Esteban G. Burchard - US grants

DESCRIPTION (provided by applicant): Asthma prevalence, morbidity and mortality are higher among Latino Americans on the east coast than on the west coast of the U.S. This is in stark contrast to the near geographic uniformity of asthma morbidity and mortality rates among African Americans and Caucasians in the U.S. The differences in asthma prevalence and severity among Latino Americans on the two coasts may reflect differences in the genetic contributions of Ancestral Native American, Spanish and African populations to the Latino population on the east coast (predominantly Puerto Rican) and west coast (predominantly Mexican). To determine whether identifiable genetic factors are associated with asthma and severe asthma among Mexican Americans, the largest U.S. Hispanic group, we will recruit Mexican American asthmatic subjects (probands) and their biologic parents (n=600) from California during a 1 year period. Probands will undergo formal phenotypic characterization. We will assemble a repository of DNA and plasma from the probands and their parents. We will identify novel single nucleotide plymorphisms (SNPs) among candidate genes at loci where there is evidence to suggest linkage to asthma in previous studies of other populations. We will determine whether novel SNPs and SNPs known to be associated with asthma in other populations are associated with asthma in Mexican Americans. We will compare the results generated from this repository to similar ongoing studies in Puerto Rican asthmatic families. The creation of a repository of DNA from well-characterized Mexican American asthmatics will enable future analysis of other genes identified in other studies. The results of this work may have important implications for the diagnosis, treatment and prognosis of asthma not only in Mexican Americans, but in other populations as well. The proposed research project is one component of a career development plan designed to prepare the applicant to lead an independent program applying novel advances in genomics to improving the diagnosis and treatment of asthma in medically underserved populations. The training component of this application includes oversight from an experienced pulmonary physician-scientist (Dr. Dean Sheppard), with a strong track-record in training successful pulmonary academicians, formal mentoring from a multidisciplinary scientific advisory committee, all collaborators from GALA, and advanced didactic training in clinical research design and genetic association studies. This proposal?s focus is consistent with the goal established by Healthy People 2010, to reduce disparities in health among different populations.

genetic susceptibility; quantitative trait loci; racial /ethnic difference; respiratory disorder epidemiology; asthma; human population genetics; health disparity; caucasian American; Mexican Americans; nucleic acid sequence; linkage mapping; African American; Puerto Rican; patient oriented research; human subject; spirometry; phlebotomy; clinical research;

DESCRIPTION (provided by applicant): In racially admixed populations genetic associations may be confounded by population stratification. To control for population stratification, statistical methods that use marker genotype data to infer population structure have been proposed as an alternative to family-based tests of association. However, there is limited empirical data on how these methods perform in real populations. This application will use well characterized populations of Mexican and Puerto Rican asthmatics, their parents, and control subjects recruited from the same sites to examine the effectiveness of approaches to correct for the effects of population stratification on case-control genetic association studies. This application has three specific aims: 1) To test and compare methods of detecting and correcting for population stratification we will genotype a total of 100 ancestral informative markers (AIMs) for 400 asthma cases and an equal number of control subjects. These AIMs will then be used with three statistical methods developed to detect and correct for population stratification. The number and characteristics of markers required to correct false positive associations between AIMs, asthma and asthma quantitative traits will be evaluated and compared 2) To compare the power of genomically adjusted case-control studies to the TDT. An allele from each of the 100 AIMS will be considered as a risk factor for a simulated "phenotype". The association between phenotypes and each AIM will be tested with the TDT and with a case-control analysis after adjustment for stratification to compare the false negative rates for these study designs. 3) To use the results from aim 1 and 2 to define an optimal approach for analysis and interpretation of case-control association studies in these populations and apply this approach to analyze the association between asthma and a series of candidate genes. The results of these studies should provide important insights into the optimal methods to control for population stratification in case-control association studies, thereby facilitating the inclusion of admixed populations in future genetic studies of complex diseases such as asthma.

