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Li Y, Wong KY, Howard AG, Gordon-Larsen P, Highland HM, Graff M, North KE, Downie CG, Avery CL, Yu B, Young KL, Buchanan VL, Kaplan R, Hou L, Joyce BT, Qi Q, Sofer T, Moon JY, Lin DY. Mendelian randomization with incomplete measurements on the exposure in the Hispanic Community Health Study/Study of Latinos. HGG Adv 2024; 5:100245. [PMID: 37817410 PMCID: PMC10628889 DOI: 10.1016/j.xhgg.2023.100245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/12/2023] Open
Abstract
Mendelian randomization has been widely used to assess the causal effect of a heritable exposure variable on an outcome of interest, using genetic variants as instrumental variables. In practice, data on the exposure variable can be incomplete due to high cost of measurement and technical limits of detection. In this paper, we propose a valid and efficient method to handle both unmeasured and undetectable values of the exposure variable in one-sample Mendelian randomization analysis with individual-level data. We estimate the causal effect of the exposure variable on the outcome using maximum likelihood estimation and develop an expectation maximization algorithm for the computation of the estimator. Simulation studies show that the proposed method performs well in making inference on the causal effect. We apply our method to the Hispanic Community Health Study/Study of Latinos, a community-based prospective cohort study, and estimate the causal effect of several metabolites on phenotypes of interest.
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Affiliation(s)
- Yilun Li
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kin Yau Wong
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Penny Gordon-Larsen
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Carolina G Downie
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christy L Avery
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria L Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Brian Thomas Joyce
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Dan-Yu Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Anwar MY, Graff M, Highland HM, Smit R, Wang Z, Buchanan VL, Young KL, Kenny EE, Fernandez-Rhodes L, Liu S, Assimes T, Garcia DO, Daeeun K, Gignoux CR, Justice AE, Haiman CA, Buyske S, Peters U, Loos RJF, Kooperberg C, North KE. Assessing efficiency of fine-mapping obesity-associated variants through leveraging ancestry architecture and functional annotation using PAGE and UKBB cohorts. Hum Genet 2023; 142:1477-1489. [PMID: 37658231 DOI: 10.1007/s00439-023-02593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/10/2023] [Indexed: 09/03/2023]
Abstract
Inadequate representation of non-European ancestry populations in genome-wide association studies (GWAS) has limited opportunities to isolate functional variants. Fine-mapping in multi-ancestry populations should improve the efficiency of prioritizing variants for functional interrogation. To evaluate this hypothesis, we leveraged ancestry architecture to perform comparative GWAS and fine-mapping of obesity-related phenotypes in European ancestry populations from the UK Biobank (UKBB) and multi-ancestry samples from the Population Architecture for Genetic Epidemiology (PAGE) consortium with comparable sample sizes. In the investigated regions with genome-wide significant associations for obesity-related traits, fine-mapping in our ancestrally diverse sample led to 95% and 99% credible sets (CS) with fewer variants than in the European ancestry sample. Lead fine-mapped variants in PAGE regions had higher average coding scores, and higher average posterior probabilities for causality compared to UKBB. Importantly, 99% CS in PAGE loci contained strong expression quantitative trait loci (eQTLs) in adipose tissues or harbored more variants in tighter linkage disequilibrium (LD) with eQTLs. Leveraging ancestrally diverse populations with heterogeneous ancestry architectures, coupled with functional annotation, increased fine-mapping efficiency and performance, and reduced the set of candidate variants for consideration for future functional studies. Significant overlap in genetic causal variants across populations suggests generalizability of genetic mechanisms underpinning obesity-related traits across populations.
