution maps of mammalian chromosomes. Science 250: 245-250. - PubMed
    1. Dobbins, D., Joe, B., Hashiramoto, A., Salstrom, J., Dracheva, S., Ge, L., Wilder, R., and Remmers, E. 2002. 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 mapping. J. Bone Miner. Res. 17: 1761-1767. - PubMed

WEB SITE REFERENCES

    1. http://corba.ebi.ac.uk/RHdb/; a repository of radiation hybrid vector data.
    1. http://rgd.mcw.edu/VCMAP/mapview.shtml; a tool at the Rat Genome Database for dynamic integration of various genome maps (genetic, RH, genome, QTL) and cross-species comparative maps between rat, human, and mouse.
    1. http://rgd.mcw.edu/pub/rhmap/3.4; ftp site to obtain vector and map information for the rat v3.4 RH maps.
    1. http://rgd.mcw.edu/pub/publications/1999/steen_genome_research/; ftp site to obtain reference rat genetic maps and our previous version of the rat RH maps as published in Steen et al. 1999.
    1. http://genome.cse.ucsc.edu/cgi-bin/hgGateway; Genome browser at the University of California at Santa Cruz providing sequence and annotation of the rat genomic sequence assemblies.

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