The Barbados Asthma Genetics Study originated in 1993 with an aim to test for linkage and association for asthma and asthma severity and associated traits, and in 1993 we initiated the collection of DNA samples and expansion of families for a family-based genetic epidemiologic study of asthma. In 2007 we performed a genome-wide association study (GWAS) on 655,352 SNPs using the Illumina Infinium™ II HumanHap650Y BeadChip v.1.0 (Illumina Inc.) on a subset of 1,000 Barbados participants. Of those, 48% are male, and 22% are children; the mean age of the full population is 30.63 ±17.06, and all but one individual (adult relative) self-reported as African Caribbean. According to admixture analyses, the proportion of African ancestry is 77.4% among 298 Barbadian founders. All subjects have previously provided informed consent. The primary outcome measure is asthma, and the approach for characterizing asthma in the Barbados population is based on the validated Respiratory Health Questionnaire (RHQ) designed from the 1978 American Thoracic Society questionnaire (ATS; Am Rev Respir Dis 1987; 136(1):225-244), which includes: (1) a reported history of asthma using the RHQ, (2) a history of physician-diagnosed asthma (past/current) and (3) a reported history of wheezing without an upper respiratory infectionor two out of the following four symptoms: wheezing with a URI, cough without a URI, shortness of breath, tightness of chest. Additional phenotype data include asthma severity, total serum IgE, and serum levels of IL-13, IFN-γ, and serum sCD14 in a subset of the population. The family-based population is highly atopic (71.4%), with a mean total serum IgE of 433.5 ng/mL (range 385.6-487.3). In most cases both parents are available for asthma probands; in the event that a parent is missing, genotype is inferred from full- and half-siblings. Probands were recruited through referrals at local polyclinics or the Accident and Emergency Department at the Queen Elizabeth Hospital, and their nuclear and extended family members were subsequently recruited. All subjects gave verbal and written consent as approved by the Johns Hopkins Institutional Review Board (IRB) and the Barbados Ministry of Health.
GRAAD African American case-control study:
The set of self-reported African American asthma cases and non-asthmatic controls are comprised pediatric and adult African American populations, plus one study on healthy African Americans, recruited through Johns Hopkins University and/or Howard University, in the Baltimore-Washington, D.C. metropolitan area (mean age 29.55 ± 18.10). Using GWAS data as described for the Barbados study, the estimated proportion of African ancestry is similar for African American cases and controls (72.3% and 72.5%, respectively) to the proportion among Barbadians. Because asthma is often characterized by onset during childhood, there was a deliberate decision to favor adults in the control group to minimize including controls with some potential for developing asthma; consequently, the mean age of GRAAD asthmatics is 23.78 ± 17.85 years, and of non-asthmatic controls the mean age is 35.23 ± 16.51 years. Informed consent was obtained from each study participant, and the study protocol was approved by the institutional review board at either the Johns Hopkins University or Howard University. Among all cases, asthma was defined as both a reported history of asthma and a documented history of physician-diagnosed asthma (past or current). For each of the asthma studies, a standardized questionnaire based on either the ATS RHQ or International Study of Asthma and Allergy in Childhood (ISAAC; Eur Resp J 1998; 12(2):315-335) was administered by a clinical coordinator. Asthma status on 50 controls participating in a study of the genetics of human pigmentation (Hum Genet 2005; 116(5): 402-6) was not explicitly determined, although “known clinical disease” was among the exclusion criteria. All other controls were administered a standardized questionnaire and determined to be negative for a history of asthma. The asthma cases are largely atopic, with a mean total serum IgE level of 315.6 (270.4-368.3), compared to a mean of 143.3 (123.8-165.8) among non-asthmatic controls (70% atopic).
