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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
(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
• Describe Asthma and Complex Trait Genetics
• Heritability
• Genome-wide linkage analysis• Example: ADAM33
• Fine-mapping efforts and genetic association• Example: Chromosome 12q
Outline
Complex Genetic Disease
Airway anatomy
Mucin Production
Lymphocyte signaling
Epithelium Integrity
Smooth Muscle Properties
Cytokine metabolism
Genetic Heterogeneity
Eosinophil behavior
Complex Genetic Disease
Genes confer increased risk of disease, not causative alone!
Simple Disease Complex Disease
• Describe Asthma and Complex Trait Genetics
• Heritability
• Genome-wide linkage analysis• Example: ADAM33
• Fine-mapping efforts and genetic association• Example: Chromosome 12q
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
• Describe Asthma and Complex Trait Genetics
• Heritability
• Genome-wide linkage analysis• Example: ADAM33
• Fine-mapping efforts and genetic association• Example: Chromosome 12q
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: 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
• Describe Asthma and Complex Trait Genetics
• Heritability
• Genome-wide linkage analysis• Example: ADAM33
• Fine-mapping efforts and genetic association• Example: Chromosome 12q
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
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.
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
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