US Genetics of Asthma Resources
Benjamin A. Raby, MD, MPH
Assistant Professor of Medicine
Channing Laboratory
Brigham and Women’s Hospital
Harvard Medical School
Outline
• Childhood Asthma Management Program (CAMP)
• Other Resources at Channing Laboratory
– Genetic Epidemiology of Asthma in Costa Rica
– Crimson Asthma Cohort
• US Asthma GWAS Consortium: EVE
Childhood Asthma Management Program (CAMP)
• NIH/NHLBI initiative to determine the long term
efficacy and safety of inhaled anti-inflammatory
medication in childhood asthma
• 4.5 year RTC comparing inhaled budesonide,
nedocromil and placebo in children ages 5-12 with
mild-to-moderate asthma
CAMP: Childhood Asthma Management Program
Dust
Eosinophils
IgE
Methacholine
Spirometry
Questionnaire
S1-4
n = 1,041
Year 1
Budesonide
Placebo
Nedocromil
Year 2
Year 3
• Inclusion criteria:
• MD diagnosis of asthma
• Methacholine PC20 no greater than 12.5mg/dl
• Asthma symptoms or medication use for 6 months in past year
• Run-in period: 28-days off all controller medication (S2-S4)
• Enrolled 1,041 children ages 5-12 years
• Follow-up >95% through 4.5 years.
Year 4
Characteristics of CAMP cohort
Variable
Median (IQR) or Count (%)
Male
621 (59.6%)
Self-reported white race
711 (68.3%)
Moderate asthma
543 (52.2%)
Parental history of asthma
427 (41.0%)
Pre-BD FEV1
1.58 (1.30–1.93)
Pre-BD FEV1/FVC
0.80 (0.75–0.86)
Methacholine PC20
1.03 (0.50–2.96)
Total serum IgE level, ng/ml
433 (173–1,221)
Hay Fever
557 (53.5%)
Atopic dermatitis
298 (28.6%)
CAMP Genetics Ancillary Study
• At S3 visit, DNA collected from 963 CAMP
participants (574 white probands)
• 652 complete trios (470 white)
• 272 parent-child duos
• 55 sib-pairs
CAMP Genetics Ancillary Study
• Illumina 550K SNP array for 422 probands and
parents
• Illumina 610 Quad array for additional 152
probands
• Affymetrix 6.0 SNP array for all white probands and
parents
CAMP Study
CAMP Continuation Studies
CD4+ selection
(n = 397)
DNA
(n = 963 )
S1-4
n = 1,041
CAMP
Budesonide
Placebo
Nedocromil
CAMP CS
CAMP CS2
CAMP CS3
NHLBI has funded three consecutive continuation
studies to assess long term effects of ICS use,
natural history of asthma (lung function)
By end of study (2011), will have 16 years of
recurrent measures of lung function, questionnaires.
CAMP Study
Integrative Genomics Study
CD4+ selection
(n = 397)
DNA
(n = 963 )
S1-4
n = 1,041
CAMP
Budesonide
Placebo
Nedocromil
CAMP CS
CAMP CS2
CAMP CS3
RNA Study
Collection of peripheral blood CD4+ T-cells from
397 CAMP CS2 participants
Blood Draw
CD4+ T-cell Selection
RNA isolation
Expression
CPT tubes
Miltenyi Anti-CD4+
Microbeads
Qiagen RNA Easy
Illumina
HumanRef8 v2
Baltimore, Boston,
Denver, St. Louis
17 cc whole blood
~106
cells, ≥ 90% purity
2.7 ug average yield
rRNA 28s:18s 1.7-1.9
20,694 probes
16,709 genes
CAMP Genetics Resources
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DNA for 963 subjects (652 trios)
GWAS data - Illumina and Affymetrix (574 probands)
Expression data – 324 subjects
CNV data: Illumina and Affy 6.0; Agilent x 11,000 loci in 2009
Cell lines – 755 probands
Stored serum ( Vitamin D levels)
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Questionnaire data (symptoms, tobacco, meds, exacerbations)
Spirometry, Methacholine
IgE (total and specific) and eosinophils
Treatment response: BD and ICS
• Dust samples
Publications
• Linkage on chromosome 12q (2003 – 12913068)
• VDR receptor polymorphisms associated with asthma (2004 - 15282200)
• Mitochondrial haplotype U associated with asthma (2007 – 17666217)
• GWAS in CAMP identifies PDE4D as asthma candidate gene (2009)
• Dust mite exposure:
– modifies IL10 SNP associations on allergy and asthma exacerbations (2008 – 18440625)
– modifies the effect of TGFB1 SNPs on PC20 and asthma exacerbations (2008 – 19096005)
• Pharmacogenetic papers: CRHR1, TBX21, 17q inversion, others
• Candidate gene associations: TBX21, Eotaxin, IL12B, VEGF, others
• Statistical methods papers: FBAT, PBAT, PC-FBAT, CNV-FBAT …
• Epidemiology papers: natural history, parent of origin, BMI,
Genetic epidemiology of asthma in Costa Rica
• Family-based study of asthmatic children from the Central
Valley of Costa Rica.
