Genetic Research Projects
Our genetic research focuses on identifying genetic risk factors and developing novel therapeutic targets for asthma.
Projects overview
Our Study Populations form the basis for our research below:
Jump below to:
- Ancestry and admixture
- Genome-wide association studies (GWAS) and admixture mapping
- Moving Beyond GWAS: projects honing in on genetic risk factors for asthma and related traits
- Methylation
Ancestry and admixture
Humans migrated >200,00 years ago from Africa. Throughout the years, the migratory populations grew more and more genetically distinct from each other. However, with the founding of the New World, individuals from Europe and Africa migrated west and began genetically mixing with each other and the Native populations of the Americas. This genetic mixture produced what is termed genetically admixed populations.
Latinos are primarily descendants of pre-Columbian Native Americans, Africans, and Europeans, whereas African Americans have varying proportions of European and African ancestry.
Scientists have been able for a long time to use genetic markers to differentiate populations that had been geographically separated for generations. This is possible because the relative frequency of these markers differentiates over time among groups that do not intermix, a process known as genetic drift.
Recent advances in genetics have allowed us to go further and estimate the relative proportions of ancestral groups in admixed populations such as Latinos and African Americans.
Race and ethnicity are complex concepts that incorporate both sociocultural and genetic factors. For this reason, their use in clinical practice is controversial. However, race and ethnicity are used to define the normal values in pulmonary function tests (PFTs), and different equations are used to determine expected lung volumes for African Americans, Mexican Americans, and Whites. Since measured lung function is compared to the expected values derived from these reference equations, ensuring that these reference equations are accurate has profound implications in diagnosing disease, determining severity, establishing disability claims, and determining priority for lung transplantation.
In “Genetic ancestry in lung-function predictions,” published July 2010 in New England Journal of Medicine, we found that the proportion of European and African ancestry in African Americans was associated with lung function across three different studies. Genetic ancestry was determined using genome-wide genetic data. We also demonstrated that including ancestry measures improved predicted lung function compared to the current race-based clinical standards, which considers all African Americans as a single, homogenous group.
We are extending this work by looking at how the variation in ancestry affects lung function in other admixed groups, such as Latinos. We are also exploring whether other traits, such as the levels of IgE also correlate with genetic ancestry. Finally, we are extending the concepts of ancestry associations with a technique known as admixture mapping, in which we use sophisticated statistical software to infer the ancestry of each region of the genome. We then look across the genome to see whether the ancestry in any region is associated with a trait or disease. We hypothesize that genetic variants exclusive or more common to a particular ancestral variant are associated with a trait or disease.
Genome-wide association studies (GWAS) and admixture mapping
Identification of new loci associated with total IgE levels in Latinos
Immunoglobulin E (IgE) is a key mediator of allergic inflammation and is frequently elevated in allergic disorders. Total serum IgE levels are known to vary by race/ethnicity in the United States, with higher levels reported in both African American and Latino individuals. In addition, African ancestry has been associated with higher IgE levels in African American and Latino populations. In spite of these differences in IgE levels, only 1% of the discovery samples included in previous genome-wide association studies (GWAS) for this trait were Latinos.
Percentage of individuals included in the discovery phases of previous GWAS by population group.
We identified novel loci associated with total IgE levels in 3,334 Latino children from the Genes-environments & Admixture in Latino Americans study (GALA II) through traditional GWAS, admixture mapping, and exon sequencing of three genes implicated in our studies. We replicated associations in 454 Latinos, 1,564 European Americans, and 3,187 African Americans from independent studies. Our results highlight the importance of studying diverse, multi-ethnic populations, and the use of both GWAS and admixture mapping to uncover novel loci associated with total IgE levels.
GWAS and asthma
Very large disparities exist in the prevalence and mortality of asthma among different racial and ethnic groups, even among those groups that are frequently aggregated, such as Mexicans and Puerto Ricans. By collecting the largest study population for gene-environment studies of asthma in U.S. minority children, our research team is poised to identify genetic, social and environmental risk factors, which will help to explain these disparities.
More than 96% of contemporary genetic association studies have been performed in European populations. We have found that more than 82% of candidate genes that were associated with asthma in other racial/ethnic populations were not associated with asthma in Mexicans and Puerto Ricans in the GALA study. Of those that were associated with asthma in this study, we found that some candidate genes were what can be considered “cosmopolitan” and are risk factors for both Puerto Ricans and Mexicans. Other genes, however, were ethnic-specific, and had differential effects in the two populations.
We also seek to discover novel risk factors for asthma in Latinos and African Americans. Using the complementary techniques of genome-wide association analyses (GWAS) and admixture mapping, we identified new regions of the genome that are associated with asthma.
In GWAS, we simultaneously genotype hundreds of thousands of single nucleotide polymorphisms (SNPs), variants in the genetic code that could confer risk for disease. We have verified that a region in chromosome 17, which had originally been associated with asthma in European populations, was also associated with asthma in Latinos and African Americans.
In admixture mapping, we use sophisticated statistical software to infer whether a particular region of the genome was passed from African, European, or Native American ancestors, the three ancestral groups that combined to give rise to modern Latinos. We then look across the genome to see whether any of these ancestries are associated with asthma. We found that having Native American ancestry in the HLA region in chromosome 6, a region important for immune function, protects against asthma in Latinos. We have projects in progress to sequence the HLA region, which is one of the most diverse regions in the genome, so that we can identify which variants and genes are responsible for this protection against asthma.
Moving Beyond GWAS
Candidate gene sequencing
Genome-wide association studies (GWAS) have identified numerous associations with common variants for asthma and asthma-related traits, including bronchodilator drug response (BDR) and total serum IgE. In many cases the variants identified through GWAS are not the actual mutations that cause disease, and therefore we must identify these variants through sequencing prior to additional studies.
