QTL Mapping in Heterogeneous Stocks Talbot et al, Nature Genetics (1999) 21: Mott et at, PNAS (2000) 97:

Chromosome 1Chromosome 15 QTL Detection in F2 to get 30cM resolution Chromosome 10 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 V ma phenotype for individual with genotype a,b is V ma + V mb Estimate V ma ‘s by analysis of variance Conclude QTL linked to marker m if some V ma 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

Failures 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 HS QTL Mosaic 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 A/J AKR BALB C3H C57 DBA I RIII allele ND allele allele allele allele

m m+1 s t s’ t’ P mi (s,t)Q m+1,i (s’,t’) QTL dmdm cd m 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:

HAPPY web resources HAPPY home page: Web Server: 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 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 F2 chromosome Fine Map using HS 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

Fine-mapping

Combined

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 TalbotAl Collins Jeanne Wehner John DeFries Wellcome Trust Centre for Human Genetics, Oxford Institute for Behavioral Genetics, Boulder