• Inclusion criteria:
• 1) Physician-diagnosed asthma and ≥ 2 attacks or respiratory symptoms in
the prior year
• 2) A high likelihood that at least 6 great-grandparents were born in the
Central Valley.
• 8 extended pedigrees and 611 family trios
• Extensive phenotyping, including spirometry,
methacholine challenge, IgE, eosinophils, dust samples
Comparability of Costa Rica with CAMP
Hersh et al. Am J Respir Crit Care Med. 2007 176: 849-57
Crimson Asthma Cohort
• Initiative to develop community-based case-control cohort of
asthmatics through use of EMR data mining approaches
• 40,000 asthmatics treated through Partner’s Health Care.
• Discarded blood samples used for DNA collection
• 7,597 samples collected to date (since October 2007):
African American
Caucasian
Cases
Controls
750
2,058
2,306
2,483
Eve Consortium
• Collaborative initiative supported by NHLBI to bring
together all US groups with asthma GWAS data
• 9 participating groups across the US
• 12,000 asthmatics (30,000 subjects)
• 50% NH-white, 30% AA, 20% Hispanic
Eve Consortium
Chairs:
Participants:
Carole Ober, Ph.D.
The University of Chicago
Kathleen Barnes, Ph.D.
Johns Hopkins University
Christoph Lange, Ph.D.
Harvard School of Public Health
Scott T. Weiss, M.D., M.S.
Harvard Medical School
Eugene Bleecker, M.D.
Wake Forest University
Stephanie London, Ph.D.
NIEHS, NIH
NHLBI
Division of Lung Diseases
Esteban G. Burchard, M.D.
UCSF
Fernando D. Martinez, M.D.
The University of Arizona
James P. Kiley, Ph.D.
Director
William James Gauderman, Ph.D.
USC
Deborah A. Meyers, Ph.D.
Wake Forest University
Susan Banks-Schlegel, Ph.D.
Senior Scientific Advisor
Airway Biology and Disease Branch
Frank Gilliland, M.D., Ph.D.
USC
Dan Nicolae, Ph.D.
University of Chicago
Hakon Hakonarson, M.D., Ph.D.
University of Pennsylvania
Benjamin Raby, M.D., MPH
Harvard Medical School
Weiniu Gan, Ph.D.
Genetics, Genomics,
and Advanced Technologies
Eve Consortium
Study
Ethnicity
Design
Sample Size
Platform
Phenotypes
CAMP
NH-white
Trios
470
Illumina 550K
Affy 6.0
PC20, IgE, RNA,
Drug, Dust, ETS
Mexican
Trios
492
Illumina 550K
skin-tests,
ETS/ pollution
Hispanic
Trios
CC
700
2000 / 2000
Affy 6.0
ETS, IgE
African-American
Trios
CC
700
1000 / 1000
Affy 6.0
ETS, IgE
Martinez
57% NHW
20% AA
Trios
700
Affy 6.0
Skin-tests, IgE
FeNO
USC
56% NHW
CC
1447 / 1918
African-American
CC
464 / 471
Ober, Nicolae
36% NHW
46% AA
CC
318 / 429
TENOR
80% NHW
Cohort
600
Illumina 370K
Difficult to treat
asthma
60% NHW
30% AA
CC
1500 / 700
Illumina 1M
ETS, IgE
100% NHW
100% AA
CC
CC
1400 / 3000
1400 / 3000
Illumina 550K
Weiss / Raby
NIEHS
London
GALA1
Burchard
SAGE
Burchard
CARE
Gauderman, Gilliland
GRAAD
Barnes
Chicago
Bleeker, Meyers
STAMPEED
Bleeker, Meyers, Barnes
CHIP
Hakonarson
Illumina 550K
Pollution
Illumina 550K
PC20, IgE, Skintest, ETS
* CAMP, CARE and ACRN (not in Eve) were genotyped with Affy 6.0 as part of the SHARP initiative
Timeline
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July 2008:
September 2008:
December 2008:
February 2009:
April 2009:
May 2009 (ATS):
Summer 2009:
Fall 2009:
Eve formalized
Phenotype definitions
MTAs completed
Analysis plan devised
Genotype imputations
Meta-analysis completed
Replications
International collaboration
Questions?