Baltimore Asthma Severity Study (BASS)
Participants in BASS include individuals with the full range of mild to moderate to severe asthma, frequency-matched on age and gender with non-asthmatic controls. To be eligible for screening, participants had to self-identify as African American; a resident of Baltimore City; 8 to 40 years of age; parents, participant-identified as both African American. The entire study population was identified through clinics affiliated with Johns Hopkins University, including the East Baltimore Medical Center (EBMC), the Wyman Park Medical Center, Berea Medical Center and Johnson Medical Center, all of which are located in inner city Baltimore, and were part of the Johns Hopkins Community Physicians, an integrated delivery system. Study participants were identified by review of administrative databases for asthma related visits as defined by primary or secondary ICD-9-CM code 493 from claims data. Patients were contacted by a Research Assistant to determine eligibility and assess their interest in participating in the study. Data included a detailed family history, with a focus on asthma and allergic diseases; sociodemographic variables; smoking; history of environmental and (if applicable) occupational exposures, and medical history, including comorbid conditions. For individuals with asthma, the questionnaire included a module designed to capture information about duration of asthma, current medications, frequency of symptoms, nocturnal awakenings due to asthma; and history of asthma exacerbations. Such information is essential, together with baseline spirometry (which is part of the methacholine challenge test), for the assessment of disease severity. In addition, at the second visit, case subjects were asked to respond to a brief questionnaire on current medication use and symptoms, information that is essential for pharmacogenetic analysis for b2-adrenergic responsiveness. Data from the clinical tests was used to validate the diagnosis of asthma (cases) and/or the lack of an asthma diagnosis (controls), assess disease severity and allergic status. The study protocol, recruitment procedures, and consent forms were approved by the Institutional Review Board of Johns Hopkins University.
Reducing Emergency Asthma Care in Harlem (REACH)
The REACH study consists of adult residents of Central Harlem or West Harlem who visited the Harlem Hospital Center ED for an asthma exacerbation, and spoke English. During the REACH study period, 1,391 adults visited the ED for asthma, and 726 patients (52%) were eligible. Non-asthmatic controls were selected from the same ED. Of the eligible participants, 52% consented to participate and came for their scheduled interview at an outpatient chest clinic ~3 weeks following the ED visit. Patients were contacted by a Research Assistant to determine eligibility and assess their interest in participating in the study. Data included a detailed family history, with a focus on asthma and allergic diseases; sociodemographic variables; smoking; history of environmental and (if applicable) occupational exposures, and medical history, including comorbid conditions. For individuals with asthma, the questionnaire included a module designed to capture information about duration of asthma, current medications, frequency of symptoms, nocturnal awakenings due to asthma; and history of asthma exacerbations. Data from the clinical tests was used to validate the diagnosis of asthma (cases) and/or the lack of an asthma diagnosis (controls), assess disease severity and allergic status. The study protocol, recruitment procedures, and consent forms were approved by the Institutional Review Board of Columbia University.
Brazilian Immunogenetics of Asthma and Schistosomiasis (BIAS)
The study was conducted in the rural district of Conde, Bahia—located 200 km north of the city of Salvador—in 5 communities where schistosomiasis is endemic (Buri, Camarao, Genipapo, Sempre Viva, and Cobo). Previous investigations in this region verified the endemicity of schistosomiasis (Araujo et al Int Arch Allergy Immunol 2000;123:145–8). Regular, publicly administered mass‐treatment campaigns against helminthic infection last occurred during 2001. The population of Brazil represents a mixture of West African, European, and Amerindian ancestral populations, with substantial African admixture in Bahia. All participants self-reported as African Caribbean. Subjects were recruited through a whole-population ascertainment scheme between July and September 2004, and 822 subjects were enrolled from an estimated total population of 1,700. The dataset is comprised of 2 large pedigrees with 535 and 310 members collapsed into 318 nuclear families 822 schistosomiasis infected individuals and asthmatics. Children represent 49.6% of the cohort. There are 360 males and 462 females in the dataset. Local health liaisons informed volunteers about the study, in a concerted effort to reach all households, and volunteers attended the regional public health clinic or a makeshift clinic set up in a school in the 2 larger villages (Cobo and Sempre Viva) or in Buri, which is accessible from the 2 other smaller villages (Genipapo and Camarao). Children under 6 years old were excluded. Blood was collected through venipuncture and serum was separated for measuring tIgE level. Two fecal samples were collected from subjects at an interval of 2–40 days. All adults provided written consent (or verbal consent recorded by a witness); children gave verbal assent, and written consent for children's participation was obtained from a parent or guardian. The research protocol was approved by institutional review boards at Johns Hopkins University School of Medicine and the Federal University of Bahia and was endorsed by the National Commission for Ethics in Human Research in Brazil. A total of 812 DNA samples are available for the current application.
