Benjamin A. Raby, MD, MPH

Assistant Professor of Medicine

Channing Laboratory

Brigham and Women’s Hospital

Harvard Medical School

US Genetics of Asthma Resources

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

• Inclusion criteria:• MD diagnosis of asthma

• Methacholine PC 20 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.

S1-4 Year 1 Year 2 Year 3 Year 4BudesonidePlaceboNedocromil

n = 1,041

Dust

Eosinophils

IgE

Methacholine

Spirometry

Questionnaire

Characteristics of CAMP cohortVariable 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 Continuation Studies

S1-4 CAMP CAMP CS CAMP CS2 CAMP CS3

CD4+ selection(n = 397)

BudesonidePlaceboNedocromil

n = 1,041

DNA (n = 963 )

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.

Integrative Genomics Study

CPT tubesBaltimore, Boston,Denver, St. Louis17 cc whole blood

Miltenyi Anti-CD4+ Microbeads

~106 cells, ≥ 90% purity

Qiagen RNA Easy2.7 ug average yield

rRNA 28s:18s 1.7-1.9

IlluminaHumanRef8 v220,694 probes 16,709 genes

Blood Draw CD4+ T-cell Selection RNA isolation Expression

S1-4 CAMP CAMP CS CAMP CS2 CAMP CS3

CD4+ selection(n = 397)

BudesonidePlaceboNedocromil

n = 1,041

DNA (n = 963 )

Collection of peripheral blood CD4+ T-cells from 397 CAMP CS2 participants

CAMP Genetics Resources• 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)

• 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):

Cases Controls

African American 750 2,058

Caucasian 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:Carole Ober, Ph.D.

The University of Chicago

Scott T. Weiss, M.D., M.S.

Harvard Medical School

 

James P. Kiley, Ph.D.

Director

Susan Banks-Schlegel, Ph.D.

Senior Scientific Advisor

Airway Biology and Disease Branch

 

Weiniu Gan, Ph.D.

Genetics, Genomics,

and Advanced Technologies

Participants:Kathleen Barnes, Ph.D.

Johns Hopkins University

 

Eugene Bleecker, M.D.

Wake Forest University

 

Esteban G. Burchard, M.D.

UCSF

 

William James Gauderman, Ph.D.

USC

 

Frank Gilliland, M.D., Ph.D.

USC

 

Hakon Hakonarson, M.D., Ph.D.

University of Pennsylvania

NHLBIDivision of Lung Diseases

Christoph Lange, Ph.D.

Harvard School of Public Health

Stephanie London, Ph.D.

NIEHS, NIH

 

Fernando D. Martinez, M.D.

The University of Arizona

 

Deborah A. Meyers, Ph.D.

Wake Forest University

 

Dan Nicolae, Ph.D.

University of Chicago

 

Benjamin Raby, M.D., MPH

Harvard Medical School

 

Study Ethnicity Design Sample Size Platform Phenotypes

CAMPWeiss / Raby

NH-white Trios 470Illumina 550K

Affy 6.0PC20, IgE, RNA, Drug, Dust, ETS

NIEHSLondon

Mexican Trios 492 Illumina 550Kskin-tests,

ETS/ pollution

GALA1Burchard

HispanicTriosCC

7002000 / 2000

Affy 6.0 ETS, IgE

SAGEBurchard

African-AmericanTriosCC

7001000 / 1000

Affy 6.0 ETS, IgE

CAREMartinez

57% NHW20% AA

Trios 700 Affy 6.0Skin-tests, IgE

FeNO

USCGauderman, Gilliland

56% NHW CC 1447 / 1918 Illumina 550K

Pollution

GRAADBarnes

African-American CC 464 / 471 Illumina 550K

ChicagoOber, Nicolae

36% NHW46% AA

CC 318 / 429PC20, IgE, Skin-test,

ETS

TENORBleeker, Meyers

80% NHW Cohort 600 Illumina 370KDifficult to treat

asthma

STAMPEEDBleeker, Meyers, Barnes

60% NHW30% AA

CC 1500 / 700 Illumina 1M ETS, IgE

CHIPHakonarson

100% NHW100% AA

CCCC

1400 / 30001400 / 3000

Illumina 550K

Eve Consortium

* CAMP, CARE and ACRN (not in Eve) were genotyped with Affy 6.0 as part of the SHARP initiative

Timeline• July 2008: Eve formalized• September 2008: Phenotype definitions• December 2008: MTAs completed• February 2009: Analysis plan devised• April 2009: Genotype imputations• May 2009 (ATS): Meta-analysis completed• Summer 2009: Replications• Fall 2009: International collaboration

Questions?