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Affiliation(s)
- Mohammad Yaser Anwar
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Roelof Smit
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Victoria L Buchanan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Eimear E Kenny
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA, 16802, USA
| | - Simin Liu
- Department of Epidemiology and Center for Global Cardiometabolic Health, School of Public Health, Brown University, Providence, RI, 02903, USA
| | - Themistocles Assimes
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - David O Garcia
- Department of Health Promotion Sciences, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, 85724, USA
| | - Kim Daeeun
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger Health, Danville, PA, 17822, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Steve Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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3
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Young K, Buchanan VL, Graff M, Krishnan M, Highland H, Yu B, Avery CL, Buyske S, Cai J, Daviglus ML, Howard AG, Isasi CR, Kaplan R, Loos R, Qi Q, Rohde R, Rotter JI, Van Horn L, Gordon-Larsen P, Boerwinkle E, North KE. Abstract P552: Mendelian Randomization Analysis of Metabolites Associated With Severe Obesity in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.p552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Obesity remains a global public health burden, with 4.7 million premature deaths globally attributed to obesity. Severe obesity (SevO: defined as body mass index (BMI)≥40) is a major risk factor for other comorbidities, including heart disease and Type 2 Diabetes, which disproportionately impact historically marginalized populations, including Hispanic/Latinos. Based on BRFSS data, 24.5% of US Hispanic/Latino adults are projected to have severe obesity by 2030. However, the etiology of the underlying metabolic dysfunction remains unknown.
To address this gap, we identified metabolites associated with SevO in genotyped participants aged ≥20 with 25 < BMI ≥ 40 and metabolic data in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). We investigated cross-sectional associations between Blom-transformed metabolites and baseline SevO, adjusting for age, study center, background group, smoking status, and principal components of ancestry, stratified by sex (SUGEN), and meta-analyzed (SAS 9.4). For the top 20 metabolites, we extracted publicly available HCHS/SOL metabolite GWAS (mGWAS) summary statistics to derive metaboQTLs, and summary statistics from a multi-population meta-analysis of SevO (N>70,000) and implemented forward MR analysis using the MendelianRandomization R package (v0.3.0), which provides various robust causal estimation methods for summary data.
Anthropometry and data for 640 known Metabolon metabolites were available for 551 females (mean age: 43.3 years, 27% SevO) and 371 males (mean age 43.4 years, 15% SevO). We identified Bonferroni-corrected significant SevO associations (p<0.05/640) for 224 metabolites in the meta-analysis. Of the top 20 metabolites associated with SevO, we excluded six with no genome-wide significant SNPs in the mGWAS. For the remaining 14, we included independent SNPs with p<1E-6 as instrumental variables in the MR for each metabolite. After excluding SNPs ±500kb from known BMI loci, two metabolites showed causal associations with SevO, cytidine (penalized robust MR-Egger: ß (SE) =0.121 (0.051), p=0.018) and indoleproprionate (penalized weighted median-MR: ß (SE) =-0.138 (0.043), p=0.001).
Cytidine is a pyrimidine nucleoside consisting of D-ribose and cytosine, which is a precursor of cytidine triphosphate required in the one-carbon metabolism pathway to convert phosphatidylcholine (PC) to phosphatidylethanolamine (PE). PC biosynthesis is higher in adipose tissue macrophages in obese mice and humans. Indoleproprionate is a microbial metabolite of tryptophan produced by gut bacteria. Indoleproprionate levels have been shown to be associated with higher microbiome diversity and lower incidence of T2D. Our work points to future efforts to validate findings in other cohorts, including reverse MR to further elucidate the causal relationship between metabolites and severe obesity.
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Affiliation(s)
| | | | | | | | | | - Bing Yu
- UNIV OF TX HEALTH SCI CTR HOUSTON, Houston, TX
| | | | | | | | | | | | | | | | - Ruth Loos
- Icahn Sch of Medicine at Mount Sinai, New York City, NY
| | - Qibin Qi
