La GenLa Genéética del Asma in Hispanos tica del Asma in Hispanos
Juan C. CeledJuan C. Celedóón, M.D., Dr.P.H.n, M.D., Dr.P.H.Channing Laboratory Division of Pulmonary and Critical Care MedicineBrigham and Women’s HospitalDepartment of MedicineHarvard Medical School
BRIGHAM AND WOMEN’S HOSPITAL
HARVARDMEDICAL SCHOOL
• Definition of the term Hispanic• Asthma among Hispanics in the United States• The Genetics of Asthma in Hispanics • Study of Asthma Genetics in Costa Rica
– Heritability Analysis – Genome-wide linkage analysis of asthma and
airway responsiveness– Future Directions
Outline
Definition of the Term “Hispanic”
1.
Introduction
• 2000 Census: ~32.8 million Hispanics in the United States (~12% of the population)
• “Hispanic”: Common heritage of language and culture
Asthma in Hispanics
2.
Asthma in Hispanics
• Asthma is a significant cause of morbidity in certain Hispanic subgroups in the U.S. (e.g., Puerto Ricans) and Hispanic America (e.g., Costa Ricans)
• Little is known about genetic and environmental influences on asthma in Hispanics
Hunninghake GM, Weiss ST, Celedón JC. State of the Art: Asthma in Hispanics. Am J Respir Crit Care Med 2006; 173:143-163.
The Genetics of Asthma in Hispanics
3.
The Genetics of Asthma in Hispanics
• To date, genome-wide analyses for linkage to asthma phenotypes have been conducted in 18 distinct populations– Until recently, only one genome scan included any
Hispanic individuals
Results of Selected CandidateResults of Selected Candidate--Gene Association Studies for Gene Association Studies for Asthma and/or AsthmaAsthma and/or Asthma--Related Phenotypes in HispanicsRelated Phenotypes in Hispanics
Raby B, et al3
No association between any of the SNPs tested and asthma or asthma-related phenotypes.
17
47 Hispanic families of children with asthma
Lind D, et al2
No association between any of the SNPs tested and asthma or asthma-related phenotypes.
6
Mexican (n=265) and Puerto Rican (n=318) families of individuals with asthma
Howard T, et al1
Two SNPs in ADAM33 were associated with asthma and allergen sensitization.
8
Hispanics with (n=112) and without (n=126) asthma
ADAM33
ReferenceResultsNumber of SNPsStudied
Study SampleGene
Candidate-Gene Association Studies in Hispanics: Limitations
• Small sample size• Inadequate definition of Hispanic subgroups• Heterogeneity of populations studied• Lack of correction for multiple comparisons• Lack of adequate data on environmental
exposures• (For case-control studies): lack of detection and
control of potential population stratification
The Genetics of Asthma in Costa Rica
4.
Rationale and Study Design
4.a.
• Prosperous Latin American Country– Universal access to health care– High literacy rate (~95%)
• High prevalence of childhood asthma in Costa Rica (~23%)
Asthma in Costa Rica
• 1697 Census–2,100 Spaniards–1,400 Amerindians–300 individuals of African descent–160 Mestizos
Costa Rica
• Most Costa Ricans live in a Central Valley separated from the coasts by mountain ranges
• Minimal migration in and out of the Central Valley until the late 1800s
The Central Valley of Costa Rica
Family-based Study of Asthma Genetics in Costa Rica
•• Rationale:Rationale:– To study “complex” diseases, a useful
strategy is to study communities that are relatively isolated genetically
•• Study HypothesisStudy Hypothesis:– A small number of chromosomal regions
contribute to the expression of asthma in Costa Ricans
• Funded by the NHLBI since March of 2001• Phenotypic and genotypic data collected in
2,471 individuals– 671 members of large families of children with
asthma– 1,800 members of nuclear families of children with
asthma
Family-based Study of Asthma Genetics in Costa Rica
Data Collected in Members of Family Pedigrees
• Children and adults:– Questionnaire information– Spirometry with B.D.R.– Methacholine challenge testing– Total and specific serum IgE– Eosinophil count– Skin test reactivity to allergens – Blood sample for DNA extraction
Subject Characteristics and Heritability Analysis
4.b.
Table 1. Characteristics of Family Members (n=687)
99.9 (45.8-115.9)% Predicted Post-BD FEV1/FVC, mean (range)
102.4 (33.6-152.4) % Predicted Post-BD FEV1, mean (range)
2 (0 to 9)Number of positive skin tests, median (range)
208.4 (30 to 7,500) Eosinophil count (cells/mm3), geometric mean (range)
97.0 (0-5,000)Total serum IgE (IU/ml), geometric mean (range)
29.5 (6.4-92.6)Age in years, mean (range)
368 (52.7)Female sex, n(%)
Table 1. Characteristics of Family Members (n=687)
47 (6.8)Current smoker, n (%)
109 (15.9) Ever smoker, n (%)
52 (29.9)87 (17.0)
Physician-diagnosed asthma and current wheezing, n (%)Age <13 yearsAge >=13 years
64 (36.8)166 (32.4)
Current wheezing, n (%)Age <13 yearsAge >=13 years
69 (39.7)128 (25.0)
Physician-diagnosed asthma, n(%)Age <13 yearsAge >=13 years
Table 2. Heritability Analysis of Asthma-Related Traits
14.3% (6.3%)Post-BD FEV1/FVC*
23.0% (6.5%)Post-BD FEV1 (L)*
49.9% (9.2%)Airway responsiveness (d.r.s. to methacholine)*
29.3% (7.6%)Eosinophil count (cells/mm3)&
56.6% (6.5%)Total serum IgE (IU/ml)&
h2N (standard error)
& Variance components analysis adjusted for age and sex.*Variance components analysis adjusted for age, sex, and height.Note: All heritability (h2
N) values > 0 with p<0.0001
Genome-wide Linkage Analysis
4.c.
