gene by environment effects
DESCRIPTION
Gene by environment effects. Elevated Plus Maze (anxiety). Modelling E, G and GxE. H 0 : phenotype ~ 1. H 1 : phenotype ~ covariate. H 2 : phenotype ~ covariate + LocusX. H 3 : phenotype ~ covariate + LocusX + covariate:LocusX. - PowerPoint PPT PresentationTRANSCRIPT
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Gene by environment effects
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Elevated Plus Maze (anxiety)
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Modelling E, G and GxE
H1: phenotype ~ covariate
H2: phenotype ~ covariate + LocusX
H3: phenotype ~ covariate + LocusX + covariate:LocusX
H0: phenotype ~ 1
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PRACTICAL: Inclusion of gender effects in a genome scan
To start:1. Copy the folder faculty\valdar\FridayAnimalModelsPractical to your owndirectory.2. Start R3. File -> Change Dir… and change directory to yourFridayAnimalModelsPractical directory4. Open Firefox, then File -> Open File, and open “gxe.R”in the FridayAnimalModelsPractical directory
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H0: phenotype ~ sex
H1: phenotype ~ sex + marker
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scan.markers(Phenotype ~ Sex + MARKER,
h0 = Phenotype ~ Sex,
... etc)
H0: phenotype ~ sex
H1: phenotype ~ sex + marker
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scan.markers(Phenotype ~ Sex + MARKER,
h0 = Phenotype ~ Sex,
... etc)
H0: phenotype ~ sex
H1: phenotype ~ sex + marker
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scan.markers(Phenotype ~ Sex + MARKER,
h0 = Phenotype ~ Sex,
... etc)
H0: phenotype ~ sex
H1: phenotype ~ sex + marker
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head(ped.gender0)
anova(lm(Phenotype ~ Sex + m1 + Sex:m1, data=ped.gender0))
head(ped.gender1)
anova(lm(Phenotype ~ Sex + m1 + Sex:m1, data=ped.gender1)
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New approaches
Advanced intercross lines
Genetically heterogeneous stocks
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F2 Intercross
x
Avg. Distance BetweenRecombinations
F1
F2F2 intercross
~30 cM
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Advanced intercross lines (AILs)
F0
F1
F2
F3
F4
Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199-1207.
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Chromosome scan for F12
position along whole chromosome (Mb)
goodness of fit(logP)
0 100cM
significance threshold
QTL
Typicalchromosome
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PRACTICAL: AILs
To start:1. Open Firefox, then File -> Open File, and open “ail_and_ghosts.R”in the FridayAnimalModelsPractical directory
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Genetically Heterogeneous Mice
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F2 Intercross
x
Avg. Distance BetweenRecombinations
F1
F2F2 intercross
~30 cM
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Pseudo-random matingfor 50 generations
Heterogeneous Stock F2 Intercross
x
Avg. Distance Between Recombinations:
F1
F2HS
~2 cMF2 intercross
~30 cM
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Pseudo-random matingfor 50 generations
Heterogeneous Stock F2 Intercross
x
Avg. Distance Between Recombinations:
F1
F2HS
~2 cMF2 intercross
~30 cM
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High resolution mapping
0
1
2
3
4
5
6
7
8
64 64.2 64.4 64.6 64.8 65 65.2
position (cM)
-logP
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Relation Between Marker and Genetic Effect
Observable effect
QTL Marker 1
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Relation Between Marker and Genetic Effect
Observable effect
QTLMarker 2 Marker 1
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Relation Between Marker and Genetic Effect
No effect
observableObservable
effect
QTLMarker 2 Marker 1
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Hidden Chromosome Structure
Observed chromosome structure
Multipoint method (HAPPY) calculates the probability that an allele descends from a founder
using multiple markers
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Haplotype reconstruction using HAPPY
chromosome
genotypes
haplotypeproportionspredicted byHAPPY
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HAPPY model for additive effects
Strain f (strain)LP.J 0.04
DBA.2J 0.05CBA.J 0.03
C57BL.6J 0.07C3H.HeJ 0.36BALB.cJ 0.07AKR.J 0.03
A.J 0.36
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Genome scans with HAPPY
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Results for our HS
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Many peaks
mean red cell volume
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How to select peaks: a simulated example
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How to select peaks: a simulated example
Simulate 7 x 5% QTLs
(ie, 35% genetic effect)
+ 20% shared environment effect
+ 45% noise
= 100% variance
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Simulated example: 1D scan
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Peaks from 1D scan
phenotype ~ covariates + ?
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1D scan: condition on 1 peak
phenotype ~ covariates + peak 1 + ?
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1D scan: condition on 2 peaks
phenotype ~ covariates + peak 1 + peak 2 + ?
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1D scan: condition on 3 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + ?
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1D scan: condition on 4 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 +peak 4 + ?
