5. Genetic Mapping Requires informative markers -- polymorphic and a population with known relationships Best if a measured between “close” markers. Unit of distance in genetic maps = centimorgans, cM 1 cM = 1% chance of recombination between markers
6. Genetic Mapping A 2 B 2 A 2 B 2 A 2 B 2 A 2 B 2 A 2 B 2 A 2 B 2 A 2 B 2 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 1 A 1 B 2 A 2 B 1 A 1 B 2 A 2 B 1 NR NR NR NR NR R R = # recombinant / # total = 2/7 = 0.286
7. Genetic Mapping Theta calculation with inbred population… bn det+ det+ bn bn+ det det bn+ bn det+ det bn+ bn det det bn bn+ det det bn bn det+ det bn bn det det bn bn+ det+ det bn banded detached banded, detached wild-type 483 512 2 3 x x = # recombinant # total = 5/1000 = 0.005
11. Restriction Mapping Restriction maps show the relative location of a selection of restriction sites along linear or circular DNA. HindIII BamHI PstII PstII BamHI HindIII EcoRI
19. Somatic Hybrid Mapping Probe1 Probe2 Probe3 1 2 3 4 5 Chromosome 0 1 1 1 1 1 1 1 1 0 0 0 0 0 0 Probe1 -- maps to chromosome 2 Probe2 -- maps to chromosomes 3 and 4 -- possible paralogs, pseudogene, or low-copy repeat Probe3 -- maps to all chromosomes -- possible high-copy repeat or ribosomal genes
20. Somatic Hybrid Mapping A subset of the data used to map the Blood Coagulating Factor III to human chromosome 1.
21. Somatic Hybrid Mapping Finer mapping (higher resolution) can be obtained if hybrids are present in the panel that contain partial chromosomes. (E.g., translocations) Such a strategy is expensive, because numerous hybrids have to be screened to identify hybrids containing the partially retained chromosomes. A more cost-effective and high-resolution alternative is Radiation Hybrid Mapping.
22. Radiation Hybrid Mapping Radiation hybrid mapping is a method for high-resolution mapping. Exploits the ability of rodent cells (hamster cells) to stably incorporate genetic material from fused cells. Pro: Resolution is “tunable”, relatively cheap Con: Difficult to compare results from different groups
27. Comparative Mapping Can be very useful in utilizing animal models of human disease, and also in exploring the causes of complex diseases. Comparing gene content, localization and ordering among multiple species.
28. Comparative Mapping Sources of Information sequence mapping BLAST potential orthologs colocalization sequence mapping Putative orthologs and syntenic segments
The construction of comparative maps requires the analysis of data from multiple locations. As I mentioned previously, the current version was created only using RH mapping information. The mapping resources used include GeneMap99 from NCBI, which contains 42,000 mapped human ESTs and 12,500 mapped human genes, 2) the recent releases from the Mouse RH Consortium, which currently have approximately 3000 mouse genes and ESTs on their placement maps, and 3) the rat EST placement maps that we have created at the UI. In addition to the mapping information, these sources are also used to identify the underlying sequences that were mapped, which were necessary to the map construction.
The construction of comparative maps requires the analysis of data from multiple locations. As I mentioned previously, the current version was created only using RH mapping information. The mapping resources used include GeneMap99 from NCBI, which contains 42,000 mapped human ESTs and 12,500 mapped human genes, 2) the recent releases from the Mouse RH Consortium, which currently have approximately 3000 mouse genes and ESTs on their placement maps, and 3) the rat EST placement maps that we have created at the UI. In addition to the mapping information, these sources are also used to identify the underlying sequences that were mapped, which were necessary to the map construction.
Currently, we have developed a initial draft of human-rat and mouse-rat comparative maps using only radiation hybrid data. As a baseline for comparison, the initial comparative maps between human, mouse and rat were developed using approximately 500 previously identified orthologs. From the 8800 placed ESTs on the UIowa maps, over 1000 had significant hits to mouse genes, and more than 7500 had significant blast hits to either human ESTs or the non-redundant nucleotide database. In all there are over 2000 mapped rat ESTs in the preliminary human-rat comparative map, and over 500 mapped rat ESTs in the preliminary mouse-rat comparative map.
To begin, I’m going to give two examples - each of which is a portion of a comparative map that we have created. The first, shown here between Rat Chr 18 and Mouse Chr 18, illustrates the high amount of conservation between the rat and the mouse. To a large extent, the portion of Mouse Chr 18 is conserved in the rat, with an apparent deletion of the region from 300 to 850 cR in the mouse map.
A more complex example is shown here between portions of Rat Chr 4 and Human Chr7. Here you can see the numerous rearranges that have occurred during the evolution of the rat and human. Note that in addition to multiple conserved segments to human Chr 7, there are also segments on rat Chr 4 to Human Chr 11 and to a distinct region of Human Chr7 about 300 cR away. Similarly, the human chromosome 7 shows a few small conserved segements to Rat Chr’s 12 and 5 within the overall segment with Rat Chr 4.
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