QTL Mapping in Heterogeneous Stocks Talbot et al, Nature Genetics (1999) 21:305-308 Mott et at, PNAS...
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Transcript of QTL Mapping in Heterogeneous Stocks Talbot et al, Nature Genetics (1999) 21:305-308 Mott et at, PNAS...
QTL Mapping in Heterogeneous Stocks
•Talbot et al , Nature Genetics (1999) 21:305-308•Mott et at, PNAS (2000) 97:12649-12654
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Chromosome 1 Chromosome 15
QTL Detection in F2 to get 30cM resolution
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cM
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Gershenfeld et al Behav Genetics, 1997
Heterogeneous Stocks (HS)
• A murine cross formed from 8 inbred founders
• Randomly outbred for >60 generations, • 40 mating pairs per generation• Each chromosome is a random mosaic of
the founders• Average distance between recombinants is
1/60=1.7cM
Fine Mapping with HS
QTL
Mosaic of progenitor strains
Region Scan with microsatellites or SNPs.
Test for association between marker and trait by ANOVA
Mapping by Single-Marker Association
Look for association between the phenotype and each marker in the genome scan:
• A marker m has alleles 1…k• Assume phenotypic effect for allele a is Vma • phenotype for individual with genotype a,b is
Vma + Vmb
• Estimate Vma ‘s by analysis of variance• Conclude QTL linked to marker m if some Vma are
significantly different
Single-marker QTL mapping
• Genotype and phenotype ~750 HS mice over 5 regions where QTL detection indicated the presence of a QTL
• Test for the association between the phenotype and marker allele as with F2 cross
• Two QTL fine-mapped to <1cM
HS provides High Resolution
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Distance (cM)
D1Mit264
D1Mit394
D1Imm103
D1Mit100
D1Mit423
D1Mit198D1Mit194
D1Mit102
D1Mit289
D1Mit369
-lo
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Failures
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Chromosome 10 Chromosome 15
Single-Marker Analysis Can Fail
Only 2/5 QTL detected in the F2 cross were confirmed by SM in the HS mice. Why ?
• Genetic Drift eliminated some of the QTL. Simulations indicate this is unlikely.
Single-Marker Analysis Can Fail
Only 2/5 QTL detected in the F2 cross were confirmed by SM in the HS mice. Why ?
• Chromosomes with the same marker allele may be descended from different strains, and so have different trait effects.
Wrong Phase, No Effect
Marker 1: No effect
observable
Marker 2: Observable
effect
QTL
Single-Marker Analysis Can Fail
Only 2/5 QTL detected in the F2 cross were confirmed by SM in the HS mice. Why ?
• Chromosomes with the same marker allele may be descended from different strains, and so have different trait effects.
• Need to test for association between trait and strain rather than trait and marker
Fine Mapping with HSQTLMosaic of progenitor strains – Hidden Data
Region Scan with microsatellites or SNPs. Observed Genotypes
Loss of information because #alleles < #strains & phase unknown
Must infer progenitors from genotypes and test for presence of QTL in each interval
marker D1MIT498 5 alleles position 64.000
A/J AKR BALB C3H C57 DBA I RIIIallele ND 0.125 0.125 0.125 0.125 0.125 0.125 0.125 0.125allele 132 0.500 0.000 0.000 0.500 0.000 0.000 0.000 0.000allele 155 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000allele 153 0.000 0.000 0.250 0.000 0.250 0.250 0.250 0.000allele 130 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000
m m+1s
t
s’
t’
Pmi(s,t) Qm+1,i(s’,t’)
QTL
dm
cdm
HS Interval Mapping
Comparison of SM and DP QTL localisation (a)
Comparison of SM and DP QTL localisation (b)
Summary(1)
• Heterogeneous Stocks provide an experimental means for fine-mapping QTL of small effect
• Dynamic Programming provides a powerful statistical means for analysing HS data
• 5/5 QTL for behaviour were detected and fine-mapped
• Mott et al (2000) PNAS 97:12649-12654
HAPPY web resources
HAPPY home page:
http://www.well.ox.ac.uk/happy
Web Server:
http://zeno.well.ox.ac.uk:8080/git-bin/happy.cgi
HAPPY is a program to map QTLs in Heterogeneous Stocks
Tea !
Future Directions (1)Mapping Traits in Parallel
• We propose to genotype 3000 markers 1cM apart on 2000 HS mice
• Measure as many phenotypes as possible affecting asthma, diabetes, behaviour etc on these animals
• Map all genes affecting these traits in parallel• Much cheaper than scanning diseases separately• Simulations indicate >90% probability of
detecting any gene accounting for >2.5% of phenotypic variance at genome-wide 5% significance level
Future Directions(2)Mapping Modifier Genes
• Over 2500 mouse models transgenic for human
• On inbred or backcross background
• HS x transgenic hybrid can be used for mapping modifiers
• Need to extend analysis for F2 HS x inbred
Inbred-Outbred Cross
• Detection phase – a genome scan with ~100 markers at 20-30 cM seperation
• Fine-Mapping Phase – rescan at 1cM spacing only those regions which were detected
Simultaneous Detection And Fine Mapping Using an Inbred
Outbred Cross
x
Genome Scan using F2chromosome
Fine Map usingHS chromosome
HS Mouse Inbred strain (knockout) F2
Inbred-Outbred Analysis
• QTL detection depends on variance between HS and background
• Fine-mapping depends on variance within HS
• Power depends on how total variance is split between the detection and fine-map
• phases
Power depends on the modifier allele frequency
Variance under Dominance Model
detection
full
difference
HS
Proportion of HS carrying modifier
Simulation Results for the Inbred Outbred Design
• QTL explaining 10% of phenotypic variance
• 1,500 animals, 500 simulations
• 5 markers per 100 cm detection phase
• Markers at 1 cm interval for fine-mapping
• (We haven’t explored all parameters yet)
Detection Phase
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Combined
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Position Estimates
Summary(2)
• Mapping in a genetically heterogeneous stock of known ancestry can achieve sub-centimorgan resolution
• Theoretically, crosses between inbreds and outbreds can detect and fine-map a genetic effect in one experiment
Acknowledgements
• Chris Talbot • Al Collins• Jeanne Wehner• John DeFries
Wellcome Trust Centre for Human Genetics, Oxford
Institute for Behavioral Genetics, Boulder