DESCRIPTION (provided by applicant): In the United States, asthma prevalence is highest in Puerto Ricans (26%) and lowest in Mexicans (10%). This is paradoxical since both groups are considered "Hispanic" or "Latino". Although there are many potential explanations for this observation, including environmental and socioeconomic factors, one potential explanation is that the genetic predisposition to asthma differs among subgroups within the Latino population. Latinos are admixed and share varying proportions of African, Native American and European ancestry. The mixed ancestry of Latinos provides unique opportunities in epidemiological and genetic studies and may be useful in untangling complex gene-gene and gene-environment interactions in disease susceptibility. This proposal will take advantage of clinical data and genomic DNA on 2,100 Puerto Rican and 1,500 Mexican asthma cases and controls collected as part of two large studies of asthma in Latinos (GALA 1 and GALA 2). The goal of this proposal is to perform genome-wide association analyses to identify genetic factors associated with asthma and related phenotypes in Puerto Ricans and Mexicans. In addition, potential interactions between these genetic factors and other genes and environmental variables will be investigated. Specifically, we will: 1) genotype Puerto Rican and Mexican asthma cases and controls using the Affymetrix state-of-art 500K GeneChip arrays, 2) perform genome-wide association analysis on 500K GeneChip data to identify SNPs associated with asthma, asthma severity and bronchodilator response. The analysis will include clinical and demographic characteristics, environmental factors and individual admixture estimates to correct for potential confounders. In addition, admixture mapping analysis will be performed to complement the genome-wide association analysis. Admixture mapping may identify novel regions that harbor racial/ethnic specific alleles for asthma and related phenotypes;and 3) fine map SNPs significantly associated with asthma and related phenotypes in genome-wide analyses (initial-hit SNPs). To our knowledge this is the first proposal to perform a genome-wide association analysis for asthma and related phenotypes in Latinos. Due to the size and scope of this project, the results of this study should substantially increase our understanding of the etiology of asthma and drug response. By gaining a better understanding of asthma risk factors in diverse populations, this proposal is consistent with the goals established by Healthy People 2010, which are to eliminate health disparities among different segments of the population.

Asthma is characterized by allergic airway inflammation and airway remodeling which underlie the clinical characteristics of airflow limitation, bronchial hyperresponsiveness, and susceptibility to exacerbation. Important questions remain for how asthma develops, the mechanisms of allergen sensitization, and the factors that contribute to the persistence of asthmatic airway changes over a lifetime. Here we propose clinical studies to investigate fundamental questions about the role of chitinases and TGFp in initiating and perpetuating allergic asthma. We will combine comprehensive genetic studies with detailed translational studies to address hypotheses for how polymorphisms in chitinase and TGFp pathway genes influence allergen sensitization, asthma susceptibility and expression of asthma-related phenotypes. Aim 1 will determine the independent and dependent effects of genetic variants in chitinases (AMCase/CHIT1) on sensitization to fungal aeroallergens and other asthma outcomes. Genetic variants in the CHIT1 and AMCase genes will be tested for association with skin test sensitivity to fungal aeroallergens and other asthma phenotypes in a cohort of 1700 asthma cases provided by the Asthma Clinical Research Network and independent cohorts of Latino and African American subjects. Aim 2 will examine the autonomous and interactive effects of genetic variants in 26 TGFp pathway genes on asthma and asthma-related phenotypes in several large, well-characterized, ethnically diverse asthma family based and case-control cohorts. Associated SNPs will be replicated in independent populations. Aim 3 will evaluate the functional significance of the genes and genetic variants examined in Aims 1 and 2. We will analyze the relative gene and protein expression of CHIT1 and AMCase in specific lung compartments and the effects of genetic variants on expression of splice variants and levels of airway chitinase activity. We will determine if any of the 26 TGFp pathway genes analyzed show differential expression in the lung in asthma. Our aims are founded on preliminary data from human subjects and integrate closely with the scientific themes of projects 1 and 2. Together, our studies will greatly advance understanding of the roles of chitinases and TGFp family members in allergy and asthma and could suggest novel treatment approaches. Lay summary: We will examine the effect of genetic variation in the CHIT1, AMCase and TGFp pathway on asthma and asthma related traits in ethnically diverse populations. We will also examine the effect of genetic variation in these genes on gene and protein expression in the lungs of subjects with asthma.

DESCRIPTION (provided by investigator): Asthma is caused by the interaction of genetic and environmental factors. In the U.S., asthma prevalence, morbidity and mortality are highest in Puerto Ricans, intermediate in Dominicans and Cubans, and lowest in Mexicans and Central Americans. There are many potential explanations for this observation, including place of birth, acculturation, early life exposures and genetic predisposition. Latinos are admixed and share varying proportions of African, Native American and European ancestry. The mixed ancestry of Latinos provides unique opportunities in epidemiological and genetic studies of complex traits and may be useful in untangling complex gene-environment (G x E) interactions in disease susceptibility. We hypothesize that ancestry will modify the association between environmental risk factors and asthma prevalence and severity. We propose to investigate whether individual ancestry, genetic factors, and environmental risk factors interact to influence asthma and asthma-related traits among several Latino ethnic groups. We will collect a well-characterized sample of Latino asthmatics (n = 2000) and clinic-based controls (n = 2000), age 8-21 years, from the Bronx, NY, Chicago, IL, San Francisco, CA, Houston, TX and Puerto Rico. This application has three specific aims. 1) We will test the hypothesis that genetic ancestry interacts with environmental/demographic risk factors to modify asthma risk and asthma-related phenotypes in Latinos of high risk Puerto Rican, intermediate risk Dominican, and low risk Central American and Mexican ethnicities. 2) We will genotype fifty candidate genes that may be involved in G x E interactions relevant to asthma. We will test whether there are ethnic-specific G x E interactions that differentially affect asthma risk, severity and pharmacologic response among Latino ethnic groups. 3) We will determine whether migration and acculturation are associated with asthma and severe asthma. Place of birth and length of stay in the U.S. are indicators of migration and acculturation. We will test the hypotheses that these indicators are associated with asthma and asthma severity. We will also test the hypothesis that place of birth and length of stay in the U.S. interact with ancestry, environmental, clinical and demographic risk factors to modify their associations with asthma and asthma severity among Latinos. PUBLIC HEALTH RELEVANCE The diversity and similarity among Latinos provide a valuable opportunity to study the interactions of race, genetics, culture, and environment. By taking advantage of such diversity, we may gain a much more thorough understanding of asthma, its causes, and its distribution among Latinos and other ethnic groups.