Chicago Asthma Genetics Study (C.A.G.)
CAG was designed to identify genes that influence risk for asthma or asthma-related phenotypes in individuals representing diverse ethnic groups. European American and African American families were ascertained through affected sib pairs, trios through affected children, adults and children with severe persistent asthma, and non-asthmatic control subjects (over the age of 18 years). Asthma cases and families were recruited in the adult and/or pediatric asthma clinics at University of Chicago Hospital; controls were recruited from the medical center at large. Asthma was diagnosed as follows: 1) presence of at least 2 of 3 symptoms (cough, wheeze, shortness of breath), 2) doctor’s diagnosis of asthma, and 3) either 20% fall in baseline FEV1 after inhalation of £25 mg/ml methacholine or ³15% improvement of baseline FEV1 after inhalation of albuterol. All subjects were at least 6 years of age. Severe persistent asthma is defined as 1) FEV1 < 60% predicted, 2) using either oral steroids with or without current symptoms or inhaled steroids with current symptoms, 3) nocturnal symptoms, and 4) either 15% improvement of baseline FEV1 after inhalation of albuterol or 15% time-related reversibility on medications. Individuals with the following conflicting diagnoses were excluded from these study: birthweight <2 kb, congenital pulmonary disease, conflicting pulmonary diagnosis, TB, severe cardiac disease, isolated occupational induced asthma, systemic vasculitis including the lungs. All eligible asthmatics (and their healthy relatives in the family studies) underwent the following: spirometry to assess lung function, methacholine challenge studies if their baseline FEV1 was ³70% predicted, airway reversibility studies if their baseline FEV1 was <70% predicted, skin prick testing to 14 allergens, blood sampling for serum IgE studies, eosinophil counts, and DNA extractions.
Chicago Initiative to Raise Asthma Health Equity (CHIRAH)
The Chicago Initiative to Raise Asthma Health Equity was one of four asthma disparities centers funded by the NHLBI to evaluate the etiologies of asthma racial disparities and pilot interventions. The CHIRAH cohort is a community-based longitudinal cohort study of urban children and adults with persistent asthma. CHIRAH was designed to examine the impact of socioeconomic and psychosocial stressors on asthma status. Subjects were enrolled from February 2004 to July 2005. The cohort was established by a broad community-based screening for households with persons with asthma using a school based proportionate sampling technique. This process resulted in 4 school groups (high/low AA and mid/low income). School screening of 48,917 elementary school-aged children led to 3,676 households with persons with asthma (either the child or a household adult if the child did not have asthma) who agreed to be contacted for research. Eight hundred thirty-nine child-caregiver dyads and 519 adults were verified eligible and ultimately 561 child-caregiver dyads, and 353 adults were enrolled and completed the baseline protocol between January 24, 2004 and July 30, 2005. For the current application, 353 African American subjects provided informed consent to genetic samples being taken and used for future studies of asthma. Of these 190 are children, and 131 are adults (123 males and 198 females). The mean age of the children was 10.5±1.9 years for children and 30.7±6.0 years for adults. Persistent symptomatic asthma was defined as physician diagnosed asthma and requiring at least 8 weeks of asthma medication over the previous 12 months. Biologic phenotypes collected as part of the study include spirometry, salivary cotinine, ImmunoCAP atopy testing (house dust mite (Dermatophagoides pteronyssinus) and cockroach (Blattella germanica). Inclusion criteria are: (English-speaking adults (age 18-40) with persistent symptomatic asthma and children (age 8-14) with persistent symptomatic asthma (and their primary caregivers). Exclusion criteria include: not fluent in spoken English, no telephone in household, not residing in the Chicago Metropolitan area. The genetic substudy was approved by all 3 institutions involved, including Children’s Memorial Hospital, Northwestern University, and John H. Stroger Cook County Hospital.