- ALBERT EINSTEIN COLLEGE OF MEDICINE, Bronx, NY
| | - Rebecca Rohde
- Univ of North Carolina at Chapel Hill, Chapel Hill, NC
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Fernández-Rhodes L, Graff M, Buchanan VL, Justice AE, Highland HM, Guo X, Zhu W, Chen HH, Young KL, Adhikari K, Palmer ND, Below JE, Bradfield J, Pereira AC, Glover L, Kim D, Lilly AG, Shrestha P, Thomas AG, Zhang X, Chen M, Chiang CW, Pulit S, Horimoto A, Krieger JE, Guindo-Martínez M, Preuss M, Schumann C, Smit RA, Torres-Mejía G, Acuña-Alonzo V, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, González-José R, Poletti G, Rothhammer F, Hakonarson H, Igo R, Adler SG, Iyengar SK, Nicholas SB, Gogarten SM, Isasi CR, Papnicolaou G, Stilp AM, Qi Q, Kho M, Smith JA, Langefeld CD, Wagenknecht L, Mckean-Cowdin R, Gao XR, Nousome D, Conti DV, Feng Y, Allison MA, Arzumanyan Z, Buchanan TA, Chen YDI, Genter PM, Goodarzi MO, Hai Y, Hsueh W, Ipp E, Kandeel FR, Lam K, Li X, Nadler JL, Raffel LJ, Roll K, Sandow K, Tan J, Taylor KD, Xiang AH, Yao J, Audirac-Chalifour A, Peralta Romero JDJ, Hartwig F, Horta B, Blangero J, Curran JE, Duggirala R, Lehman DE, Puppala S, Fejerman L, John EM, Aguilar-Salinas C, Burtt NP, Florez JC, García-Ortíz H, González-Villalpando C, Mercader J, Orozco L, Tusié-Luna T, Blanco E, Gahagan S, Cox NJ, Hanis C, Butte NF, Cole SA, Comuzzie AG, Voruganti VS, Rohde R, Wang Y, Sofer T, Ziv E, Grant SF, Ruiz-Linares A, Rotter JI, Haiman CA, Parra EJ, Cruz M, Loos RJ, North KE. Erratum: Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium. HGG Adv 2022; 4:100149. [PMID: 36268164 PMCID: PMC9576563 DOI: 10.1016/j.xhgg.2022.100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
[This corrects the article DOI: 10.1016/j.xhgg.2022.100099.].
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Kim D, Justice AE, Chittoor G, Blanco E, Burrows R, Graff M, Howard AG, Wang Y, Rohde R, Buchanan VL, Voruganti VS, Almeida M, Peralta J, Lehman DM, Curran JE, Comuzzie AG, Duggirala R, Blangero J, Albala C, Santos JL, Angel B, Lozoff B, Gahagan S, North KE. Genetic determinants of metabolic biomarkers and their associations with cardiometabolic traits in Hispanic/Latino adolescents. Pediatr Res 2022; 92:563-571. [PMID: 34645953 PMCID: PMC9005573 DOI: 10.1038/s41390-021-01729-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 06/08/2021] [Accepted: 08/17/2021] [Indexed: 01/05/2023]
Abstract
BACKGROUND Metabolic regulation plays a significant role in energy homeostasis, and adolescence is a crucial life stage for the development of cardiometabolic disease (CMD). This study aims to investigate the genetic determinants of metabolic biomarkers-adiponectin, leptin, ghrelin, and orexin-and their associations with CMD risk factors. METHODS We characterized the genetic determinants of the biomarkers among Hispanic/Latino adolescents of the Santiago Longitudinal Study (SLS) and identified the cumulative effects of genetic variants on adiponectin and leptin using biomarker polygenic risk scores (PRS). We further investigated the direct and indirect effect of the biomarker PRS on downstream body fat percent (BF%) and glycemic traits using structural equation modeling. RESULTS We identified putatively novel genetic variants associated with the metabolic biomarkers. A substantial amount of biomarker variance was explained by SLS-specific PRS, and the prediction was improved by including the putatively novel loci. Fasting blood insulin and insulin resistance were associated with PRS for adiponectin, leptin, and ghrelin, and BF% was associated with PRS for adiponectin and leptin. We found evidence of substantial mediation of these associations by the biomarker levels. CONCLUSIONS The genetic underpinnings of metabolic biomarkers can affect the early development of CMD, partly mediated by the biomarkers. IMPACT This study characterized the genetic underpinnings of four metabolic hormones and investigated their potential influence on adiposity and insulin biology among Hispanic/Latino adolescents. Fasting blood insulin and insulin resistance were associated with polygenic risk score (PRS) for adiponectin, leptin, and ghrelin, with evidence of some degree of mediation by the biomarker levels. Body fat percent (BF%) was also associated with PRS for adiponectin and leptin. This provides important insight on biological mechanisms underlying early metabolic dysfunction and reveals candidates for prevention efforts. Our findings also highlight the importance of ancestrally diverse populations to facilitate valid studies of the genetic architecture of metabolic biomarker levels.