DESCRIPTION (provided by applicant): Over the last ten years, the world has witnessed unprecedented advances in biomedical research and discovery. We have observed technological miracles including isolation of human embryonic stem cells, completion of the human genome project, generation of new heart valves from stem cells and the discovery of novel genetic risk factors through genome-wide screens. With the rapid development and application of new technologies to biomedical research, enormous progress has been made in understanding basic human biology and disease. In contrast, the translation of this knowledge to the discovery, development and optimal use of pharmacological therapies has been slow. This slow progress can be attributed, in large part, to a severe shortage of well-trained, qualified clinical pharmacology investigators nationally who can fulfill this need for translational research and, paradoxically, a marked contraction of training opportunities within the U.S. At UCSF, we are keenly aware of what has been described as an "overwhelming mandate" to train the next generation of clinical pharmacologist researchers. For the past 30 years, the Clinical Pharmacology Training program at UCSF has consistently produced clinical pharmacologists of the highest caliber. Therefore, our UCSF training program is in an excellent position to "address (this) unfortunate shortage of qualified investigators in the field" by developing a well-trained and diverse contingent of clinical-scientist investigators who will serve as tomorrow's leaders in clinical pharmacology research and practice in academia as well as the pharmaceutical and biotechnology industries. We recognize the strengths of our faculty and clinical institutions and believe strongly that we are uniquely positioned to fulfill the growing and evolving dynamic needs of adult and pediatric clinical pharmacology through the recruitment of an expanded group of diverse and highly-motivated M.D., Pharm.D. and Ph.D. fellows into our research-intensive Clinical Pharmacology post-doctoral fellowship program. We propose to continue and expand our training program to educate and develop highly qualified researchers in modern clinical pharmacology. These scientists will be leaders in the translation of basic discoveries to clinical research and patient care. Herein, we describe the continuation and expansion of our training program with an emphasis on new developments including new leadership and expanded research and training directions. RELEVANCE: There is a severe shortage of qualified clinical pharmacology investigators who can translate advances in biomedical research to the discovery, development and use of pharmacological therapies. The UCSF Clinical Pharmacology Training Program will address this shortage by educating and developing highly qualified researchers in modern clinical pharmacology.

Clinical Studies Research will maintain SOPHIE, Studies Of Pharmacogenetcs in Ethnically Diverse Populations, a cohort of healthy volunteers who have agreed to be called back for further pharmacogenetic studies. This team will conduct mechanistic genotype driven clinical studies and participate in collaborative studies with PGRN investigators. Members of this team will lead our large clinical study focused on metformin, an anti-diabetic drug that interacts with multiple transporters

Asthma and obesity are leading public health concerns that disproportionately affect low-income and minority children. Epidemiologic studies have consistently shown an association between asthma and obesity. Among all US populations, asthma prevalence is highest in Puerto Ricans and lowest in Mexican Americans. Obesity is high in both populations. Obese asthma may be a unique phenotype of asthma, with a more difficult clinical course and altered response to asthma controller therapy. Independent risk factors for both obesity and asthma disproportionately impact low income and minority children. Shared early-life exposures are known risk factors. Shared genetic risk factors are also important Twin studies indicated that 8% of the genetic component of obesity is shared with asthma. A comprehensive study of low income minority children will help to uncover the contributions of genetics, socio-demographic, and early-life events to the co-occurrence of asthma and obesity in this population. Latinos are an ideal population to tease apart the genetic, social and environmental risk factors associated with obesity and asthma. Latinos are the largest minority population in the United States and the largest demographic group among all U.S. children. Latinos are admixed with considerable variation in genetic ancestry, both at the individual and group levels, and this can be leveraged to untangle complex associations between asthma and obesity susceptibility. We performed the largest admixture mapping scan of asthma and obesity in the U.S. We identified three admixture mapping peaks that were associated with both asthma and obesity, suggesting there are pleiotropic risk variants in these regions that contribute to both asthma and obesity in Latino populations. The goal of this roposal is to identify novel genetic variants associated with both asthma and obesity by deep resequencing of candidate regions identified through admixture mapping. We will also test for correlations between the genetic variation and levels of gene expression to identify putative expression quantitative trait loci (eQTLs) that are associated with each condition. Finally, we will test identified eQTLs in several independent populations from the NHLBI sponsored EVE asthma consortium.