Howard University Family Study (HUFS)
The main objective of the “Howard University Family Study” was to enroll and examine a randomly ascertained cohort of 350 African American families with members in multiple generations from the Washington, D.C. metropolitan area. A follow-up study entitled “Admixture Mapping for Hypertension in African Americans’ aimed to build additional resources for hypertension cases and matched controls. Protocols for both studies were approved by the HU-IRB. Hypertension was defined by a BP>140/90 mm Hg or treatment for it. To qualify as a control, participants were required to have SBP<120 mm Hg and DBP<80 mmHg and have never taken antihypertensive medication. A total of 261 asthma participants were identified from these studies. Participants were not ascertained based on disease condition; their asthma status is based on self-report of a doctor’s diagnosis. A subset of 200 asthma cases and 200 controls are included in this application.
Jamaican Adolescent Asthma Study (JAAS)
Participants in this study comprise a cross-sectional look at the prevalence of asthma and allergies in Jamaican Adolescent’s at 18 years study. Asthmatic subjects and controls who will participate in this protocol were recruited from an existing longitudinal birth cohort of young African Caribbean adults in Jamaica. Participants’ mothers were initially recruited into the Jamaica Perinatal Mortality Survey of 1986 (a study for which there are over 33 peer-reviewed manuscripts in PubMed), which included all children born in Jamaica in September-October 1986. Children were contacted at ages 11 and 16 as part of a child development study, and again at age 18 for a cardiovascular study. For the current asthma genetics study, 897 participants of the original birth cohort were consented to participate. They are now 18-20 years old and currently live in the metropolitan area (Kingston, St. Andrew, or St. Catherine). The primary outcome is asthma. Unequivocal asthma cases and non-asthmatic controls were defined according to results from a modified ISAAC questionnaire (The International Study of Asthma and Allergies in Childhood (ISAAC) Steering Committee. Lancet 1998; 351:1225-32) and (ii) a history of physician-diagnosed asthma (past/current). Basic demographic information and data on environment exposure was ascertained. Willing participants were asked to give blood samples for storage and future genotyping and for serum for measuring total IgE levels. Asthma associated phenotypes including serum inflammatory cytokine levels, total and specific IgE and gene/environment interactions (smoking exposure) are also analyzed. Demographic, phenotype, and outcome data related to asthma and allergy lung function, morbidity, and mortality is available for the genetic analysis. All subjects provided informed written consent to participate in the study as approved by the University of the West Indies, Mona campus.
Proyecto Genes Candidatos en Asma (PGCA)
The Colombian cases/control and family-based study population (N = 2,075) comprised participants in the program “Prevalence and Risk Factor for Asthma and Allergies”, a study conducted for the Institute for Immunological Research of The University of Cartagena (Colombia). The aim of this program is to identify environmental and genetic risk factors for asthma and allergies, in subjects from Cartagena, a tropical city located in the province of Bolivar in the Caribbean Coast of Colombia. The primary outcome measure of both the case/control and the family based study is asthma. For the case-control study, 836 unrelated cases and 574 controls self-reporting as African Caribbean were recruited from the Social Security Clinic and outpatient health centers in Cartagena from 2002 to 2005. Asthma was defined according to the Global Initiative for Asthma Criteria (GINA 2005) using a standardized Respiratory Health Questionnaire (RHQ) designed from the 1978 American Thoracic Society questionnaire, well-suited for population-based studies and validated in the Collaborative Studies on the Genetics of asthma (CSGA) Barnes et al 1999 JACI Oct;104(4 Pt 1):791-6). Extensive phenotypic data and blood samples were collected at the time of the recruitment for DNA extraction and total and specific IgE (sIgE) levels measurements. Total serum IgE was measured in duplicate using a commercial enzyme-linked immunosorbent assay (ELISA) kit (RIDASCREEN® Total IgE; R-Biopharm, Darmstadt, Germany). Atopic status was assessed by specific IgE levels against Blomia tropicalis (Bt) and Dermatophagoides pteronyssinus (Dp) extracts since these two mites are the main source of sensitization in tropical environments and the prevalence of IgE sensitization to other aeroallergens is very low in Cartagena; specific IgE was determined by indirect ELISA in all individuals. Atopy was defined as positive spIgE to at least one of the two mite extracts tested. The Colombian genetic family-based study is an existing study comprised of 655 individuals in 167 nuclear and extended families. The families were ascertained based in the proband who met the criteria mentioned above. 100% of the family members self-report as Colombians. After a full verbal explanation of the investigation, all subjects or their guardian/responsible adult gave written consent for their inclusion in the present study as approved by the Bioethics Committee of the School of Medicine of The University of Cartagena.