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Affiliation(s)
- Daeeun Kim
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Anne E. Justice
- Department of Population Health Sciences, Geisinger, Danville, PA
| | - Geetha Chittoor
- Department of Population Health Sciences, Geisinger, Danville, PA
| | - Estela Blanco
- Division of Academic General Pediatrics, Child Development and Community Health at the Center for Community Health, University of California at San Diego, San Diego, CA,Department of Public Health, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Raquel Burrows
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Victoria L. Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - V. Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis NC
| | - Marcio Almeida
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Juan Peralta
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Donna M. Lehman
- Departments of Medicine and Epidemiology and Biostatistics, University of Texas Health San Antonio, San Antonio, TX
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | | | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Brownsville, TX
| | - Cecilia Albala
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - José L. Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bárbara Angel
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Betsy Lozoff
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| | - Sheila Gahagan
- Division of Academic General Pediatrics, Child Development and Community Health at the Center for Community Health, University of California at San Diego, San Diego, CA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Avery CL, Howard AG, Ballou AF, Buchanan VL, Collins JM, Downie CG, Engel SM, Graff M, Highland HM, Lee MP, Lilly AG, Lu K, Rager JE, Staley BS, North KE, Gordon-Larsen P. Strengthening Causal Inference in Exposomics Research: Application of Genetic Data and Methods. Environ Health Perspect 2022; 130:55001. [PMID: 35533073 PMCID: PMC9084332 DOI: 10.1289/ehp9098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Advances in technologies to measure a broad set of exposures have led to a range of exposome research efforts. Yet, these efforts have insufficiently integrated methods that incorporate genetic data to strengthen causal inference, despite evidence that many exposome-associated phenotypes are heritable. Objective: We demonstrate how integration of methods and study designs that incorporate genetic data can strengthen causal inference in exposomics research by helping address six challenges: reverse causation and unmeasured confounding, comprehensive examination of phenotypic effects, low efficiency, replication, multilevel data integration, and characterization of tissue-specific effects. Examples are drawn from studies of biomarkers and health behaviors, exposure domains where the causal inference methods we describe are most often applied. Discussion: Technological, computational, and statistical advances in genotyping, imputation, and analysis, combined with broad data sharing and cross-study collaborations, offer multiple opportunities to strengthen causal inference in exposomics research. Full application of these opportunities will require an expanded understanding of genetic variants that predict exposome phenotypes as well as an appreciation that the utility of genetic variants for causal inference will vary by exposure and may depend on large sample sizes. However, several of these challenges can be addressed through international scientific collaborations that prioritize data sharing. Ultimately, we anticipate that efforts to better integrate methods that incorporate genetic data will extend the reach of exposomics research by helping address the challenges of comprehensively measuring the exposome and its health effects across studies, the life course, and in varied contexts and diverse populations. https://doi.org/10.1289/EHP9098.
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Affiliation(s)
- Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anna F Ballou
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victoria L Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason M Collins
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolina G Downie
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephanie M Engel
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Moa P Lee
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adam G Lilly
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Sociology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brooke S Staley
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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7
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Fernández-Rhodes L, Graff M, Buchanan VL, Justice AE, Highland HM, Guo X, Zhu W, Chen HH, Young KL, Adhikari K, Palmer ND, Below JE, Bradfield J, Pereira AC, Glover L, Kim D, Lilly AG, Shrestha P, Thomas AG, Zhang X, Chen M, Chiang CW, Pulit S, Horimoto A, Krieger JE, Guindo-Martínez M, Preuss M, Schumann C, Smit RA, Torres-Mejía G, Acuña-Alonzo V, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, González-José R, Poletti G, Rothhammer F, Hakonarson H, Igo R, Adler SG, Iyengar SK, Nicholas SB, Gogarten SM, Isasi CR, Papnicolaou G, Stilp AM, Qi Q, Kho M, Smith JA, Langefeld CD, Wagenknecht L, Mckean-Cowdin R, Gao XR, Nousome D, Conti DV, Feng Y, Allison MA, Arzumanyan Z, Buchanan TA, Ida Chen YD, Genter PM, Goodarzi MO, Hai Y, Hsueh W, Ipp E, Kandeel FR, Lam K, Li X, Nadler JL, Raffel LJ, Roll K, Sandow K, Tan J, Taylor KD, Xiang AH, Yao J, Audirac-Chalifour A, de Jesus Peralta Romero J, Hartwig F, Horta B, Blangero J, Curran JE, Duggirala R, Lehman DE, Puppala S, Fejerman L, John EM, Aguilar-Salinas C, Burtt NP, Florez JC, García-Ortíz H, González-Villalpando C, Mercader J, Orozco L, Tusié-Luna T, Blanco E, Gahagan S, Cox NJ, Hanis C, Butte NF, Cole SA, Comuzzie AG, Voruganti VS, Rohde R, Wang Y, Sofer T, Ziv E, Grant SF, Ruiz-Linares A, Rotter JI, Haiman CA, Parra EJ, Cruz M, Loos RJ, North KE. Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium. HGG Adv 2022; 3:100099. [PMID: 35399580 PMCID: PMC8990175 DOI: 10.1016/j.xhgg.2022.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/06/2022] [Indexed: 02/05/2023] Open