DESCRIPTION (provided by applicant): Over the last ten years, the world has witnessed unprecedented advances in biomedical research and discovery. We have observed technological miracles including isolation of human embryonic stem cells, completion of the human genome project, generation of new heart valves from stem cells and the discovery of novel genetic risk factors through genome-wide screens. With the rapid development and application of new technologies to biomedical research, enormous progress has been made in understanding basic human biology and disease. In contrast, the translation of this knowledge to the discovery, development and optimal use of pharmacological therapies has been slow. This slow progress can be attributed, in large part, to a severe shortage of well-trained, qualified clinical pharmacology investigators nationally who can fulfill this need for translational research and, paradoxically, a marked contraction of training opportunities within the U.S. At UCSF, we are keenly aware of what has been described as an overwhelming mandate to train the next generation of clinical pharmacologist researchers. For the past 30 years, the Clinical Pharmacology Training program at UCSF has consistently produced clinical pharmacologists of the highest caliber. Therefore, our UCSF training program is in an excellent position to address (this) unfortunate shortage of qualified investigators in the field by developing a well-trained and diverse contingent of clinical-scientist investigators who will serve as tomorrow's leaders in clinical pharmacology research and practice in academia as well as the pharmaceutical and biotechnology industries. We recognize the strengths of our faculty and clinical institutions and believe strongly that we are uniquely positioned to fulfill the growing and evolving dynamic needs of adult and pediatric clinical pharmacology through the recruitment of an expanded group of diverse and highly-motivated M.D., Pharm.D. and Ph.D. fellows into our research-intensive Clinical Pharmacology post-doctoral fellowship program. We propose to continue and expand our training program to educate and develop highly qualified researchers in modern clinical pharmacology. These scientists will be leaders in the translation of basic discoveries to clinical research and patient care. Herein, we describe the continuation and expansion of our training program with an emphasis on new developments including new leadership and expanded research and training directions. RELEVANCE: There is a severe shortage of qualified clinical pharmacology investigators who can translate advances in biomedical research to the discovery, development and use of pharmacological therapies. The UCSF Clinical Pharmacology Training Program will address this shortage by educating and developing highly qualified researchers in modern clinical pharmacology.

DESCRIPTION (provided by applicant): The goal of this program is to launch the careers of an outstanding group of next generation scientists equipped to use omics approaches to help transform lung research and pulmonary medicine. UCSF is one of the world's leading health sciences campuses and this program will build on existing strengths in pulmonary research, omics, and education and training. Two physician-scientists with experience in applying genomics and genetics tools to basic, translational and clinical pulmonary research will direct the program. An exceptionally accomplished group of mentors with strong records of interdisciplinary collaboration will bring complementary expertise in other key areas, including proteomics, microbiome research, metabolomics, computational biology, biostatistics, and career development program management. An Advisory Committee will work with the program directors to select K12 Scholars, monitor the progress of the Scholars, and identify opportunities for improving the program. The Scholar recruitment process will benefit from access to a large and diverse pool of internal candidates from UCSF's well-established postdoctoral training programs and provide additional opportunities for us to continue to recruit the most promising young faculty from other outstanding programs. Each Scholar will work with mentors on their career development committee to establish goals and identify didactic and hands-on training experiences to meet these goals. Scholars will have access to classes and seminars sponsored by multiple graduate programs and the UCSF Clinical and Translational Sciences Institute, and to a large assortment of omics-oriented core facilities at UCSF. K12 program activities, including a new UCSF Omics of Lung Diseases conference, will benefit Scholars who are directly support by K12 funding as well as other UCSF faculty, postdoctoral trainees, and students seeking to integrate omics approaches into pulmonary research.

