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US Genetics of Asthma Resources

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

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US Genetics of Asthma Resources

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  1. US Genetics of Asthma Resources Benjamin A. Raby, MD, MPH Assistant Professor of Medicine Channing Laboratory Brigham and Women’s Hospital Harvard Medical School

  2. 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

  3. 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

  4. CAMP: Childhood Asthma Management Program Dust Eosinophils IgE Methacholine Spirometry Questionnaire • 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. S1-4 Year 1 Year 2 Year 3 Year 4 Budesonide n = 1,041 Placebo Nedocromil

  5. Characteristics of CAMP cohort

  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

  7. 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

  8. CAMP Study CD4+ selection (n = 397) CAMP Continuation Studies DNA (n = 963 ) S1-4 CAMP CAMP CS CAMP CS2 CAMP CS3 Budesonide n = 1,041 Placebo Nedocromil 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.

  9. CAMP Study CD4+ selection (n = 397) Integrative Genomics Study DNA (n = 963 ) S1-4 CAMP CAMP CS CAMP CS2 CAMP CS3 Budesonide n = 1,041 Placebo Nedocromil Collection of peripheral blood CD4+ T-cells from 397 CAMP CS2 participants RNA Study Expression Blood Draw CD4+ T-cell Selection RNA isolation Illumina HumanRef8 v2 20,694 probes 16,709 genes CPT tubes Baltimore, Boston, Denver, St. Louis 17 cc whole blood Miltenyi Anti-CD4+ Microbeads ~106 cells, ≥ 90% purity Qiagen RNA Easy 2.7 ug average yield rRNA 28s:18s 1.7-1.9

  10. 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

  11. 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,

  12. 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

  13. Comparability of Costa Rica with CAMP Hersh et al. Am J Respir Crit Care Med. 2007 176: 849-57

  14. 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):

  15. 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

  16. Eve Consortium Chairs: 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 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 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 NHLBI Division of Lung Diseases

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

  18. 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

  19. Questions?

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