Download - Inherit the Wheeze: The Genetics of Asthma Benjamin Raby, MD.CM, MPH, F.R.C.P.C. Respiratory Environmental and Genetic Epidemiology Channing Laboratory

Inherit the Wheeze:The Genetics of Asthma

Benjamin Raby, MD.CM, MPH, F.R.C.P.C.Benjamin Raby, MD.CM, MPH, F.R.C.P.C.Respiratory Environmental and Genetic EpidemiologyChanning LaboratoryBrigham and Women’s HospitalBoston, MA

BRIGHAM AND WOMEN’S HOSPITAL

HARVARDMEDICAL SCHOOL

The Post-Genomic Era: February 13th, 2001

Growth of Genomic Information: 1992-2002

Venter et al. 2003 Nature Genetics 33:219

(Some) Notable Events in Pulmonary Genetics

• 1960s: Alpha-1 Antitrypsin genetics

• 1985-1990: PCR for diagnosis of M.Tb

• 1989: CFTR identified as cause of Cystic Fibrosis

• 1994: INH-resistance gene

• 1994: GM-CSF and Pulmonary Alveolar Proteinosis

• 2000: BMPR2 mutations identified in Primary Pulmonary Hypertension

• 2001: Surfactant C mutations in Interstitial Fibrosis

• 2002: ADAM33 identified as an asthma gene

Overview of Complex Trait Genes

Demonstrate Familial Aggregation of Complex TraitDemonstrate Familial Aggregation of Complex Trait

Positional CloningPositional Cloning Candidate Gene ApproachCandidate Gene Approach

Localize Susceptibility Gene(s)Localize Susceptibility Gene(s)

Identify Disease Susceptibility Gene and Functional VariantsIdentify Disease Susceptibility Gene and Functional Variants

DiagnosticsDiagnostics Determine Fraction of Determine Fraction of Explained VariationExplained Variation

TreatmentTreatment

• Describe Asthma and Complex Trait Genetics

• Heritability

• Genome-wide linkage analysis• Example: ADAM33

• Fine-mapping efforts and genetic association• Example: Chromosome 12q

Outline

Recessive InheritanceDominant Inheritance

Asthma

?

Complex Genetic Disease

Airway anatomy

Mucin Production

Lymphocyte signaling

Epithelium Integrity

Smooth Muscle Properties

Cytokine metabolism

Genetic Heterogeneity

Eosinophil behavior


Environmental Phenocopy

RSVinfection

RADS SmokerBronchitis

COPD


Reduced Penetrance


Genes confer increased risk of disease, not causative alone!

Simple Disease Complex Disease

The Genetics of Asthma


• Heritability



Outline

Risk to relatives

Risk to relatives: disease more common among individuals with family history compared to those with out.

Relative risk

0

5

10

15

20

Yes No

Family History

Dis

ease

pre

vela

nce

(%

)

Twin studies

Twin concordance studies: phenotype more similar among monozygotic vs. dizygotic twins even though environment shared

Trait Concordance

0

0.5

1

1.5

2

2.5

3

3.5

4

4.5

5

Tra

it p

air

-dif

fere

nc

e

MZ DZ Unrelatedtwins twins pairs

Heritability estimates

Heritability estimates: variability in trait explained by familial resemblance

Trait variability

0

0.5

1

1.5

2

2.5

3

0 1 2 3 4 5

Family number

Tra

it va

lue

Asthma and intermediate phenotypes are highly heritable.

• Risks to relatives 2-4 times for asthma» Sibbald et al. Thorax 1980

• Heritability of Airways responsiveness 30-66%» Hopp et al. JACI 1984» Palmer et al. AJRCCM 2000

• Atopy-related phenotypes highly heritable– Total and specific serum IgE levels: 56-79%

» Hopp et al. JACI 1984» Hanson et al. AJHG 1991» Palmer et al. AJRCCM 2000

– Skin test reactivity heritable» Hanson et al. AJHG 1991

Australian Twin Studies : 3,808 PairsAustralian Twin Studies : 3,808 Pairs

0.640.64

11

Hay feverHay fever AtopyAtopy AsthmaAsthma

0.80.8

0.60.6

0.40.4

0.20.2

00

0.120.12

0.860.86

0.210.21

0.760.76

0.190.19

MZ

DZ

MZ

DZ

Duffy et al. AJRCCM 1990


• Heritability



Outline

Linkage AnalysisAnalyze the distribution of DNA markers within families to determine if a

region of the genome contains a gene related to the phenotype

Intermarker DistanceIntermarker Distance

Trait LocusTrait Locus(alleles unobserved)(alleles unobserved)

Marker LociMarker Loci(alleles unobserved)(alleles unobserved)