PROJECT SUMMARY/ABSTRACT Albuterol, a short-acting ?2-agonist, is the most commonly prescribed asthma medication in the world. There are marked differences in the therapeutic response to albuterol between racial and ethnic groups. We demonstrated that Puerto Rican and African American children with asthma were significantly less responsive to albuterol than Mexican children. Our goal is to understand the biological basis of differential drug response in diverse pediatric populations with asthma. We hypothesize that rare exonic and promoter variants, with potentially larger effect sizes than common snps, contribute to racial/ethnic differences in albuterol response. We will test our hypothesis with three specific aims. Specific Aim 1: Perform ?Exome Plus? DNA sequencing on extreme phenotypes of bronchodilator response (BDR) among minority children with asthma. A total of 1500 minority children with asthma and extreme drug response phenotypes will be selected for sequencing, including Puerto Ricans (n=500), Mexicans (n=500) and African Americans (n=500). With the ?Exome-Plus? approach, the target capture probe set is designed to capture human exons (38 Mb), >1000 non-coding RNAs, and 6 Mb of custom sequences. We will focus the ?Plus? sequencing on the identification of cis-regulatory variants in a set of 2,153 candidate genes identified as being expressed in airway smooth muscle cells and our own GWAS results. Specific Aim 2: Identify genetic variation associated with bronchodilator response. We will perform association testing on individual and pooled variants between high and low drug responders in the discovery phase (n=1500), and test for an association of the top hits with BDR in a large, independent group of Latino and African American subjects with asthma (n=2,235). We will then replicate our findings in an additional 4,980 individuals. Specific Aim 3: Determine whether promoter variants associated with bronchodilator response cause differential gene expression in primary airway smooth muscle cells. We have developed a chromatin based promoter reporter assay that will provide a next-generation system for the high- throughput study of non-coding and promoter variants believed to be so important in human disease and drug response.

DESCRIPTION (provided by applicant): Asthma is a multifactorial disease with environmental and genetic contributions. We demonstrated that the harm caused by early-life exposures to air pollution and tobacco varies among different racial/ethnic groups. Our recent genome-wide association studies have identified both shared and ethnic-specific genetic risk factors for asthma and asthma-related traits. Our findings imply that both genes and early-life environmental exposures are important contributors to asthma susceptibility in minority children. We hypothesize that racial/ethnic differences in asthma susceptibility are due to gene-environment interactions resulting from early-life exposure to air pollution and tobacco. We will use existing genome-wide SNP genotypes and two distinct but complimentary approaches-admixture mapping and novel genome-wide GxE interaction scanning methods-to investigate the relationship between genetics, early-life air pollution and tobacco smoke exposures, and asthma risk. Specific Aim 1: Ancestry by environment interaction analysis of asthma in minority children. We will use genome-wide estimates of local chromosomal ancestry (African, European, and Native American) to perform an admixture mapping by environment (AxE) scan in 6,536 Latino and African American children from across the U.S. We will fine map AxE interaction peaks by performing targeted GxE analyses of genotyped and imputed SNPs from CAAPA and the Thousand Genomes Project. Results will be replicated using similar outcomes and exposures in the Mexico City Childhood Asthma Study (MCCAS). Specific Aim 2: Genome-wide by environment (GxE) interaction analysis of asthma in ethnically diverse children with and without asthma. We will use a novel two-step analytical method to perform a genome-wide scan at 38.9 million SNPs for GxE interactions with air pollution and tobacco smoke exposure. Scans will be performed in our combined resource of 8,138 children, as well as within Latino, European, and African American subgroups. Results will be replicated using similar outcomes and exposures in MCCAS. EXPECTED OUTCOMES: We will identify genes and genetic loci whereby gene-environment interactions play an important role in asthma etiology, and thus retrieve part of the missing heritability of asthma. We will identify significant shared and ethnic specific gene-environment interactions, which will further our understanding of racial/ethnic differences in asthma susceptibility.

? DESCRIPTION (provided by applicant): Asthma affects 5% of the world population. In the U.S., asthma death rates are four-fold higher in Latinos and African Americans compared to Whites. Latinos and African Americans have varying degrees of African, European, and Native American genetic ancestry. This genetic heterogeneity has important clinical implications. In fact, we demonstrated that we can improve the diagnosis of lung disease among African Americans by as much as 15% by including genetic measures of ancestry into clinical lung function prediction equations (NEJM). We improved upon our results by incorporating sub-continental Native American ancestry into clinical lung function prediction equations for Latinos (Science). We also demonstrated that exposure to air pollution is associated with increased asthma risk among Latino and African American children, and that this increase in risk was greatest among African American children (AJRCCM). Subsequently, we demonstrated that environmental and social risk factors cannot fully explain the correlation between genetic ancestry and asthma severity and lung function (JACI). Clearly, we demonstrated that ancestry plays a strong role in determining normal clinical measures such as lung function and asthma severity. We hypothesize that gene- environment interactions contribute to population differences in lung function and asthma severity following exposure to air pollution. Racial/ethnic differences in the frequency and composition of genetic variation likely play an important role in asthma severity. To test this hypothesis we recruited the largest gene-environment study of asthma among minority children in the U.S. (N > 10,000). Our goal is to use integrative genomics to identify gene-by-air pollution interactions that influence lung function and asthma severity in minority children. We will leverage existing 1,600 whole genome sequences with air pollution-induced gene expression in nasal airway epithelial cells (NECs) from children with mild and severe asthma. We will integrate individual-level whole genome sequencing data with precise cell-level genetic and exposure-response experiments. We will identify genetic risk factors and gene-environment interactions that contribute to asthma severity, and determine cellular response mechanisms that mediate poor lung function and severe asthma using NECs exposed to air pollution.

