Accounting for age-specific sex-limitation in IgE QTL linkage analysis: example of 11p13

1. Accounting for age-specific sex-limitation in IgE QTL linkage analysis: example of 11p13 Manuel A R Ferreira, David Duffy & Nick Martin Queensland Institute of Medical Research Australia

2. Accounting for non-additive genetic effects in IgE QTL linkage analysis: example of 11p13 Manuel A R Ferreira, David Duffy & Nick Martin Queensland Institute of Medical Research Australia

3. Genetics of asthma DPP10 GPRA EHF, ELF5 (11p13) FCER1B PHF11 ADAM33 1 9 10 11 12 13 21 22 X Y 2 14 15 16 17 18 19 20 3 4 5 6 7 8 Replicated regions @ p<0.01 (LOD>1.2) – Ober et al. (2000) Positionally cloned genes EHF and ELF5 (11p13) not replicated

4. Linkage and association of asthma to 11p13 Brooks-Wilson et al. (1998) filed a US patent for ELF5 and EHF, asthma susceptibility genes One extended pedigree from Tristan-da-Cunha island (n=282), with high prevalence of asthma. Own replication with a small sample of Canadian nuclear families with 1+ asthmatic children. Patent reports suggestive linkage (p = 0.0001) of asthma to D11S907 and association to D11S2008 (p < 0.0001) Baron et al. (2002) failed to replicate association of asthma to ELF5 and EHF, small number of SNPs (4+3) 6/27

5. Problem: can we replicate linkage of asthma to 11p13? 7/27

6. Replication of Linkage to 11p13 – large Australian dataset 1995-1998 QIMR Asthma & Allergy study 802 families, mean size 4 (range 1-10), mostly parents and children Each family with at least 1 asthmatic child 2500+ individuals with phenotypic and genotypic data at candidate regions Extensive respiratory questionnaire (American Thoracic Society) Total Immunoglobulin E, Eosinophils, BHR, atopy, FEV1/FVC Dataset includes 490 DZ twin pairs and 312 MZ pairs 8/27

7. Chr11 IgE Significant VC lod D11S2008 D11S907 Replication Chr11 1 Mb 100 Kb EHF ELF5 Similar with other phenotypes Variance components (VC) Additive QTL effects only Multipoint IBD

8. Have we failed to replicate linkage of asthma to 11p13? Can it be a false negative result? 10/27

9. 1. Hypothesis A: power? 11/27

10. Overall (n = 497) α = 0.0001 NCP VC linkage test Size 3 (n = 128) Size 2 (n = 325) α = 0.01 Size 4 (n = 38) Size 5+ (n = 6) QTL magnitude (proportion total variance) r = 0.25 Biallelic single QTL Additive effects only Perfect marker information θ = 0 Sham et al. (2000) 12/27

11. Enough power QTL >25% variance Comparable or better than most published asthma linkage studies 13/27

12. 2. Hypothesis B: sex-specific age-of-onset? 14/27

13. Cumulative incidence Age (years) Males have earlier onset of asthma/atopy n = 949 doctor diagnosed asthmatics Kaplan-Meier survival curves for age of first wheeze Similar results for atopy Mean age-of-onset. Males: 8.2 (7.2-9.2). Females: 11.8 (11-12.5) 15/27

14. Can this affect linkage analysis? yes, it if affects the expression of phenotypes, such as IgE 16/27

15. n = 858 sib-pairs r = 0.23 Opposite-sex sib-pairs Same-sex sib-pairs Young (age ≤ 20) r = 0.08 r = 0.36 (-0.07-0.23) (0.24-0.47) Sib 2 IgE Older (age > 20) r = 0.25 r = 0.16 (0.12-0.37) (0.04-0.28) Sib 1 IgE 17/27 Not observed with other phenotypes

16. True heterogenous sib-pair correlation for IgE confounder linkage analysis When tested formally by maximum likelihood estimation, only 8/802 (1%) families were found to be significantly inconsistent with a model that assumed homogenous sib-correlation. Follow up of these families did not reveal any plausible epidemiological explanation for male/female discordance Low IgE correlation young opposite-sex sib-pairs was unrelated to sex-specific age-of-onset, likely to be of stochastic nature 18/27

17. Other issues could explain failure to replicate 11p13? 19/27

18. 3. Hypothesis C: non-additive genetic effects? 20/27

19. Dizygotic twins Monozygotic twins IgE r = 0.17 r = 0.68 (0.07-0.27) (0.61-0.74) Twin 2 Eosinophils r = 0.13 r = 0.56 (0.00-0.25) (0.43-0.67) Twin 1 Suggestive of dominance, epistasis? 21/27

20. Chr11 IgE Significant VC lod Replication Chr11 100 Kb EHF ELF5 2-df test Fulker et al. (1999) linkage & association model implemented in QTDT (Abecasis et al. 2000). Similar results with SOLAR (Almasy & Blangero 1998) 22/27

21. D11S2008 Chr11 Eosinophils 774F D11S907 Significant VC lod Replication Chr11 100 Kb EHF Type 1 error? ELF5 23/27

22. Empirical type 1 Error Eosinophils Marker 774F 16.91 (LOD = 2.98), p = 0.008 Frequency 9 10 11 12 13 21 22 23 24 0 1 2 14 15 16 17 18 19 20 25 26 3 4 5 6 7 8 Chi-square Meets criteria for replication (p < 0.01) Simulated genotypic data for the 11p13 region (9 markers), unlinked to the trait 5,000 replicates 2-df test Replicates and IBDs obtained from Merlin (Abecasis et al. 2002) Analysis performed with QTDT (Abecasis et al. 2000) 24/27

23. Have we replicated linkage of asthma to 11p13? 25/27

24. Summary 1. Initially failed to replicate linkage to 11p13 on an additive model 2. Enough power to detect a QTL >25% of total variance 3. Failure to replicate not a consequence of unaccounted sex differences 4. Failure to replicate due to unmodelled non-additive genetic effects ? 5. Replication when modelling dominance 6. Statistical validity of dominance tests to be investigated 26/27

25. Acknowledgements 1. All participating families 2. Project team Perth Sydney [Sequana] Melbourne Brisbane Peter LeSouef Nigel Dore Sunalene Devadason Jennifer Peat Brett Toelle Janet Li Lon Cardon Colin Robertson Tim Newson Marita Dalton Dixie Statham Barbara Haddon Olivia Zheng Louise Mattick 3. Everyone @ Genetic Epidemiology, QIMR Nick Martin David Duffy 4. Scholarship SFRH/4824/2001, FCT - Portugal 27/27