1. Mapping

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

9. Genetic Mapping

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

12. Restriction Mapping BglII BamHI PstI BglII +BamHI BglII +PstI BamHI +PstI 4.2 5.2 3.6 3.5 3.3 2.6 1.7 1.7 1.4 1.4 1.2 1.2 1.0 1.0 1.2 0.7 0.9 0.5 0.3 0.3 0.3 BglII BamHI PstI BglII PstI 0.3 0.7 2.6 0.9 0.5 1.2

15. Cytogenetic Mapping Cytogenetic mapping refers to observing a map location in reference to a chromosomal banding pattern.

16. Cytogenetic Mapping These methods allow a rough determination of location, but to not yield a direct measure of distance.

17. Cytogenetic Mapping

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

23. Radiation Hybrid Mapping

26. Summary of Mapping Strategies

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

31. Comparative Mapping Examples RNO18 MMU18 300 600 900 1200 0 100 200 300 400

32. Comparative Mapping Examples } HSA11 400 500 600 700 } { 100 200 300 RNO4 HSA7 } { { } } { } HSA7p 0 RNO5 { RNO12 { RNO12 { } HSA4

33. Resources Genome browsers http://genome.ucsc.edu/goldenPath/hgTracks.html http://www.ensembl.org http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search GeneMap99 http://www.ncbi.nlm.nih.gov/genemap99