Isolated PopulationIsolated Population Outbred PopulationOutbred Population

sib

pa

irs

sib

pa

irs

ped

igre

es

ped

igre

es

Recombination

A

B

C

D

A

B

C

D

A

B

C

D

DuplicationA

B

C

D

A

B

C

D

Cross-over

A

B

C

D

A

B

C

D

Recombination

Linkage Analysis

A2A5 A1A6

A1A2 A3A4

A1A3 A2A3 A1A4 A1A4 A2A4 A2A3

NR NR NRNR NR R

Linkage Analysis: Non-Parametric ModelsAffected Sib-Pair Allele Sharing

A1A2 A3A4 A1A2 A3A4

A1A3 A1A3 = 35%A1A4 = 35%A2A3 = 15%A2A4 = 15%

A1A3 A1A3

A1A4 A2A3

A2A4

= 50%

= 25%

= 25%

Positional Cloning of ADAM33

• 460 Caucasian families

• Affected sib-pairs

• Asthma diagnosis and medication use

• Genome-wide linkage analysis

• Chromosome 20p13

• 2.5 Megabase region Van Eerdewegh et al. Nature 2002

2-allele sharing (%) LOD score

Asthma 31% 2.94

Asthma + BHR

35% 3.93


• Heritability



Outline

0.04

Asthma Linkage to 12q: Genome-wide and Regional Screens

0.0295.56 -101.1AsthmaGerman

0.01154 -159AsthmaDanish

0.00003133.3EosinophilsFrench

0.03130AsthmaU.S Hispanic

0.001111.9 -125.3AsthmaJapanese

<0.001109.5 -125.3AsthmaNetherlands

0.03111.9AHRFrench

0.00493.65AsthmaU.S Caucasian

83.19AsthmaFrench

0.00880.52AsthmaHutterites

0.0162.1- 75.2AHRGerman

P-valueChromosome position (in cM from pter)

PhenotypePopulation

0.002

0.0009

0.000887.9AsthmaAfro-Caribbean

0.0283.19AtopyFrench Canadian

0.000467.63AsthmaItalian

95.56IgEGerman

133.33AsthmaU.S. Caucasian

Asthma Linkage to Chromosome 12q in 55 Sib-pairs

Hum Mol Gen 2003 12:1973

Fine-Mapping of Chromosome 12q Asthma Locus

Goal: Perform association mapping of 28.5 Mb centromeric locus on chromosome 12q using high-resolution SNP map

Study Design:Family-based association study using 400 Caucasian parent-offspring trios ascertained through an asthmatic child participating in the Childhood Asthma Management Program (CAMP)

Linkage disequilibrium mapping using LD-tagging SNPs identified from the HapMap project.

Association Studies

Family-BasedFamily-Based Case Control Case Control

Transmission Disequilibrium Test (TDT)

AA AG

AG:AA50:50

AA AG

AG

AG AA

AA

AA AG

AG

AG AA

AG

AA AG

AA

AG AA

AA

AA AG

AG

AG AA

AA

AA AG

AG

AG AA

AG

AA AG

AG

AG AA

AA

AA AG

AG:AA66:33

Linkage Disequilibrium

RecombinationRecombination

Ancestral chromosomes

a b c d

Contemporarychromosomes

a b c d

0

1

2

3

4

Marker

-lo

g(p

-va

lue

)

a b c d

SNP Selection From HapMap

Data reduction of 2525 SNP across region to 1611 with high residual LD

SNP Associations With Asthma in CAMP

Haplotype Block Associations

0

0.5

1

1.5

2

2.5

3

3.5

0 5 10 15 20 25 30

Marker order

-lo

g(p

-val

ue)

Frequency T:U ratio p-value

0.58 180:158 0.23

0.18 78:124 0.001

0.14 92:82 0.45

0.07 44:43 0.92

0.03 23:12 0.06

Summary and Future Directions

This initial fine mapping effort has identified 19 regions totaling ~2Mb with evidence of association with asthma.

These regions contain 46 expressed genes, few of which have been previously implicated in asthma pathobiology.

We intend to further characterize the genetic patterns across these regions using higher resolution maps and to attempt to replicate our associations in other asthmatic populations.

Replicated regions will then be resequenced to identify disease-susceptibility variants for functional analysis.

Acknowledgements

Channing LaboratoryScott WeissEdwin SilvermanRoss LazarusMany others…

Harvard School of Public HealthKristel Van SteenChristoph Lange

McGill UniversityThomas HudsonAlexandre MontpetiteJean-Francois Olivier

FundingNational Institutes of Health National Heart Lung Blood InstituteCanadian Institutes of Health Research

We thank all the CAMP children and their parents for their ongoing participation in this study

Download - Inherit the Wheeze: The Genetics of Asthma Benjamin Raby, MD.CM, MPH, F.R.C.P.C. Respiratory Environmental and Genetic Epidemiology Channing Laboratory

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