Abstract
Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite their notable anthropometric variability, ancestry proportions, and high burden of growth stunting and overweight/obesity. To address this knowledge gap, we analyzed densely imputed genetic data in a sample of Hispanic/Latino adults to identify and fine-map genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (stage 1, n = 59,771) and generalized our findings in 9 additional studies (stage 2, n = 10,538). We conducted a trans-ancestral GWAS with summary statistics from HISLA stage 1 and existing consortia of European and African ancestries. In our HISLA stage 1 + 2 analyses, we discovered one BMI locus, as well as two BMI signals and another height signal each within established anthropometric loci. In our trans-ancestral meta-analysis, we discovered three BMI loci, one height locus, and one WHRadjBMI locus. We also identified 3 secondary signals for BMI, 28 for height, and 2 for WHRadjBMI in established loci. We show that 336 known BMI, 1,177 known height, and 143 known WHRadjBMI (combined) SNPs demonstrated suggestive transferability (nominal significance and effect estimate directional consistency) in Hispanic/Latino adults. Of these, 36 BMI, 124 height, and 11 WHRadjBMI SNPs were significant after trait-specific Bonferroni correction. Trans-ancestral meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our findings demonstrate that future studies may also benefit from leveraging diverse ancestries and differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification.
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Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Biobehavioral Health, Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA 16802, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria L. Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anne E. Justice
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA 17822, USA
| | - Heather M. Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Wanying Zhu
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristin L. Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, MK7 6AA Milton Keynes, UK
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan Bradfield
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - LáShauntá Glover
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daeeun Kim
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam G. Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Poojan Shrestha
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alvin G. Thomas
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinruo Zhang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Charleston W.K. Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Sara Pulit
- Vertex Pharmaceuticals, W2 6BD Oxford, UK
| | - Andrea Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - Jose E. Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - Marta Guindo-Martínez
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Novo Nordisk Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Preuss
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claudia Schumann
- Hasso Plattner Institute, University of Potsdam, Digital Health Center, 14482 Potsdam, Germany
| | - Roelof A.J. Smit
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriela Torres-Mejía
- Department of Research in Cardiovascular Diseases, Diabetes Mellitus, and Cancer, Population Health Research Center, National Institute of Public Health, Cuernavaca, Morelos 62100, Mexico
| | | | - Gabriel Bedoya
- Molecular Genetics Investigation Group, University of Antioquia, Medellín 1226, Colombia
| | - Maria-Cátira Bortolini
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Samuel Canizales-Quinteros
- Population Genomics Applied to Health Unit, The National Institute of Genomic Medicine and the Faculty of Chemistry at the National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Rolando González-José
- Patagonian Institute of the Social and Human Sciences, Patagonian National Center, Puerto Madryn U9120, Argentina
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | | | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sharon G. Adler
- Division of Nephrology and Hypertension, Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Susanne B. Nicholas
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
| | | | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Lynne Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Roberta Mckean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, Department of Biomedical Informatics, Division of Human Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Darryl Nousome
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Matthew A. Allison
- Department of Family Medicine, University of California, San Diego, CA 92161, USA
| | - Zorayr Arzumanyan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Thomas A. Buchanan
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Pauline M. Genter
- Department of Medicine, Division of Endocrinology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Willa Hsueh
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Eli Ipp
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
- Department of Medicine, Division of Endocrinology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Fouad R. Kandeel
- Department of Translational Research & Cellular Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Kelvin Lam
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jerry L. Nadler
- Department of Pharmacology at New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Leslie J. Raffel