Study of African Americans, Asthma, Genes, and Environments (SAGE)
The majority of subjects recruited into SAGE were children under the age of 21, with equal proportions of male and female subjects. Whole blood was collected and processed and genomic DNA was isolated and anonymously stored at the UCSF DNA Bank Core facility. Additional phenotype data include IgE levels, cotinine and other biomarkers including cytokines. All samples were anonymously bar coded and free of all patient identifiers. Cases and controls were asked to come to a one time visit. For asthmatic and healthy child/adolescent subjects, the parent[s] was the primary contact and through whom we assess interest in their and their child’s participation, general eligibility, and willingness to contact other potentially eligible family members. Written informed consent was obtained on all participants as approved by the IRB at the University of California, San Francisco.
Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-ethnicity (SAPPHIRE): The genomewide association data that will be included as part of this application will be those African American patients that met the following entry criteria: age ≥12 years, a physician diagnosis of asthma (identified by using encounter data prior to screening and by the survey administered at the clinic visit), bronchodilator reversibility on pulmonary function testing (i.e., improvement in baseline FEV1 of ≥12%), no smoking in the preceding year or <10 pack-year smoking history total, no oral or inhaled corticosteroid use in the 4 weeks preceding enrollment, and not pregnant at the time of enrollment or during the 6-week treatment period. Individuals to be included for the replication studies are those who, at the time of initial screening, did not meet all of the above criteria, but were aged 12-56 years, had a physician diagnosis of asthma, and did not have a prior diagnosis of congestive heart failure or chronic obstructive pulmonary disease. The study has been approved by the Institutional Review Board (IRB) at HFHS and is compliant with its Health Insurance Portability and Accountability Act policy. Written assent and consent was obtained from all children and parents/guardians, respectively, for minors to participate in the study. Written consent was obtained for all adult participants. Each site investigator and staff member involved has completed training in the areas of patient confidentiality. In anticipation of the NIH policy for sharing data obtained in NIH supported genome-wide association studies (notice# NOT-OD-07-088), this language was incorporated into our patient consent forms prior to enrollment to notify patients of the possibility of data sharing.
Severe Asthma Research Program (SARP)
All volunteers participating in SARP protocols provided informed written assent/consent, including a separate assent/consent to grant permission to share information with the other studies. Subjects >7 years of age with asthma were included in the research design first by participating in clinical testing to characterize the severity of asthma. Clinical testing for all subjects included: pulmonary function testing, methacholine challenge, allergy testing, measurement of exhaled nitric oxide and collection of exhaled breath condensate and induced sputum. Subjects were not required to perform all evaluations. The subject population for SARP was based on the enrollment of subjects at all 8 of the SARP sites. At Wake Forest there was enrollment of 1,284 African American nonsevere asthmatics and severe asthmatics and 458 African American healthy controls. There is a predominance of females in the adult population as 65% of the SARP I subjects were women. Exclusion criteria for asthmatic subjects includes: a greater than five pack year history of smoking, a prior diagnosis of vocal cord dysfunction, cystic fibrosis or chronic obstructive pulmonary disorder as well as any other lung disease besides asthma, or any coronary artery disease, hypertension, diabetes or renal failure that is not well-controlled as deemed by the principal investigator. Subjects of all ages and all races were originally recruited (range >7 years of age). In our experience, children younger than 7 years of age are unable to perform rigorous pulmonary function testing in an accurate or reproducible manner and will be excluded for this reason. Because of the interaction of several of our procedural medications with pregnancy, pregnant women are excluded from the study. All volunteers participating in SARP protocols provided informed written assent/consent approved by the IRB at Wake Forest University.