? DESCRIPTION (provided by applicant): The NHGRI Genome Sequencing Program (GSP) will identify genomic variants relevant to health and disease by genome sequencing over 225,000 participants across a multitude of diseases. The GSP will also serve as a pilot for the Precision Medicine Initiative that aims to enroll and sequence more than a million people representative of U.S. ethnic diversity. Here, we propose a GSP analysis center focused on Multi- and Trans- ethnic Mapping of Mendelian and Complex Diseases. There is a growing recognition of the substantial scientific advantages, as well as public health importance, of conducting biomedical research across ethnically diverse cohorts. We propose to develop scalable methods that incorporate ancestry to optimize medical genomic study design and improve power for uncovering the role of common and rare variants in disease. Achieving this goal requires expertise across diverse domains of knowledge including: medical and population genomics, algorithm development for complex disease mapping, and expertise in management of large-scale databases. Here, we have assembled a world-class team of medical and population geneticists, computer scientists, statisticians and clinicians, with leading expertise in the development of novel and scalable strategies for characterizing sequence variants and their role in disease. Importantly, our group has been at the forefront of development of resources, study designs and methods to enable genomic research in U.S. minority populations. Our project has three main objectives. First, we will develop an Automated Scalable Ancestry Pipeline (ASAP) for common disease mapping in diverse populations. ASAP will improve the computational efficiency of existing state-of-the-art methods for ancestry inference and develop important extensions to linear mixed models (LMMs) and other mapping strategies leveraging local and global ancestry. We will also develop methods to refine phenotypes and identify common controls for disease studies and define endpoints. Secondly, we will develop tools and resources for trans- and multi-population rare variant discovery that incorporate patterns of local and sub-continental ancestry. We will also develop machine-learning tools for variant annotation that leverage ancestral information, patterns of sequence evolution, and protein structure in a unified framework. Furthermore, we will incorporate population-specific patterns of cellular phenotypes to improve functional prediction algorithms for non-coding and coding variants. Lastly, we will disseminate our results through web-based resource that empower the biomedical research community. We will augment existing resources including ClinGen by annotating and characterizing pathogenic variants across diverse populations. We will develop a secure web-server that allows sharing of summary statistics and analysis pipelines to enable discovery, fine-mapping and functional prediction of genetic variants. Our team has ample experience with NIH-funded consortia and is dedicated to meeting the overall GSP project goals through collaborative work with NHGRI leadership and other funded investigators.

PROJECT SUMMARY Identifying genetic variants associated with complex diseases via genome-wide SNP and whole genome sequencing (WGS) studies has outpaced our ability to translate these findings into actionable biologic and clinical insights. We need to use in silico methods that integrate multiple layers of data, including transcriptomic, epigenetic, social, and environmental, to focus experimental validation on the most impactful targets. Asthma-related deaths are 4-fold higher in minority children than white children. Moreover, minority children with asthma have markedly decreased drug response to albuterol, a bronchodilator rescue medication that is the most commonly prescribed asthma medication in the world, and to glucocorticoids, anti-inflammatory medications that decrease symptoms and exacerbations. Our goal is to understand the biological basis of differential drug response that leads to observed racial/ethnic asthma disparities. In this proposal, we use two cloud-based apps we developed to identify functional biologic mechanisms of genes that are associated with racial/ethnic variation in asthma therapies. Specifically, our apps 1) provide gene-centric WGS association findings in the context of integrated multi-tissue omic results, and 2) reprioritize WGS association results using machine-learned tissue-specific networks constructed from gene expression, known protein-protein interactions, and established functional pathways. Our results will increase knowledge about the biological role of genes associated with asthma therapy and facilitate design of experiments to understand their function.