Overview of Complex Trait Genetics
Demonstrate Familial Aggregation and/or Heritability of Trait
Localize Susceptibility Gene(s)
Identify Disease Susceptibility Gene and Functional Variants
Positional Cloning Candidate Gene Approach
Diagnostics Determine Fraction of Explained Variation Treatment
How to find a disease-susceptibility gene?
page
‘chromosomal region’
This is a sentence in a paragraph…
‘gene’
This it a sentence in a paragraph…
‘mutation’
• Difficult challenge: like finding a misspelled word in a set of encyclopedias!
Plausible candidate genes>100 !
‘which chromosome?’
Vol 7
A1
Z247
•• DefinitionDefinition:: A group of methods that analyze the distribution of DNA markers within families to determine if a particular region of the genome contains a gene related to the phenotype of interest.
•• LOD ScoreLOD Score:: Result of a statistical test to determine if genetic loci are linked, expressed as log10 of the odds that the loci are linked. LOD scores of 3-3.6 correspond to highly significant linkage.
Linkage Analysis
Whole Genome Scans
• A genome scan consists of ~400 STR markers spread across all 23 human chromosomes. These markers are like a dragnet, enabling us to pinpoint the location of genomic regions containing disease susceptibility genes.
• Shown on the right is a map of human chromosome 1 with different type of markers (SNPs and STR or microsatellite markers) overlaid on the map.
• Genome scan was completed in November of 2004 at the Genome Quebec Innovation Centre in 671 individuals– 380 short-tandem repeat (STR) markers, with an average
spacing of 8.2 cM (ranging from 6.2 cM on chromosome22 to 9 cM on chromosome 17)
- Marker locations were determined on the basis of the deCODE map
Genome Scan for Asthma and Asthma-related Phenotypes in Costa Rica
Short-Tandem Repeats: Repetitive elements flanked by unique sequence
GTC GTC GTC GTC
CAG CAG CAG CAG
1 2 3 4
5’ 3’
CAG CAG CAG CAG CAG CAG CAG
1 2 3 4 5 6 7
GTC GTC GTC GTC GTC GTC GTC
GF GM Mom Dad Son Ladder8765432
7/4 8/5
7/5 8/2
7/2
• Phenotype:– Dose-response slope to methacholine, which was log-
transformed (residual kurtosis <0.9)
• Variance component linkage analysis conducted with the SOLAR program– Age, sex, height, smoking (ever), pack-years, and quadratic
terms were considered for inclusion in final models
• All analyses were repeated in nonsmokers only
Genome-wide Linkage Analysis of Airway Responsiveness
1.01
1.32
1.75
All subjects(n=488)
Maximum LOD score
15
12
10
6
Chromosome
119
146
23
147
134
cM
1.04
2.33
1.50
1.41
Nonsmokers(n=423)
Table 1. Genome-wide Linkage Analysis of Airway Responsiveness
Staged Genomic Search
• A genome scan (Stage 1 or “Random Genome Scan”) is carried out at a low marker density and then those regions which may be linked to the trait of interest are investigated by typing more markers (Stage 2 or “Fine Mapping Linkage Analysis”)
• First genome-wide linkage analysis of airway responsiveness in a Hispanic population
• Chromosome 12q24 likely contains a locus (or loci) that influence airway responsiveness, a critical intermediate phenotype of asthma
Discussion
Sex Differences in Total Serum IgE in Costa Rican Pedigrees
p=0.003
Comparisons adjusted for age, age2, ever smoking, pack-years (py) and py2.
Narrow-sense heritability of log10IgE=0.556 (S.E=0.065), p=10-35
Genome-wide Linkage Analysis of Total Serum IgE in Costa Rican Pedigrees
Sex-specific Linkage to Total Serum IgE in Costa Rican Pedigrees
• First demonstration of a distinct genetic architecture of total serum IgE in males and females
• Chromosome 20p12 likely contains a gene(s) that influence total serum IgE in males
Discussion
Future Directions
4.d.
• Fine-mapping linkage analysis to confirm and narrow regions linked to asthma and/or asthma-related traits – Currently on chromosomes 1p, 7q, 20p
• Fine-mapping association analysis to identify gene(s) associated with asthma and/or its intermediate phenotypes (in nuclear families)– First region: chromosome 12q24
Family-based Study of Asthma Genetics in Costa Rica
• Channing Laboratory, Brigham and Women’s Hospital(Boston, MA): Jody Senter, Barbara Klanderman, Craig Hersh, Matt Hunninghake, Ngoc Ly, Ross Lazarus, Steve Lake, Catherine Liang, Dan Laskey, Jessica Su, Ed Silverman, and Scott T. Weiss
• Dept. of Biostatistics, Harvard School of Public Health(Boston, MA): Christoph Lange and Nan Laird
Collaborators
• Genome Quebec Innovation Centre (Montreal, Canada): Thomas Hudson
• Hospital Nacional de Niños (San José, Costa Rica): Manuel Soto-Quiros, Lydiana Avila, Eduardo Fournier,and Mitzi Spesny
Collaborators
The Genetics of The Genetics of Asthma in Costa Asthma in Costa
RicaRica
HL66289, HL04370HL66289, HL04370
The Genetics of COPD in The Genetics of COPD in Costa RicaCosta Rica
HL073373HL073373
Genes, Allergens, and Genes, Allergens, and Asthma in Puerto RicansAsthma in Puerto Ricans
HL079966HL079966
Genome Scan/Linkage →Flanking Markers/Linkage →Positional Candidates/Association →Animal Models/Function
Genetic Studies of Asthma and COPD in Hispanics at BWH