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1D scan: condition on 5 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + ?
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1D scan: condition on 6 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + peak 6 + ?
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1D scan: condition on 7 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + peak 6 + peak 7 + ?
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1D scan: condition on 8 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + peak 6 + peak 7 + peak 8 + ?
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1D scan: condition on 9 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + peak 6 + peak 7 + peak 8 + peak 9 + ?
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1D scan: condition on 10 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + peak 6 + peak 7 + peak 8 + peak 9 + peak 10 + ?
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1D scan: condition on 11 peaks
phenotype ~ covariates + peak 1 + peak 2 + peak 3 + peak 4 + peak 5 + peak 6 + peak 7 + peak 8 + peak 9 + peak 10 + peak 11 + ?
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Peaks chosen by forward selection
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Bootstrap sampling
1
2
3
4
5
6
7
8
9
10
10 subjects
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Bootstrap sampling
1
2
3
4
5
6
7
8
9
10
1
2
2
3
5
5
6
7
7
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10 subjects
sample withreplacement
bootstrap samplefrom
10 subjects
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Forward selection on a bootstrap sample
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Forward selection on a bootstrap sample
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Forward selection on a bootstrap sample
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Bootstrap evidence mounts up…
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In 1000 bootstraps…
Bootstrap Posterior Probability(BPP)
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Results
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Tea Break
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Study design
2,000 mice
15,000 diallelic markers
More than 100 phenotypes
each mouse subject to a battery of tests spread over weeks 5-9 of the animal’s life
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101 Phenotypes
Anxiety (conditioned and unconditioned tasks) [24]
Asthma (plethysmography) [13]
Biochemistry [15]
Diabetes (glucose tolerance test) [16]
Haematology [15]
Immunology [9]
Weight/size related [8]
Wound Healing [1]
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High throughput phenotyping facilityHigh throughput phenotyping facility
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Photo ID
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Open Field
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Open Field
Anxious mouse
Non anxious mouse
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Elevated Plus Maze (anxiety)
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Food hyponeophagia(reluctance to try new food)
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“Home Cage” activity
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Startle&
Conditioning
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Plethysmograph
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Plethysmograph
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Glucose Tolerance Test (diabetes)
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Wound healing
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PRACTICAL: http://gscan.well.ox.ac.uk
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END
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An individual’s phenotype follows a mixture of normal distributions
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m
Maternal chromosomePaternal chromosome
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mChromosome 1Chromosome 2
ABCDEF
Strains
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Markers
m
ABCDEF
Strains
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Markers
m
ABCDEF
Strains
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Markers
m
0.5 cM
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Markers
m
0.5 cM 1 cM
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Markers
m0.5 cM 1 cM
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Analysis
Probabilistic Ancestral Haplotype Reconstruction (descent mapping): implemented in HAPPY
http://www.well.ox.ac.uk/~rmott/happy.html
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M1
Q
M2
m1
q
m2
M1
?
m2
recombination
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M1
Q
M2
m1
q
m2
m1
Q
M2
M1
q
m2
M1
q
m2
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M1
Q
M2
m1
q
m2 M1
Q
m2
M1
Q
m2
m1
q
M2
m1
Q
M2
M1
q
m2
M1
q
m2
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M1
Q
M2
m1
q
m2
M1
m2
M1
m2
m1
m2
m1
M2
M1
m2
M1
m2
Q q
Q q q
Q
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M1
?
m2
m1
?
m2
1c
2c
cM distancesdetermineprobabilities
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0|Pr
5.0|Pr
5.0|Pr
2121
2121
2121
mmmMQQ
mmmMqQ
mmmMqq
M1
?
m2
m1
?
m2
1c
2c
cM distancesdetermineprobabilities
Eg,
![Page 104: Gene by environment effects](https://reader036.vdocuments.us/reader036/viewer/2022062720/568134ab550346895d9bbe21/html5/thumbnails/104.jpg)
Interval mapping
M1 M2
m1 m2
M1m1
M2m2
LODscore
![Page 105: Gene by environment effects](https://reader036.vdocuments.us/reader036/viewer/2022062720/568134ab550346895d9bbe21/html5/thumbnails/105.jpg)
Interval mapping
M1 M2
m1 m2
M1m1
M2m2
LODscore
![Page 106: Gene by environment effects](https://reader036.vdocuments.us/reader036/viewer/2022062720/568134ab550346895d9bbe21/html5/thumbnails/106.jpg)
Interval mapping
M1 M2
m1 m2
M1m1
M2m2
LODscore
![Page 107: Gene by environment effects](https://reader036.vdocuments.us/reader036/viewer/2022062720/568134ab550346895d9bbe21/html5/thumbnails/107.jpg)
Interval mapping
M1 M2
m1 m2
M1m1
M2m2
LODscore