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

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

2 4 53 7 86 10 119 12 13 14 15 16 17 18 19 201 21 22 X Y

Replicated regions @ p<0.01 (LOD>1.2) – Ober et al. (2000)

ADAM33

PHF11

DPP10

EHF, ELF5 (11p13)FCER1B

GPRA

Positionally cloned genes

Genetics of asthma

EHF and ELF5 (11p13) not

replicated

Patent reports suggestive linkage (p = 0.0001) of

asthma to D11S907 and association to D11S2008 (p <

0.0001)

Brooks-Wilson et al. (1998) filed a US patent for ELF5

and EHF, asthma susceptibility genes

6/27

Linkage and association of asthma to 11p13

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.

Baron et al. (2002) failed to replicate association of asthma

to ELF5 and EHF, small number of SNPs (4+3)

Problem: can we replicate linkage of asthma to

11p13?

7/27

1995-1998 QIMR Asthma & Allergy study

8/27

Replication of Linkage to 11p13 – large

Australian dataset

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

0.0

1.0

2.0

3.0

4.0Significan

t

Replicatio

n

EHF

100 Kb

VC

lod

IgE

Variance components (VC)Additive QTL effects onlyMultipoint IBD

Chr11

Chr11

ELF5

D11S200

8D11S907

Similar with other phenotypes

1 Mb

Have we failed to replicate linkage of asthma to

11p13?Can it be a false negative result?

10/27

1. Hypothesis A: power?

11/27

α = 0.01

α =

0.0001

Size 3 (n =

128)Size 2 (n =

325)Size 4 (n =

38)

Size 5+ (n = 6)

Overall (n =

497)

QTL magnitude (proportion total

variance)

NC

P V

C lin

kag

e t

est

r = 0.25Biallelic single QTLAdditive effects onlyPerfect marker informationθ = 0 Sham et al. (2000) 12/27

Comparable or better than most published asthma

linkage studies

Enough power QTL >25% variance

13/27

2. Hypothesis B: sex-specific age-of-

onset?

14/27

Cu

mu

lati

ve

incid

en

ce

Age (years)

0

0.2

0.4

0.6

0.8

1

0 20 40 60 80

Males (n = 431)

Females (n = 518)

Excess asthmatic males

Logrank p < 0.001

n = 949 doctor diagnosed asthmaticsKaplan-Meier survival curves for age of first wheezeSimilar results for atopyMean age-of-onset. Males: 8.2 (7.2-9.2). Females: 11.8 (11-12.5)

Males have earlier onset of

asthma/atopy

15/27

Can this affect linkage analysis?

yes, it if affects the expression of phenotypes, such as IgE

16/27

-4

-2

0

2

4

-4 -2 0 2 4

-4

-2

0

2

4

-4 -2 0 2 4

-4

-2

0

2

4

-4 -2 0 2 4

-4

-2

0

2

4

-4 -2 0 2 4

Same-sex sib-

pairs

Opposite-sex sib-

pairs

Young

(age ≤ 20)

Older

(age > 20)

17/27

r = 0.08(-0.07-0.23)

r = 0.36(0.24-0.47)

r = 0.25(0.12-0.37)

r = 0.16(0.04-0.28)

Sib

2 Ig

E

Sib 1 IgE

n = 858 sib-pairsr = 0.23

Not observed with other phenotypes

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.

Low IgE correlation young opposite-sex sib-pairs was

unrelated to sex-specific age-of-onset, likely to be of

stochastic nature

18/27

True heterogenous sib-pair correlation for IgE

confounder linkage analysis

Follow up of these families did not reveal any plausible

epidemiological explanation for male/female

discordance

Other issues could explain failure to replicate

11p13?

19/27

3. Hypothesis C: non-additive genetic

effects?

20/27

-4

-2

0

2

4

-4 -2 0 2 4

-4

-2

0

2

4

-4 -2 0 2 4

-4

-2

0

2

4

-4 -2 0 2 4

-4

-2

0

2

4

-4 -2 0 2 4

Monozygotic

twins

IgE

Eosinophils

21/27

r = 0.17(0.07-0.27)

r = 0.68(0.61-0.74)

r = 0.13(0.00-0.25)

r = 0.56(0.43-0.67)

Dizygotic twins

Suggestive of dominance, epistasis?

Tw

in 2

Twin 1

0.0

1.0

2.0

3.0

4.0Significan

t

Replicatio

n

VC

lod

ELF5EHF

100 Kb

Chr11

22/27

2-df testFulker et al. (1999) linkage & association model implemented in QTDT (Abecasis et al. 2000). Similar results with SOLAR (Almasy & Blangero 1998)

Chr11IgE

0.0

1.0

2.0

3.0

4.0Significan

t

Replicatio

n

ELF5EHF

100 Kb

Chr11

VC

lod

Eosinophil

s

23/27

Type 1 error?

Chr11D11S2008

774F

D11S907

1 20 4 53 7 86 10 119 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26

Fre

qu

en

cy

Chi-square

16.91 (LOD = 2.98), p =

0.008

Marker 774F

Eosinophil

s

24/27

Meets criteria for replication (p

< 0.01)Simulated genotypic data for the 11p13 region (9 markers), unlinked to the trait5,000 replicates 2-df testReplicates and IBDs obtained from Merlin (Abecasis et al. 2002)Analysis performed with QTDT (Abecasis et al. 2000)

Empirical type 1

Error

Have we replicated linkage of asthma to 11p13?

25/27

1. Initially failed to replicate linkage to 11p13 on an additive model

26/27

2. Enough power to detect a QTL >25% of total variance

3. Failure to replicate not a consequence of unaccounted sex differences

6. Statistical validity of dominance tests to be investigated

SummarSummaryy

4. Failure to replicate due to unmodelled non-additive genetic effects ?

5. Replication when modelling dominance

Acknowledgements

1. All participating families2. Project team

3. Everyone @ Genetic Epidemiology, QIMRNick Martin

David Duffy

Melbourne

Colin Robertson

Tim Newson

Marita Dalton

Perth

Peter LeSouef

Nigel Dore

Sunalene Devadason

Sydney

Jennifer Peat

Brett Toelle

Janet Li

[Sequana]

Lon Cardon

Brisbane

Dixie Statham

Barbara Haddon

Olivia Zheng

Louise Mattick

27/27

4. Scholarship SFRH/4824/2001, FCT - Portugal