University of Chicago/Nigeria, Asthma, Environment and the Genes Study
The purpose of this research is to determine asthma risk factors in a black population with similar ancestral origin as African Americans. The main objective is to see how "similar" or "different" the Nigerian Yorubas are with respect to the genetic contributions to asthma. Our long-term goal is to identify the genetic variation and environmental factors that contribute to risk and severity ofasthma among African populations with a view to closing the global gaps that exist in asthma outcomes. This study was designed as a case control study to determine the prevalence of asthma in children in the 6 to 18 age group living in rural and urban settings in Southwest, Nigeria. In the Phase I, a total of 1690 school children living in rural communities were interviewed using the validated ISAAC questionnaire as in the approved protocol. Based on our preliminary review of the questionnaires responses, 104 subjects appear to have symptoms consistent with asthma. We also identified 121 control subjects, which were matched with the asthma cases based on sex and age in a 1:1 ratio. Both asthmatics and controls then underwent spirometry, allergy skin testing to 8 environmental allergens using the OMNI Skintestor kit, stool evaluation for ova and parasites, serum IgE levels, and eosinophil count. All participants also had DNA extracted to conduct studies to identify variations in areas of interest that may confirm risk for asthma.
Asthma Genomics in Ethnic Populations of Honduras
The populations included in this study are the Garifuna, as well as other indigenous autochthonous groups inhabiting Honduras, a Central American country. The Garifuna populations included in CAAPA are composed of individuals of West African descent who arrived to Honduras mare than two centuries ago, peopling the entire Caribbean coast of the country. The structure and history of Garifuna in Honduras is described in Am J Hum Biol 2010; 22(1):36-44. We visit the communities and contact asthmatic subjects through community leaders. The goal in each community is to recruit every possible asthmatic individual over age five, as well as healthy controls. Each subject who agrees to enter the study fills a questionnaire from the ISAAC (Lancet 1998; 351:1225-32), and answers basic demographic and environmental questions. Asthmatic patients are those with a history of asthma symptoms and/or medical diagnosis of asthma. Blood samples for storage and future determination of serum IgE concentration, expression profile (RNA), and genetic/genomic analyses are taken. Participants are asked to provide stool samples for coproparasitoscopic analysis whenever possible. We performed lung function tests to all asthmatic patients. All subjects provide informed written consent to participate in the study as approved by the Ethics Committee of Universidad Católica de Honduras, Campus San Pedro y San Pablo. Asthmatic patients and healthy controls from five communities have being sampled to this day.
The village of San Basilio de Palenque was established by Benkos Bioho sometime in the 16th century. It has a population of about 3,500 inhabitants and is located in the foothills of the Montes de María, southeast of the regional capital, Cartagena. San Basilio is populated mainly by Afro-Colombians which are direct descendants of African slaves brought by the Spanish during the Colonization of the Americas and have preserved their ancestral traditions and have developed also their own language. The population is predominatly black and still preserves traditions and language from their African ancestors. San Basilio is the only “palenque” that survives from those that existed previously which were funded by slaves that escaped from their owners. Many of the oral and musical traditions have roots in Palenque's African past. In 2005 the Palenque de San Basilio village was proclaimed “Masterpiece of the Oral and Intangible Heritage of Humanity” by UNESCO. The selection of individuals for the current study was based on the knowledge of their African ancestors, and their residency in the village. The gathering was promoted by community leaders, and the individuals were selected with a minimum degree of relatedness as possible in such inbreed community. The assistance of Professor of Ethno-education program Regina Miranda, was critical in the recruitment and enrolling of the individuals. All individuals gave informed consent as approved by the Ethics committee of the University of Cartagena.