Download Radiation Hybrid (RH) mapping

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
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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
Genomic Maps :
• Genetic maps.
• Physical maps.
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Low resolution
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.
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
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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:
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http://www.waisman.wisc.edu/cytogenetics/procedures/FISH/FISHmethod.html
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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
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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
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Physical Maps
The ultimate physical
map is the
complete sequence
of a chromosome.
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Radiation Hybrid (RH) Mapping
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.
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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.
http://www1.genetics.wisc.edu/466/fall99/lect13/sld011.htm
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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:
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An n-by-m matrix, indicating which marker is retained in which hybrid cell.
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Radiation Hybrid (RH) Mapping Input
Example data for radiation hybrid mapping:
Markers:
+ (1) presence
- (0) absence
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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.
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RH Computational Task
Input: n-by-m 0/1 matrix (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 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.
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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),
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a problem of “statistical nature”.
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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
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optimality of solution !
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RHO Output
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RHO Results
Chromosome 1 analysis:
There are 132 markers and 93 hybrids.
Results for the Maximum Likelihood estimation method:
Whitehead
Institute data
vs
RHO
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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.
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Comparison of Genetic Map and RH Map of Chromosome 8q24
Genetic
map
Common sites
Adapted from: Lewis et al., 1995
RH
map
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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/
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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 ?
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Which genes are located on a particular chromosome
and in what order ?
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Other links from Entrez, for a gene that exists in a
particular chromosomal region ?
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What is the distance between genes ?
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NCBI Map View
http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/hum_srch?chr=hum_chr.inf&query
Scale
on
chromosome
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NCBI Map View
Scale
on
chromosome
See also Map View at:
http://genome.ucsc.edu/
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