Pharmacogenetics of Asthma Treatment

Project Goal

To sequence and genotype a sample of individuals of Hispanic, non-Hispanic White, and African American ethnicity for all newly discovered single nucleotide polymorphisms (SNPs).

Detailed Goals

The goal of the PhAT is to provide the scientific community with ethnic-specific information of the allele frequency of all SNPs discovered as part of the variant discovery process. Although variants other than SNPs may also be discovered, we will concentrate in this phase on SNPs because they are much more abundant and easier to ascertain. Together with providing an estimate of allele frequency, as part of this project we will also provide pilot information as the potential association between the different SNPs discovered and four heart, lung, and blood disease phenotypes: childhood asthma, adult asthma, chronic obstructive lung disease, and myocardial infarction.

Populations used for sequencing

At the present time we utilize Corriel cell lines and cell lines from a group of asthmatic subjects and DNA from a select group of hispanic subjects for our sequencing efforts. Twenty to thirty subjects from four ethnic groups: European, African/American, and Hispanic (Mexican) asthmatics are sequenced. The total is approximately 100 subjects or 200 chromosomes.

Populations Used for Genotyping

All SNPs present in individual genes (including 5' UTR, 3' UTR, exons and part of introns) will be genotyped at the same time. Genotyping is often performed for several genes concomitantly if the number of polymorphisms discovered in each gene is not sufficient to justify separate genotyping of such polymorphisms. For details of the SNP selection strategy for a given gene see the technical lab notes.

Nurses Health Study I

The Nurses Health Study was originally designed by Dr. Frank E. Speizer to examine the relationship of diet to a variety of cancer and cardiovascular outcomes. The study was begun in 1976 and has longitudinally followed a cohort of 120,000 nurses, initially between the ages of 30 and 55, prospectively, over the past 24 years. The principal investigator for cardiovascular outcomes is Dr. Joann Manson. Dr. Meir Stampfer is the designated Channing Laboratory Co-Investigator of this proposal. Principal outcomes relevant to this proposal include physician-diagnoses based on chart review of: myocardial infarction, stroke, asthma, COPD, and various coagulation factors. 400 ug of DNA is available on 35,000 of the subjects in the Nurses cohort and, in addition, 35,000 new DNA samples are currently being collected.

Physicians Health Study

The Physicians Health Study (PHS) was initially developed as a randomized control trial of aspirin and/or antioxidant vitamins as treatments for myocardial infarction. Dr. Michael Gaziano is now the overall P.I. Dr. Meir Stampfer and Dr. Paul Ridker, both Co-Investigators in this proposal, have been Co-Investigators in this proposal since its inception. The study is of 22,000 male physicians, initially between the ages of 30 and 55 who have been followed for 18 years. All of the outcomes previously described for the Nurses' Health Study above are available on all trial participants. DNA is available on 15,000 of these physicians.

CAMP Study

The Childhood Asthma Management Program (CAMP) is a North American eight-center, double-blind, double-masked trial of inhaled steroid plus albuterol versus nedocromil plus albuterol versus PRN albuterol in three treatment arms. There are a total of 1041 children initially aged 5 to 12, who are entered into this trial, and all children and most of their parents had DNA collected for trios-based, family-based association studies. Phenotypic information is available on doctor-diagnosed asthma, airways responsiveness to methacholine, FEV1, total and specific IgE levels, and response to treatment. Exposure information is available on personal and parental smoking, allergen levels in the home, treatment regimens during the trial, and the presence or absence of pets. DNA is available on all subjects. Dr. Scott T. Weiss is the principal investigator for the Genetics Ancillary Study of CAMP.

The Normative Aging Study

The Normative Aging Study (NAS) is a longitudinal cohort study of 2180 individuals, initially aged 45 to 60, who were health screened at entry. Dr. Scott Weiss is the Principal Investigator for the lung disease outcomes. Dr. Michael Gaziano is the overall study P.I. The NAS has been ongoing for the past 30 years and 1800 of the 2180 initial subjects are still under observation. In 1990, a minority cohort and NAS wives were added to the study. Respiratory and cardiovascular outcomes available include physician-diagnosed myocardial infarction, stroke, hypertension, obesity, asthma, COPD, and coagulation factors. Sleep studies have been performed on the entire population with a sleep questionnaire, and sleep apnea and sleep disordered breathing cases have been identified. DNA is available on 2000 of the 2180 cohort participants.

The Tucson Children's Respiratory Study (TCS)

This is a longitudinal study of the risk factors for and natural history of asthma during childhood and adolescence. Over 1240 index children were enrolled at birth between 1980 and 1984 together with their nuclear families. A careful assessment of asthma symptoms has been done both in the index children and their parents for the last 16-20 years. Over 900 nuclear families were still participating in the study in 1997. Approximately 60% of children are Caucasian, 35% Hispanic and the remaining 5% of other ethnicities, as represented in the Tucson population. DNA samples extracted from blood have already been collected and stored for 630 families with 2113 individuals. Informed consent for genetic studies related to asthma and associated traits has been obtained for all subjects.

Phenotypes Used

We examine five specific conditions from the populations available in Table 1 below. We will be studying adult asthma, childhood asthma, COPD, MI, and DVT. Childhood asthma will be defined as self-report of a doctor's diagnosis with confirmation of a doctor's diagnosis by a medical record or current wheezing symptoms and a doctor's diagnosis within the past year. Adult asthma will be defined as self-report of a doctor's diagnosis with chart confirmation and/or current wheezing or asthma medication within the past year. COPD will be defined as self-report of a doctor's diagnosis or FEV1 % predicted <70% predicted on two successive yearly spirometric examinations. Myocardial infarction will be defined by the DWO criteria of classic symptoms plus enzyme or EKG changes consistent with myocardial infarction. All myocardial infarctions are chart confirmed. Deep venous thrombosis will be confirmed by physician diagnosis of deep venous thrombosis with the presence of a positive venogram and impedence plethysmography or ultrasound. While intermediate phenotypes are available for many of our studies, all studies have stable, consistent diagnoses that will allow pooling of results across studies and there is no intent to use intermediate phenotypes for anything more than diagnostic validation and confirmation for this PGA.

Table 1
POPULATION/PHENOTYPES

Individuals genotyped

Seventy cases from each available ethnic group (Hispanics, non-Hispanic White, and African American) and from each of the these lung diseases under study (childhood asthma, adult asthma, COPD), with only one ethnic group (non-Hispanic) for myocardial infarction (MI) and deep venous thrombosis (DVT) will be obtained from the available populations (Table 2). Sufficient subjects are available for 8 of the 11 possible cells, from our populations (Table 2). A group of 140 controls without the disease are available for each of the 8 cells for which cases are available. Based on the above description, a total of 1680 individuals will be genotyped for each of the newly discovered polymorphisms.

The meaning of race in PhAT Data

For the purposes of the data presented here race refers to the self designation of a racial or ethnic group by the respondent in the above named studies and cell lines. The investigators realize that there are more specific designations for each of the ethnic groups reported here and that these self designations may be inaccurate and/or misleading and should only be used for hypothesis generation purposes. It is a well known genetic fact that genetic variation within self designated ethnic groups is greater than between ethnic groups and these data should not and indeed cannot be used to generalize to a whole race. It is also recognized that race or ethnic groups are social constructs that may (or may not) be a proxy variable for variation in SNP presence or allele frequency. At best, they may offer a clue as to what might be found in a larger outbred population in the US.