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Computational Genomics Course Lecture 12 fall 2002/03 School of Computer Science

Radiation Hybrid (RH) Mapping. Computational Genomics Course Lecture 12 fall 2002/03 School of Computer Science Tel-Aviv University Instructor: Benny Chor Many slides taken (with permission…) from Metsada Pasmanik-Chor. Genomic Mapping.

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Computational Genomics Course Lecture 12 fall 2002/03 School of Computer Science

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  1. Radiation Hybrid (RH) Mapping Computational Genomics Course Lecture 12 fall 2002/03 School of Computer Science Tel-Aviv University Instructor: Benny Chor Many slides taken (with permission…) from Metsada Pasmanik-Chor

  2. Genomic Mapping A map - graphic representation that provides information about the location of sites and the spacing between them. Maps for the genome provide the relative order of items (“markers”) along the chromosome. • Two Major Types of • GenomicMaps : • Genetic maps. • Physical maps. 1

  3. Physical Maps Low resolution Cytogenetic (chromosome) map - based on the distinctive banding patterns observed by light microscope of stained chromosomes. cDNA map -locations of expressed DNA (exon regions) on the chromosome. Radiation Hybrid (RH) map - the order of DNA markers (STS), each appearing uniquely in the genome. Contig (cosmid) map - the order of overlapping DNA fragments spanning the genome. Restriction map - describes the order and distance between DNA enzyme cleavage sites. Sequence “map” - complete sequencing of a chromosome. High resolution 2

  4. Cytogenetic Map - A Low Resolution Map Looking directly at chromosomes, using the technique of Fluorescence In-Situ Hybridization (FISH). Metaphase chromosome spreads For FISH demo look at: http://www.waisman.wisc.edu/cytogenetics/procedures/FISH/FISHmethod.html 3

  5. Physical Maps (Contig Maps) Physical maps are a set of ordered DNA clones that cover the complete chromosome. These clones overlap each other to form a contiguous array (contig). clones contig (contiguous array) contig assembly 4

  6. RFLP - Genetic Markers Creating Genetic Maps of Chromosomes. A change of a single nucleotide may produce RFLP (restriction fragment length polymorphism), by changing locations of restriction enzyme recognition site. http://opbs.okstate.edu/~melcher/MG/MGW1/MG11124.html 5

  7. Physical Maps The ultimate physical map is the complete sequence of a chromosome. 6

  8. Radiation Hybrid (RH) Mapping A somatic cell technique that is used for ordering markers along a chromosome and estimating the physical distances between them. Markersare genomic sequences of length approx. 200bp, appearinguniquelyon the human genome. Markers’ locations and relative order isunknowna-priory, but should become known after the RH experiments. Analyzing the experimental data is a challenging and demanding computational task. 7

  9. Donor cells (haploid or diploid) are irradiated, and chromosomes breaks at random locations. Radiation Hybrid (RH) Mapping The irradiated cells are fused with non-radiated rodent cells. Hybrids are formed. 8 http://www1.genetics.wisc.edu/466/fall99/lect13/sld011.htm

  10. Marker Retention Patterns Approx. n ~ 100 “hybrids” are used for mapping m ~ 150 markers on one chromosome. The resulting cells are screened for the presence or absence of the markers. Experiment output: Ann-by-mmatrix, indicating which marker is retained in which hybrid cell. 9

  11. Radiation Hybrid (RH) Mapping Input Example data for radiation hybrid mapping: Markers: + (1) presence - (0) absence 10

  12. RH Pannels & Hamming Distances V = 10100110001 U = 10010001000 W = 01101110111 U, V, W are three RH panels (binary vectors) of length 11. The Hamming distance between V and U is 6. The Hamming distance between U and W is 11. 11

  13. RH Computational Task Input: n-by-m 0/1matrix (one row per marker). Desired Output: Ordered markers (a permutation on {1,2,…,n}) • Intuition: Close-by markers will be retained or lost together. • Far away markers retainedorlostindependently. • The further apart two markers are, the more likely it is that radiation will break between them, resulting in two separate chromosomal fragments. • Viewing each marker as length m binary vector, Hamming distance between vectors is indicative of markers’ distance on chromosome. 12

  14. RHO - Radiation Hybrid Ordering Amir Ben-Dor, Benny Chor and Dan Pelleg, Dept. of Computer Science, Technion. http://www.cs.technion.ac.il/~benny/RHO.pdf • A software package that implements a number of heuristics • that attempt to order genomic markers along the chromosome, • given as input the results of an RH biological experiment. • The heuristics are based on formulating an appropriate • optimization problem, “reducing” RH to the traveling salesman • problem (TSP). • Two different optimization problems: • Nonparametric: Minimum obligate chromosome break (MOB), • a problem of “combinatorial nature”. • 2. Parametric: Maximum likelihood estimation (MLE), • a problem of “statistical nature”. 13

  15. RHO - Radiation Hybrid Ordering Amir Ben-Dor, Benny Chor and Dan Pelleg, Dept. of Computer Science, Technion. http://www.cs.technion.ac.il/~benny/RHO.pdf • TSP is obviously NPH, but its symmetric version is amenable to • very efficient hueristics. • Two hueristic approaches: • Simulated annealing: Finds a tour (upper bound), typically • fairly close to optimal (but how does one know that…?) • 2. Held-Karp: Finds a minimum spanning tree (lower bound). • By modifying the underlying graph, MST becomes more and • more like a path. • Comparing results of (1) and (2) we get a good estimate of • accuracy of solution. If both are same, this proves • optimality of solution ! 14

  16. RHO Output 15

  17. RHO Results Chromosome 1 analysis: There are 132 markers and 93 hybrids. Results for the Maximum Likelihood estimation method: Whitehead Institute data vs RHO 16

  18. Other Example: In this example, RHO ordered each of the two “arms” of the chromosome in accordance with the original order. However, the first “arm” was reversed. This phenomena is fairly common, probably indicating that retention on one side of the centromer is independent of retention on the other side. 17

  19. Comparison of Genetic Map and RH Map of Chromosome 8q24 Common sites Genetic map RH map 18 Adapted from: Lewis et al., 1995

  20. Radiation Hybrid Database http://corba.ebi.ac.uk:80/RHdb/index.html Release 19.0 - 22 January 2001. This release contains: 133239 RH entries (106574 different STSs), 92 maps, 15 Panels, 229 experimental conditions and 3 species. http://www.ncbi.nlm.nih.gov/dbEST/ 19

  21. NCBI Map Viewer - A Tool for Integrating Genetic and Physical Maps http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search?chr=hum_chr.inf&query • Map Viewer: A tool for visualizing whole genomes or single chromosomes. • Where does a particular gene exist within an organism's • genome ? • Which genes are located on a particular chromosome • and in what order ? • Other links from Entrez, for a gene that exists in a • particular chromosomal region ? • What is the distance between genes ? 20

  22. NCBI Map View http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=hum_chr.inf&query Scale on chromosome 21

  23. NCBI Map View Scale on chromosome See also Map View at: http://genome.ucsc.edu/ 22

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