Week 11: Mapping

November 8, 2001
Todd Scheetz
 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
 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
 Introduction
Physical mapping

Relies upon observable experimental outcomes

• hybridization
• amplification

May or may not have a distance measure.

 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

 Genetic Mapping

A2 A2 A2 A1 A1 A1 A2 A1
B2 B2 B2 B1 B2 B1 B1 B1

A2 A1 A1 A1
B2 B1 B1 B1

A2 A1 A1 A1 A1 A1 A2 A1 A1A1 A2 A1 A2 A1
B2 B 1 B1 B1 B2 B1 B2 B 1 B1 B1 B1 B1 B2 B 1

NR NR R NR NR R NR

 = # recombinant / # total = 2/7 = 0.286

 Genetic Mapping
Theta calculation with inbred population…
bn det+ bn+ det
bn det+
x bn+ det

bn det+ bn det
bn+ det x bn det

bn det+ bn+ det bn det bn+ det+

bn det bn det bn det bn det
 = # recombinant
banded detached banded, wild-type # total
detached = 5/1000
483 512 2 3 = 0.005
 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

Genetic Mapping
 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 GAATTC G AATTC
CCGG CC GG CTTAAG CTTAA G
 Restriction Mapping
Restriction maps show the relative location of a selection of
restriction sites along linear or circular DNA.
EcoRI
HindIII

PstII BamHI
HindIII BamHI PstII
 Restriction Mapping
BglII BglII BamHI
BglII BamHI PstI
+BamHI +PstI +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 0.9 1.0
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

 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!.
A A!
1 1
if the two single-enzyme reactions generate 2 2
6 and 8 times respectively, 3 6
4 24
29,030,400 potential permutations to evaluate 5 120
6 720
7 5040
8 40,320
 Restriction Mapping
Multiple valid solutions possible.
• Reflections
• Equivalence

A = {1,3,3,12} B = {1,2,3,3,4,6}
A^B = {1,1,1,1,2,2,2,3,6}
1 3 12 3
A 4320 map
2 4 6 3 3 1
B configurations,
11 2 2 6 3 1 2 1
A^B but only 208
distinct solutions.
1 3 12 3
A’
3 3 6 1 2 4
B’
1 2 1 2 6 1 2 1 3
A^B’
 Cytogenetic Mapping
Cytogenetic mapping refers to
observing a map location in
reference to a chromosomal
banding pattern.
 Cytogenetic
Mapping
These methods allow a rough
determination of location, but to not
yield a direct measure of distance.
Cytogenetic Mapping
 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.
 Somatic Hybrid Mapping
Chromosome
1 2 3 4 5
Probe1 0 1 0 0 0
Probe2 0 0 1 1 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
 Somatic Hybrid Mapping

EXP 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X
WIL1 - - - - - - - - + - - - - - + - - + - - - + - +
WIL6 - - + - + + + + + - + + - - + - - + - + + + -
WIL7 - - + + - + + - + - + + - + + - - + + - - + - +
wil14 + + - + - - - + + - + - + - + + - + - - - - - +
SIR3 + + + + + + + + - + + + + + - - + + + + + + + +
…
% discord 0 32 17 24 31 21 21 31 21 24 30 21 21 28 14 24 21 28 17 34 41 21 27

A subset of the data used to map the Blood Coagulating Factor III
to human chromosome 1.
 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.
 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
Radiation Hybrid Mapping
 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 0100110102010001100100100000102210010..
RN_HEM 0101110102000100101100200010100110010..
 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.

 = A+B- + A-B+
TH(RA + RB - 2RARB)

d = - ln (1 - )

NOTE:   [0,1]
 Summary of Mapping Strategies
Mapping Requires Resolution How to Software
Strategy increase
resolution
Genetic Polymorphic Medium to Increase GeneHunter
Markers, and High number of
Pedigrees markers or
people
Restriction Restriction High Increase
Enzymes number of
enzymes.
Somatic Somatic Low to Increase
Cell Hybrid Hybrid Panel, Medium number of
and STSs deletion hybrids
Radiation Radiation High Use additional RHMap,
Hybrid Hybrid Panel, hybrids, or MultiMap,
and STSs make a new RHMAPPER
panel.
 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.
Comparative Mapping
Sources of Information

sequence BLAST sequence

mapping mapping

potential
orthologs

colocalization

Putative orthologs and

syntenic segments
Comparative Mapping
Sources 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
 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 GenBank’s nt database

2479 rat ESTs in preliminary human-rat comparative map

1671 rat ESTs in preliminary mouse-rat comparative map
 Comparative Mapping
Examples
RNO18 MMU18
0
1200
100
900
200
600
300
300
400
Comparative Mapping
Examples

RNO4 HSA7
0 RNO12 {
400
} {
}
{
100 RNO12 { 500
} HSA11
} {

200 { 600
} RNO5 {

300 } HSA7p
} HSA4
700
 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