NHLBI TOPMed: The Genetic Epidemiology of Asthma in Costa Rica

This study is part of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Program. TOPMed is part of a broader Precision Medicine Initiative, which aims to provide disease treatments that are tailored to an individual's unique genes and environment. TOPMed will contribute to this initiative through the integration of whole-genome sequencing (WGS) and other -omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data. In doing so, this program aims to uncover factors that increase or decrease the risk of disease, to identify subtypes of disease, and to develop more targeted and personalized treatments. Two genotype call sets derived from WGS are now available, Freeze 8 (GRCh38) and Freeze 9b (GRCh38), with largely overlapping sample sets. Information about how to identify other TOPMed WGS accessions for cross-study analysis, as well as descriptions of TOPMed methods of data acquisition, data processing and quality control, are provided in the accompanying documents, "TOPMed Whole Genome Sequencing Project - Freeze 8, Phases 1-4" and "TOPMed Whole Genome Sequencing Project - Freeze 9b, Phases 1-4". Please check the study list at the top of each of these methods documents to determine whether it applies to this study accession.

This administrative supplement to the project, "The Genetic Epidemiology of Asthma in Costa Rica" (R37 HL066289) is in response to NOT-HL-14-029 to perform whole genome sequencing (WGS) on existing NHLBI populations. We focus on asthma because of its public health significance. Asthma affects 26 million U.S. children and adults, remains a major cause of morbidity (one-half million hospitalizations a year) and is the most common cause of school and work days lost. Asthma-related costs are estimated to be over $12.7 billion annually. The Asthma Probands for both the extended pedigrees and the trios utilized in this study were selected on the basis of a physician diagnosis of asthma; a history of recurrent asthma attacks or at least 2 respiratory symptoms; and either airway hyperresponsiveness to methacholine or significant response to bronchodilator (Albuterol) administration. These criteria are identical to the criteria used in the Childhood Asthma Management Program (CAMP).

The three primary goals of this project are to: (1) identify common and rare genetic variants that determine asthma and its associated phenotypes (height, weight, IgE level, lung function, bronchodilator response, steroid treatment response) through whole genome sequencing (WGS); (2) perform novel family based association analysis of our WGS data to identify novel genes for asthma; and (3) integrate epigenomic and transcriptomic data with our WGS data and determine the epistatic interactions present using systems genomics approaches. Identification of the molecular determinants of asthma remains an important priority in translational science. Genome-wide association studies (GWAS) have been successful in this regard, identifying at least 10 novel susceptibility genes for asthma. However, as with most complex traits, the variants identified by GWAS explain only a fraction of the estimated heritability of this disorder. Herein, we propose a novel family-based study design and state-of-the-art genome sequencing techniques to map a set of sequence variants for asthma and its associated phenotypes and assess the interrelationships of the identified genes and variants using systems genomics methods. We have assembled a team of investigators highly-skilled and expert in whole genome sequencing (Drs. Michael Cho and Benjamin Raby), genetic association analysis (Drs. Scott T. Weiss, Jessica Lasky-Su and Christoph Lange), integrative genomics (Drs. Raby, Kelan Tantisira, Augusto Litonjua and Dawn DeMeo), and systems genomics (Drs. Weiss, Amitabh Sharma, Lange and Raby) to address this important problem with both a novel study design and data set.

• Study Design:
  • Family/Twin/Trios
• Study Type:
  • Parent-Offspring Trios
• dbGaP estimated ancestry using GRAF-pop
• Subject Sample Telemetry Report (SSTR)

Asthma probands for both the extended pedigrees and the trios were selected on the basis of a physician diagnosis of asthma; a history of recurrent asthma attacks or at least 2 respiratory symptoms; and either airway hyperresponsiveness to methacholine or significant response to bronchodilator (Albuterol) administration. These criteria are identical to the criteria used in the Childhood Asthma Management Program (CAMP).

