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Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins - Baxevanis A.D.

Baxevanis A.D. Bioinformatics. A Practical Guide to the Analysis of Genes and Proteins - New York, 2001. - 493 p.
ISBN 0-471-22392-1
Download (direct link): bioinformaticsapractic2001.pdf
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132
GENOMIC MAPPING AND MAPPING DATABASES
purchase from Research Genetics. Three high-resolution genome-wide maps have been constructed using these panels, each primarily utilizing EST markers. Mapping servers for each of the three human RH panels are available on-line to allow users to place their own markers on these maps. RH score data are deposited to, and publicly available from, The Radiation Hybrid Database (RHdb). Although this section covers RH mapping in humans, many RH mapping efforts are also underway in other species. More information regarding RH resources in all species are available at The Radiation Hybrid Mapping Information Web site.
In general, lower-resolution panels are most useful for more widely spaced markers over longer chromosomal regions, whereas higher-resolution panels are best for localizing very densely spaced markers over small regions. The lowest-resolution human RH panel is the Genebridge4 (GB4) panel (Gyapay et al., 1996). This panel contains 93 hybrids that were exposed to 3000 rads of irradiation. The maximum map resolution attainable by GB4 is 800-1,200 kb. An intermediate level panel was produced at the Stanford Human Genome Center (Stewart et al., 1997). The Stanford Generation 3 (G3) panel contains 83 hybrids exposed to 10,000 rads of irradiation. This panel can localize markers as close as 300-600 kb apart. The highest resolution panel (‘‘The Next Generation,’’ or TNG) was also developed at Stanford (Beasley et al., 1997). The TNG panel has 90 hybrids exposed to 50,000 rads of irradiation and can localize markers as close as 50-100 kb.
The Whitehead Institute/MIT Center for Genome Research constructed a map with approximately 6,000 markers using the GB4 panel (Hudson et al., 1995). Framework markers on this map were localized with odds >300:1, yielding a resolution of approximately 2.3 Mb between framework markers. Additional markers are localized to broader map intervals. A mapping server is provided for placing markers (scored in the GB4 panel) relative to the MIT maps.
The Stanford group has constructed a genome-wide map using the G3 RH panel (Stewart et al., 1997). This map contains 10,478 markers with an average resolution of 500 kb. Markers localized with odds = 1,000:1 are used to define ‘‘high-confidence bins,’’ and additional markers are placed into these bins with lower odds. A mapping server is provided for placing markers scored in the G3 panel onto the SHGC G3 maps.
A fourth RH map has been constructed using both the G3 and GB4 panels. This combined map, the Transcript Map of the Human Genome (GeneMap ’99; Fig. 6.4), was produced by the RH Consortium, an international collaboration between several groups (Deloukas et al., 1998). This map contains over 30,000 ESTs localized against a common framework of approximately 1,100 polymorphic Genethon markers. The markers were localized to the framework using the GB4 RH panel, the G3 panel, or both. The map includes the majority of human genes with known function. Most markers on the map represent transcribed sequences with unknown function. The order of the framework markers is well supported, but most ESTs are mapped relative to the framework with odds <1,000:1. The majority of markers on the GeneMap have a lod score <2.0, and many are <1.0. Such markers are localized with relatively low support for local order, and their map positions should be confirmed by other means if critical. A mapping server for placing markers on GeneMap ’99 is available at the Sanger Centre.
The Radiation Hybrid Database (RHdb) is the central repository for all RH data. It is maintained at the European Bioinformatics Institute (EBI) in Cambridge, UK (Rodriguez-Tome and Lijnzaad, 2000). RHdb is a sophisticated Web- and FTP-based
MAPPING PROJECTS AND ASSOCIATED RESOURCES
133
Netscape: GM98: Chr 22
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Chromosome 22: pTEL-D22S420
RHMap Genetic One О94 Q3 Map Densty
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| See also: equivalent interval on G3 map
About Ttrrt interval
Top of interval: chr22_pTEL(O.OcM) Bottom of interval: D22S420 (0.0 cM) Genetic size of bin: OcM Physical size of bin: lScRwx
TELOMERE
0.00 P>3.00 T52917 EST
1.04 P019 stSG22362 ESTs
1.15 P0.16 A005T29 BCR breakpoint cluster region
1.50 P>3.00 R41599 COMT catechol-O-methyi transferase
263 P0.07 SGC31622 SLC20A3 solute carrier family 20 (mitochondrial citr..
3.53 P>3.00 sts-T79756 ESTs
4.54 P0.74 WI-22519 ARVCF armadillo repeat gene deletes in velocardiof..
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