Asthma is a complex disease with striking disparities across racial and ethnic groups, which may be partly attributable to genetic factors. A major goal of the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) has been to discover genes conferring risk to asthma in populations of African ancestry. Genome-wide association studies (GWAS) have been successful in identifying genes associated with increased risk of asthma, but there is a substantial gap between associations discovered by GWAS and understanding how these loci control disease. A major portion of the `missing heritability' could be due to variants with smaller effects missed by traditional GWAS thresholds, emphasizing the need for a transition to integrative genetics, where transcriptome, proteome, methylome and metabolome information are brought into a unified framework. Our goal in this continuing renewal is to apply an integrative, multi-omics approach to understand the molecular architecture underlying asthma, building upon the 5-year CAAPA program, where >16,000 asthmatics and non-asthmatics have already been GWAS-genotyped, and GWAS and/or whole genome sequencing (WGS) data are available on more than 100,000 non-CAAPA samples. We propose to test if genetic variants control development of asthma by regulating gene transcription and expression, DNA methylation, metabolic profiles, and proteome variation.
The specific aims of this application leverage an international group of investigators with diverse but highly integrated areas of expertise, and include the following: (1) expand and integrate multi-omic resources for asthma research in African Diaspora populations and identify novel genetic determinants for risk of asthma by adding indigenous American and continental African genetic representation in the African Diaspora catalog, building a multi-omic repository through newly generated transcriptome, methylome, proteome, and metabolome data from CAAPA asthmatics and unaffected controls with existing GWAS data from 7 sites in North and South America, the Caribbean and Africa, and performing integrative analyses; (2) broadly disseminate CAAPA results through a web-based resource that empowers the asthma research community for new discoveries; and (3) develop and apply approaches for prioritizing CAAPA results in 3 health systems biobanks enriched for US minority populations (Nashville, New York City, and the Rocky Mountain region) by examining genomics (PheWAS) and multi-omics (PrediXcan) asthma associations identified in CAAPA and non-CAAPA datasets. These studies will advance our understanding of the molecular basis for asthma among populations of African ancestry.
The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) will expand and build a multi-omics repository in populations with African ancestry, from continental Africa and the Americas, for integrative analysis to empower discovery and functional interpretation of asthma genetic risk. We will also implement web-based technologies to develop an online community resource for asthma researchers, and investigate the impact of asthma loci in three large health systems. Overall, this work will inform the genetic and clinical asthma communities about how to implement genetic discovery using high dimensional data in a clinically useful and technologically innovative manner.
|Gour, Naina; Lajoie, Stephane; Smole, Ursula et al. (2018) Dysregulated invertebrate tropomyosin-dectin-1 interaction confers susceptibility to allergic diseases. Sci Immunol 3:|
|Sun, Xiaobo; Gao, Jingjing; Jin, Peng et al. (2018) Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files. Gigascience 7:|
|Shringarpure, Suyash S; Mathias, Rasika A; Hernandez, Ryan D et al. (2017) Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data. Bioinformatics 33:1147-1153|
|Oh, Sam S; Du, Randal; Zeiger, Andrew M et al. (2017) Breastfeeding associated with higher lung function in African American youths with asthma. J Asthma 54:856-865|
|Sherenian, M G; Cho, S H; Levin, A et al. (2017) PAI-1 gain-of-function genotype, factors increasing PAI-1 levels, and airway obstruction: The GALA II Cohort. Clin Exp Allergy 47:1150-1158|
|Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing et al. (2017) Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome. Sci Rep 7:46398|
|Thakur, Neeta; Barcelo, Nicolas E; Borrell, Luisa N et al. (2017) Perceived Discrimination Associated With Asthma and Related Outcomes in Minority Youth: The GALA II and SAGE II Studies. Chest 151:804-812|
|Abid, Z; Oh, S S; Hu, D et al. (2016) Maternal age and asthma in Latino populations. Clin Exp Allergy 46:1398-1406|
|Kessler, Michael D; Yerges-Armstrong, Laura; Taub, Margaret A et al. (2016) Challenges and disparities in the application of personalized genomic medicine to populations with African ancestry. Nat Commun 7:12521|
|Rahmani, Elior; Zaitlen, Noah; Baran, Yael et al. (2016) Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. Nat Methods 13:443-5|
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