Asthma Extended Pedigrees

At least 15 families, each having at least two siblings and no more than one parent with a physician diagnosis of asthma were ascertained and enrolled into this study in Costa Rica. All available first- and second-degree relatives of these probands were enrolled, including affected and unaffected individuals. Probands and their families were recruited from a group of 72 asthmatic children ages 6-12 yr that participated in phase II of the International Study of Asthma and Allergies in Childhood (ISAAC). The Principal Investigator for this study in Costa Rica, Dr. Manuel Soto-Quiros, has been collaborating with us first on a pilot study of the genetics of asthma in Costa Rica. Informed consent for this study was approved by the IRB of the Hospital Nacional de Ninos (San Jose, Costa Rica) and the Costa Rican Ministry of Health, and approval was obtained from the Institutional Review Board of the Brigham and Women's Hospital for genotyping and data analysis. The parents of these children provided information on their respiratory health status and that of their children. Lineages for these 72 children (the probands) were traced back at least three generations using church records. All of these children have at least 6 great-grandparents from the Central Valley of Costa Rica, and are therefore descended primarily from the original founders of the population of the Central Valley of Costa Rica. After determining eligibility, Dr. Soto-Quiros contacted the parents of eligible children. We did, however, exclude trios that are selected for pedigree extension from any of the analyses planned on parent-child trios recruited for the present study. Parents of eligible children were contacted by Dr. Soto-Quiros by mail or by phone, according to their preference. Once an asthmatic child's family was selected for extension, we gave copies of a brief study description to the proband's parents, so that they could keep a copy for themselves and distribute the others to interested relatives. We then asked the proband's parents to ask their relatives for permission to be contacted regarding the study. Relatives that had given us permission to be contacted through the proband's parents were called by telephone to explain the study and to set up interviews.

Parent-Child Trios

Probands for the trios were selected using the same asthma eligibility criteria outlined above. 1,200 asthmatic children and their parents (3,600 individuals) were ascertained and enrolled in this study in the Central Valley of Costa Rica. Probands were recruited from approximately 3,500 school children, ages 6-12 yr, from the Central Valley of Costa Rica. A short screening questionnaire was administered to the parents of these children to obtain information about the child's respiratory health status and the last names of both of his/her parents. The parents were instructed to have their child take the completed questionnaire back to school in a sealed envelope. Based on this information, we selected over 800 children with a physician diagnosis of asthma; either ≥ 2 respiratory symptoms or history of recurrent asthma attacks; and a high probability of having ≥ 6 great-grandparents from Central Valley origins, as determined by our genealogist. Once an asthmatic child's family was selected, we asked permission of the parents to conduct methacholine challenge testing on the index children to determine whether or not they are true asthmatics.

Inclusion Criteria

A family was eligible for inclusion in this study only if the asthmatic proband in that family meets all of the following criteria. Each proband must:

1. Be at least 6 years of age
2. Have a physician diagnosis of asthma and either ≥ 2 respiratory symptoms or a history of recurrent asthma attacks
3. Have either airway hyperresponsiveness to methacholine (PD20 ≤ 16 mg/ml) or (if the FEV1 is ≤ 65% of predicted) a significant bronchodilator response (an increase of at least 12% from baseline FEV1)
4. Have at least 6 great-grandparents born in the Central Valley of Costa Rica
5. Have his/her parents give voluntary written consent to participate in the study
6. Give his/her assent to participate in the study
7. Have at least 2 siblings with physician-diagnosed asthma and no more than one parent with a physician diagnosis of asthma

All first- and second-degree relatives of the proband, affected and unaffected were enrolled in the study of 15 large, multigenerational family pedigrees if available and willing to participate.

The natural mother and father of the proband were enrolled in the study of 600 parent-child trios if available and willing to participate.

Exclusion Criteria

A subject was not eligible for inclusion in this study if any of the following criteria apply. Each subject must not:

1. Be adopted
2. Have a chronic respiratory disorder other than asthma (e.g., active tuberculosis, bronchiectasis). Inactive tuberculosis is not an exclusion criterion
3. For the study of large, multigenerational pedigrees only: Have a familial relationship to any of the remaining fourteen (14) families over the last four generations.

Subject Reconsideration for Inclusion

Subjects fulfilling the following exclusion criteria below might have been eligible for inclusion in the study at a later date provided that the study physician did not feel that their participation woulld adversely influence the results of the study.

• Subjects who had taken antibiotics for respiratory disease within one month or have had respiratory infection within 6 weeks of the visit.

This study originated in 1997 when we recruited both extended pedigrees and trios in the central valley of Costa Rica. It has been continuously funded since then. Costa Rica is an ideal place to study childhood asthma as it has the highest asthma prevalence in the world and is a relative genetic isolate. We utilized the same protocol as was used in the Childhood Asthma Management Program so we could have direct comparability between the two projects. Over the years we have written a total of 77 articles on this population all of these are listed in PubMed.

• Primary Phenotype: Asthma
• Immunoglobulin E, Basic Level of, in Serum
• Body Mass Index
• Body Weight
• Body Height

• HLA-DQA1
• HLA-DQB1
• PDE4D
• SERPINE2
• PRKCA
• TGFB1
• VEGF
• INSIG2
• CRTAM
• TSLP

• BioProject
• PubMed
• Sequence Read Archive
• BioSample
• MeSH
• PMC
• Clinical Trials
  • NCT00021840

• Principal Investigator
  • Scott T. Weiss, MD, MS. Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
• Funding Source
  • R37 HL066289 "The Genetic Epidemiology of Asthma in Costa Rica". National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.