PROJECT SUMMARY/ABSTRACT Asthma prevalence in Puerto Ricans is 37% versus 12% for whites yet most studies have been conducted among the latter. This asthma burden extends to asthma morbidity and mortality, which are 2.4- and 4-fold higher among Puerto Ricans compared to whites, respectively. There is a strong association between severe, early-life viral respiratory illnesses and development of childhood recurrent wheeze and asthma. However, little is known about the mechanisms underlying these associations. Does airway dysfunction exist at birth and first manifest in early life as a severe illness in response to viral respiratory infections, and later as childhood asthma? Or does a severe, early-life respiratory illness injure a normal airway and precipitate asthma later in childhood? We will study Puerto Rican children to address these questions via three Specific Aims. Aim 1: Recruit a cohort of 3,000 newborns to longitudinally study the effects of early-life viral respiratory illnesses on nasal airway molecular endotype and risk for recurrent wheeze. We will collect yearly environmental, social, and clinical data on each participant and track all respiratory illnesses from birth to age 3. We will record severity and presence of wheezing in each child's illnesses and collect nasal swabs to determine the presence/type of virus associated with these illnesses. Aim 2: Identify viral and genetic determinants of severe early-life respiratory illnesses and whether the molecular state of the nasal airway epithelium at birth is predictive of these severe illnesses. We will perform transcriptomic and viral analyses on nasal airway swabs from subjects at birth and during respiratory illness. We will test if severe respiratory illnesses are associated with viral infection in general and/or infection with a specific viral species. We will use genome-wide genetic data to identify risk variants for severe early-life respiratory illnesses and variants influencing airway gene expression at birth and during illness (eQTLs). We will test for GxE interactions between top risk variants/eQTLs and infection with different viral species. We will also identify gene expression response to mild vs. severe early-life respiratory illnesses and determine if airway gene expression at birth is predictive of severe respiratory illness in early childhood. Aim 3: Determine the relationship between severity of early-life respiratory illness and post-illness but pre-asthma nasal airway gene expression profiles. We will perform transcriptomic and viral metagenomic analysis of nasal swabs collected from subjects at age 3. We will determine how severe respiratory illnesses affect the trajectory of airway gene expression profiles from birth to early childhood. Finally, we will determine if mild or severe respiratory illness in early life is predictive of recurrent wheeze at age 3. Our longitudinal birth cohort will [1] be the largest prospective study of minority infants, [2] provide novel and seminal information on genetic/viral risk factors for severe respiratory illnesses, and [3] identify airway endotypes that high-risk groups exhibit at birth and after respiratory illness, but prior to asthma onset. Our study will help to elucidate the relationship between early-life respiratory illness and asthma.

The NHGRI Genome Sequencing Program (GSP) will identify genomic variants relevant to health and disease by genome sequencing over 225,000 participants across a multitude of diseases. The GSP will also serve as a pilot for the Precision Medicine Initiative that aims to enroll and sequence more than a million people representative of U.S. ethnic diversity. Here, we propose a GSP analysis center focused on Multi- and Trans- ethnic Mapping of Mendelian and Complex Diseases. There is a growing recognition of the substantial scientific advantages, as well as public health importance, of conducting biomedical research across ethnically diverse cohorts. We propose to develop scalable methods that incorporate ancestry to optimize medical genomic study design and improve power for uncovering the role of common and rare variants in disease. Achieving this goal requires expertise across diverse domains of knowledge including: medical and population genomics, algorithm development for complex disease mapping, and expertise in management of large-scale databases. Here, we have assembled a world-class team of medical and population geneticists, computer scientists, statisticians and clinicians, with leading expertise in the development of novel and scalable strategies for characterizing sequence variants and their role in disease. Importantly, our group has been at the forefront of development of resources, study designs and methods to enable genomic research in U.S. minority populations. Our project has three main objectives. First, we will develop an Automated Scalable Ancestry Pipeline (ASAP) for common disease mapping in diverse populations. ASAP will improve the computational efficiency of existing state-of-the-art methods for ancestry inference and develop important extensions to linear mixed models (LMMs) and other mapping strategies leveraging local and global ancestry. We will also develop methods to refine phenotypes and identify common controls for disease studies and define endpoints. Secondly, we will develop tools and resources for trans- and multi-population rare variant discovery that incorporate patterns of local and sub-continental ancestry. We will also develop machine-learning tools for variant annotation that leverage ancestral information, patterns of sequence evolution, and protein structure in a unified framework. Furthermore, we will incorporate population-specific patterns of cellular phenotypes to improve functional prediction algorithms for non-coding and coding variants. Lastly, we will disseminate our results through web-based resource that empower the biomedical research community. We will augment existing resources including ClinGen by annotating and characterizing pathogenic variants across diverse populations. We will develop a secure web-server that allows sharing of summary statistics and analysis pipelines to enable discovery, fine-mapping and functional prediction of genetic variants. Our team has ample experience with NIH-funded consortia and is dedicated to meeting the overall GSP project goals through collaborative work with NHGRI leadership and other funded investigators.

