1. 1 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 Radiation Hybrid (RH) Mapping

2. 2 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. Genomic Mapping Two Major Types of Genomic Maps : Genetic maps. Physical maps. 1

3. 3 Physical Maps 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. Low resolution High resolution 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. Radiation Hybrid (RH) map - the order of DNA markers (STS), each appearing uniquely in the genome. 2

4. 4 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 Cytogenetic Map - A Low Resolution Map 3

5. 5 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). Physical Maps (Contig Maps) contig assembly clones contig (contiguous array) 4

6. 6 http://opbs.okstate.edu/~melcher/MG/MGW1/MG11124.html 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. 5

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

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

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

10. 10 Marker Retention Patterns Experiment output: An n-by-m matrix, indicating which marker is retained in which hybrid cell. 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. 9

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

12. 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. 13 RH Computational Task Intuition: Close-by markers will be retained or lost together. Far away markers retained or lost independently. 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. Input: n-by-m 0/1 matrix (one row per marker). Desired Output: Ordered markers (a permutation on {1,2,…,n}) 12

14. 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: 1.Nonparametric: Minimum obligate chromosome break (MOB), a problem of combinatorial nature. 2. Parametric: Maximum likelihood estimation (MLE), a problem of statistical nature. 13

15. 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: 1.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. 3.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. 16 RHO Output 15

17. 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. 18 Other Example: 17 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.

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

20. 20 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. Radiation Hybrid Database http://www.ncbi.nlm.nih.gov/dbEST/ 19

21. 21 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 ? 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 20

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

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