Week 11: Mapping

1
Week 11 Mapping

• November 8, 2001
• Todd Scheetz

2
Introduction

• What is mapping?
• determining the location of elements within a
  genome, with respect to identifiable landmarks.
• Types of mapping
• genetic mapping
• physical mapping
• restriction mapping
• cytogenetic mapping
• somatic cell mapping
• radiation hybrid mapping
• comparative mapping

3
Introduction

• Genetic mapping
• Utilize recombination events to estimate distance
  between genetic markers.
• RFLP
• STRP
• SNP
• Look at a population and estimate the
  recombination fraction
• ? recombinants / total

4
Introduction

• Physical mapping
• Relies upon observable experimental outcomes
• hybridization
• amplification
• May or may not have a distance measure.

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
A2 B2
A2 B2
A2 B2
A1 B1
A1 B1
A1 B1
A1 B2
A2 B1
A2 B2
A1 B1
A1 B1
A1 B1
A2 B2
A2 B2
A2 B2
A1 B1
A1 B1
A1 B1
A1 B1
A1 B1
A1 B1
A1 B1
A1 B1
A1 B1
A1 B2
A2 B1
NR
NR
NR
NR
NR
R
R
? recombinant / total 2/7 0.286
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Genetic Mapping
Theta calculation with inbred population
bn
det
bn
det
x
det
bn
det
bn
bn
det
bn
det
x
det
bn
det
bn
bn
det
bn
det
bn
det
bn
det
det
bn
det
bn
det
bn
det
bn
? recombinant total
5/1000 0.005
banded
detached
banded, detached
wild-type
483
512
2
3
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Genetic Mapping
? theoretical maximum of 50 Best if a
measured between close markers. Unit of
distance in genetic maps centimorgans, cM d -
0.5 ln(1 - 2?) d 0.25 ln(1 2?)/(1 - 2?) 1
cM 1 chance of recombination between markers
9
Genetic Mapping
10
Restriction Mapping
Background on restriction enzymes cut DNA at
specific sites Ex. EcoRI cuts at GAATTC sites
are often palindromic GAATTC CTTAAG may leave
blunt ends or overlaps
GGCC GG CC CCGG CC GG
GAATTC G AATTC CTTAAG CTTAA G
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Restriction Mapping
Restriction maps show the relative location of a
selection of restriction sites along linear or
circular DNA.
EcoRI
HindIII
BamHI
PstII
HindIII
BamHI
PstII
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Restriction Mapping
BamHI PstI
BglII BamHI
BglII PstI
BglII
BamHI
PstI
5.2
4.2
3.6
3.5
3.3
2.6
1.7
1.7
1.4
1.4
1.2
1.2
1.2
1.0
1.0
0.9
0.7
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
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Restriction Mapping
Creating a restriction map from a double digest
experiment is NP-complete. No polynomial-time
solution. As the number of fragments increase,
the complexity increases as A!B!. if the two
single-enzyme reactions generate 6 and 8 times
respectively, 29,030,400 potential permutations
to evaluate
A A! 1 1 2 2 3 6 4 24 5 120 6 720 7 5040 8 40,320
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Restriction Mapping

• Multiple valid solutions possible.
• Reflections
• Equivalence
• A 1,3,3,12 B 1,2,3,3,4,6
• AB 1,1,1,1,2,2,2,3,6

3
3
12
1
4320 map configurations, but only 208 distinct
solutions.
A
1
3
3
6
2
4
B
1
1
3
2
1
1
2
2
6
AB
1
3
3
12
A
1
3
3
2
4
6
B
1
1
1
3
1
2
2
2
6
AB
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Cytogenetic Mapping
Cytogenetic mapping refers to observing a map
location in reference to a chromosomal banding
pattern.
16
CytogeneticMapping
These methods allow a rough determination of
location, but to not yield a direct measure of
distance.
17
Cytogenetic Mapping
18
Somatic Hybrid Mapping
Somatic cell mapping can be used to map an
element to a portion of a genome. typically with
chromosome resolution Exploits the ability of
rodent (hamster) cells to stably integrate
genetic material from other species. Cells from
the target genome are fused with hamster cells.
The resulting cells are then screened for cells
(hybrids) that have retained one or more of the
chromosomes from the target genome. Ideally, a
complete set of hybrids can be constructed such
that each has retained a single chromosome from
the target genome.
19
Somatic Hybrid Mapping
Chromosome
1
2
3
4
5
Probe1
0
1
0
0
0
Probe2
1
1
0
0
0
Probe3
1
1
1
1
1
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
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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.
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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
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Radiation Hybrid Mapping
The data obtained from a radiation hybrid
experiment is similar to that from a somatic cell
hybrid. It is the retention data for the given
locus for each hybrid. This data is generally
displayed as a vector of numbers or letters 1 or
for retention 0 or - for non-retention 2 or ?
for ambiguous or unknown Ex. RN_ALB 0100110102010
001100100100000102210010.. RN_HEM 0101110102000100
101100200010100110010..
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Radiation Hybrid Mapping
Analytical methods -- Many ranging from
minimizing the number of obligate breaks to
sophisticated methods relying on maximum
likelihood or maximum posterior probability
methods. ? AB- A-B TH(RA RB -
2RARB) d - ln (1 - ?) NOTE ? ? 0,1
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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.
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Comparative MappingSources of Information
sequence
sequence
BLAST
mapping
mapping
potential orthologs
colocalization
Putative orthologs and syntenic segments
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Comparative MappingSources of Information

• GeneMap 99 (human)
• 42,000 ESTS
• 12,500 genes
• Mouse RH consortium (mouse)
• 14,000 ESTs
• UIowa EST placements (rat)
• 13,793 ESTs

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Current Status
Initial comparative map (Welcome Trust and Otsuka
Lab) about 500 previously identified
orthologs human-mouse-rat University of Iowa
comparative maps 13,973 placed ESTs 3057
significant mouse hits 9109 significant human EST
hits 10,148 significant hits to GenBanks nt
database 2479 rat ESTs in preliminary human-rat
comparative map 1671 rat ESTs in preliminary
mouse-rat comparative map
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Comparative MappingExamples
RNO18
MMU18
0
1200
100
900
200
600
300
300
400
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Comparative MappingExamples
HSA7
RNO4
400
0
RNO12




100
500
RNO12
HSA11


600
200

RNO5

700
300
HSA7p
HSA4
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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 GeneM
ap99 http//www.ncbi.nlm.nih.gov/genemap99