ABSTRACT Asthma is the most common chronic disease among children. Asthma prevalence, mortality, and drug response vary by race/ethnicity and genetic ancestry. In the U.S., asthma prevalence is highest among Puerto Ricans (36.5%), intermediate among African Americans (13.0%) and whites (12.1%), and lowest in Mexicans (7.5%). These disparities extend to asthma mortality, which is four-fold higher in Puerto Ricans and African Americans compared to Mexican Americans. Albuterol is the most commonly prescribed asthma medication in the world and is the mainstay of acute asthma management. Among low income and minority populations in the U.S., albuterol is often the only medication used regardless of asthma severity. Poor drug response contributes to racial/ethnic disparities in asthma morbidity and mortality. Disturbingly, Americans with the highest asthma prevalence and death rate also have the lowest drug response. Chronic albuterol use can decrease acute airway smooth muscle response to albuterol and increase airway inflammation through beta-agonist signaling in the airway epithelium, suggesting that chronic albuterol use may alter acute response through genomic and epigenomic modification of airway cells. Furthermore, acute bronchodilator drug response (BDR) to albuterol is a complex phenotype with an estimated heritability of 28.5%, indicating genetic factors contribute to BDR variability. Genome-wide and whole genome association analyses have revealed population-specific common and rare variants in non-coding regions of the genome associated with the extremes of BDR. The roles of genomic regulatory regions and population-specific variants in BDR have yet to be fully investigated. To this end, we have created an investigative system involving airway-specific cell types, patient-derived cells, and detailed clinical data to generate an encyclopedia of genes, regulatory regions, and pathways involved in BDR to albuterol. We will integrate RNA-seq, ChIP-seq, ATAC-seq, and whole genome sequencing data with detailed clinical data to identify trans-ethnic and population-specific variants contributing to differential expression and chromatin structure patterns in response to albuterol exposure. Furthermore, we will functionally characterize the regulatory regions that underlie acute and chronic albuterol BDR in multi-ethnic children with asthma using CRISPR-Cas9 activation/inhibition assays. These analyses will allow us to determine on a genomic scale the functional consequences of acute and chronic albuterol treatment on airway cells, and provide insight into potential targetable genes, regulatory elements, and pathways for improved asthma therapies in at-risk populations.

PROJECT SUMMARY Asthma is the most common chronic disorder of children, with an estimated 300 million cases worldwide and with significant increases in incidence since the early 1980s. In the United States (U.S.), asthma prevalence, morbidity, mortality, and drug response vary substantially among racial and ethnic groups. While asthma was previously regarded as being a single clinical entity with a number of diagnostic criteria, it is now widely recognized that asthma represents multiple different pathobiological and clinical subtypes, which may underlie observed racial and ethnic variation. Furthermore, an individual's risk of developing asthma reflects a summation of genetic as well as various clinical risk factors. Importantly, clinical risk factors are not randomly distributed across racial and ethnic groups, and certain populations are more burdened than others. Our goal in this work is to identify cell types, genes, and pathways altered by exposure to clinical risk factors, thereby improving mechanistic understanding of asthma subtypes and elucidating the underlying networks by which these risk factors affect asthma disparities. To achieve this goal, we will determine the epigenetic profiles of patients with and without known asthma risk factors (Aim 1), identify common and unique epigenetic profiles associated with known and novel clinical asthma subtypes (Aim 2), and examine the contribution of common and unique epigenetic changes to the association of clinical risk factors with clinical asthma subtypes (Aim 3). We hypothesize that DNA methylation will provide the bridge that ties clinical risk factors with asthma disease subtypes and that this relationship may be modified by self-identified race/ethnicity and genetic ancestry thereby contributing to asthma disparities. Strong preliminary data from our group and others have shown that methylation, a long lasting but dynamic measure of cellular states, is highly correlated with exposure to clinical asthma risk factors, including early life respiratory infection, obesity, and maternal history of asthma. To execute this research program, we have assembled an interdisciplinary team with complementary expertise in epidemiology, clinical asthma, genetics, epigenetics, and statistical methods. Our team will study a unique cohort of minority children at the extremes of asthma prevalence and mortality (high risk Puerto Ricans and African Americans, and low risk Mexican Americans), who have existing demographic data, clinical exposures, genotypes, and RNA/DNA sequences. To our knowledge, there are no other groups within or outside the U.S. with populations as detailed as ours that are large enough to be well powered for these analyses. Therefore, we are the only group with the population needed and track record to successfully complete this project. Findings from our work will help: (i) provide the clinical and biomedical research communities with the largest methylation dataset on minority children produced to date, with a substantially increased value due to existing clinical, socio-environmental, and genetic data, (ii) improve risk profiling, especially for minority children, and (iii) precisely treat patients by selecting interventions using epigenetic markers accounting for clinical risk factors.