We sequenced the coding exons plus UTRs (Untranslated Regions) of seven genes implicated through GWAS and admixture mapping studies in 2,000 Latinos, including one gene for asthma susceptibility (SMAD2), three genes for BDR (SLC24A2, SLC24A4, SLC22A15), and three genes for total serum IgE (HLA-DQB1, HLA-DRB5, ZNF365). Overall, we identified novel genetic variation associated with drug response and IgE within three of the genes sequenced, including a significant contribution of nonsynonymous rare variants in SLC24A2, SLC24A4, and HLA-DQB1. Our results suggest that deep sequencing of candidate genes identified through GWAS and admixture mapping is essential for the fine mapping of genetic associations. Resequencing in larger, multi-ethnic population samples and functional studies are required to further understand the role of rare and common variation in asthma and asthma-related traits.
SMAD2 and asthma
Mothers against decapentaplegic homolog 2 (SMAD2) is a protein involved in TGF-beta signaling. In our ongoing studies as part of the EVE consortium, we found that Native American ancestry at SMAD2 was associated with an increased risk of asthma in Latinos. This is a strong indication there are population-specific genetic mutations within or nearby the SMAD2 gene that contribute to asthma in Latino children.
We are currently pursuing sequencing and gene expression studies to identify the causal variation behind the association of local Native American ancestry at SMAD2 and asthma. Through the RS&G service at the NHLBI, we are sequencing the SMAD2 locus and its flanking gene (ZBTB7C), including contiguous non-coding regions in 2,000 Latinos with and without asthma. We hypothesize that the SMAD2 locus contains population-specific rare variants that contribute to asthma. We further hypothesize that rare variants nearby SMAD2 are associated with differential BDR and risk of asthma exacerbation through influencing SMAD2 expression.
Exome sequencing extremes of drug response
Albuterol, a short-acting β2-agonist, is the most commonly prescribed asthma medication in the world. There are marked differences in the therapeutic response to albuterol among patients and racial/ethnic groups. For example, Puerto Rican and African American children with asthma are significantly less responsive to albuterol than Mexican or Caucasian children. We are pursuing studies to understand the genetic basis of differential drug response in minority children with asthma.
We hypothesize that rare variants, with potentially larger effect sizes than common SNPS, contribute to racial/ethnic differences in albuterol response. For example, in our GWAS studies for bronchodilator drug response we identified an excess of small p-values of association driven entirely by low frequency variants. We are further testing this hypothesis by performing exome plus UTR sequencing of 1,500 African American, Puerto Rican, and Mexican asthma patients with extreme phenotypes of BDR. Specifically, we are identifying individual and pooled rare variants that are associated with BDR through association testing between high and low drug responders. Furthermore, in our ongoing studies we are testing for an interaction of genetic factors with known environmental modifiers of bronchodilator drug response.
QQplot of a GWAS for BDR in GALA II. Black indicates all SNPs, blue indicates a loss of signal after excluding less common variation (MAF<5%).
High and low bronchodilator drug response (Max BDR) in the extremes of 500 Puerto Ricans, 500 Mexicans, and 500 African Americans in GALA II and SAGE. Note: Max BDR is on a log scale.
Whole genome sequencing holds the promise to identify a more complete picture of genetic variants affecting complex traits and disease. As part of the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), we are examining patterns of variation across the genomes of 500 asthma cases and 500 asthma controls. One of the major goals of CAAPA is to use this data to develop a commercial genotyping platform that is better able to capture the high degree of genetic variation in individuals with African ancestry.
Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA).
HLA studies
Genetic variation in the major histocompatibility complex (MHC) region plays an important role in asthma susceptibility and total serum IgE. In our own studies, admixture mapping for both asthma susceptibility and IgE level in Latinos indicated that genetic variation in the MHC has a significant contribution to both of these traits. Specifically, we found Native American ancestry at the MHC class I locus to be associated with lower risk of asthma, and at the MHC class I and II loci to be associated with lower IgE.
We are currently performing pilot studies by sequencing 5 Mb of the MHC region in Latino children using targeted, high-coverage next-generation sequencing. We are currently integrating advanced MHC region capture technology plus next-generation sequencing, with classical methods of human leukocyte antigen (HLA) typing. We will use this data to identify HLA types and genetic variation in the MHC regions that are associated with asthma and total serum IgE levels. Furthermore, we hope to develop an analytic pipeline to promote the study of the MHC region in Latinos by integrating targeted next-generation sequencing data, SNP-based HLA imputation, and classical methods of HLA typing.
Methylation
It is commonly believed that the genome is almost unchanging and that the genetic code in a person is invariant. However, several biological processes are capable of turning genes on and off through what scientists call epigenetics. (epi- is a Greek prefix meaning, in this case, “above” or “on top of.”) One such process is methylation, in which a methyl group is added to certain DNA base pair patterns known as CpG sites without changing the DNA code itself. Methylation changes how likely a gene is to be converted to a protein. We have used advanced microarray technology to obtain genome-wide methylation data at hundreds of thousands of CpG sites, and we seek to correlate epigenetic changes with asthma and related traits.
Both genetic and environmental factors are capable of driving changes in methylation patterns, though the extent of each has not been fully established. We leverage the rich genetic and environmental diversity among the participants in our GALA II study to explore the extent to which genetic and environmental factors contribute to methylation patterns. We have seen that there are ethnic differences in methylation patterns, even among related ethnic groups such as Puerto Ricans and Mexicans. We have also seen that many of these differences are due to differences in ancestry between the two groups. Those differences in ancestral composition are associated with differences in genetic patterns, which in turn lead to changes in methylation pattern. This has a profound impact on complex diseases such as asthma.