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
| | - Kathryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Anny H. Xiang
- Research and Evaluation Branch, Kaiser Permanente of Southern California, Pasadena, CA 91101, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Astride Audirac-Chalifour
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Jose de Jesus Peralta Romero
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Fernando Hartwig
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas 96010-610, Brazil
| | - Bernando Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas 96010-610, Brazil
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Donna E. Lehman
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sobha Puppala
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27109, USA
| | - Laura Fejerman
- Department of Public Health Sciences, School of Medicine, and the Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA
| | - Esther M. John
- Departments of Epidemiology & Population Health and Medicine-Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carlos Aguilar-Salinas
- Division of Nutrition, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Noël P. Burtt
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Humberto García-Ortíz
- Laboratory of Immunogenomics and Metabolic Diseases, National Institute of Genomic Medicine, Mexico City 14610, Mexico
| | - Clicerio González-Villalpando
- Center for Diabetes Studies, Research Unit for Diabetes and Cardiovascular Risk, Center for Population Health Studies, National Institute of Public Health, Mexico City 14080, Mexico
| | - Josep Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, National Institute of Genomic Medicine, Mexico City 14610, Mexico
| | - Teresa Tusié-Luna
- Molecular Biology and Medical Genomics Unity, Institute of Biomedical Research, The National Autonomous University of Mexico and the Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Estela Blanco
- Center for Community Health, Division of Academic General Pediatrics, University of California at San Diego, San Diego, CA 92093, USA
| | - Sheila Gahagan
- Center for Community Health, Division of Academic General Pediatrics, University of California at San Diego, San Diego, CA 92093, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Craig Hanis
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nancy F. Butte
- United States Department of Agriculture, Agricultural Research Service, The Children’s Nutrition Research Center, and the Department Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelley A. Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | | - V. Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tamar Sofer
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Struan F.A. Grant
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andres Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
- Department of Genetics, Evolution and Environment, and Genetics Institute of the University College London, London WC1E 6BT, UK
- Laboratory of Biocultural Anthropology, Law, Ethics, and Health, Aix-Marseille University, Marseille 13385, France
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto- Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Miguel Cruz
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Ruth J.F. Loos
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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Buchanan VL, Wang Y, Blanco E, Graff M, Albala C, Burrows R, Santos JL, Angel B, Lozoff B, Voruganti VS, Guo X, Taylor KD, Chen YDI, Yao J, Tan J, Downie C, Highland HM, Justice AE, Gahagan S, North KE. Genome-wide association study identifying novel variant for fasting insulin and allelic heterogeneity in known glycemic loci in Chilean adolescents: The Santiago Longitudinal Study. Pediatr Obes 2021; 16:e12765. [PMID: 33381925 PMCID: PMC8711702 DOI: 10.1111/ijpo.12765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/25/2020] [Indexed: 12/01/2022]
Abstract
BACKGROUND The genetic underpinnings of glycemic traits have been understudied in adolescent and Hispanic/Latino (H/L) populations in comparison to adults and populations of European ancestry. OBJECTIVE To identify genetic factors underlying glycemic traits in an adolescent H/L population. METHODS We conducted a genome-wide association study (GWAS) of fasting glucose (FG) and fasting insulin (FI) in H/L adolescents from the Santiago Longitudinal Study. RESULTS We identified one novel variant positioned in the CSMD1 gene on chromosome 8 (rs77465890, effect allele frequency = 0.10) that was associated with FI (β = -0.299, SE = 0.054, p = 2.72×10-8 ) and was only slightly attenuated after adjusting for body mass index z-scores (β = -0.252, SE = 0.047, p = 1.03×10-7 ). We demonstrated directionally consistent, but not statistically significant results in African and Hispanic adults of the Population Architecture Using Genomics and Epidemiology Consortium. We also identified secondary signals for two FG loci after conditioning on known variants, which demonstrate allelic heterogeneity in well-known glucose loci. CONCLUSION Our results exemplify the importance of including populations with diverse ancestral origin and adolescent participants in GWAS of glycemic traits to uncover novel risk loci and expand our understanding of disease aetiology.
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Affiliation(s)
- Victoria L Buchanan
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yujie Wang
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Estela Blanco
- Division of Academic General Pediatrics, Child Development and Community Health, University of California at San Diego, San Diego, California, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Cecilia Albala
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology, University of Chile, Santiago, Chile
| | - Raquel Burrows
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology, University of Chile, Santiago, Chile
| | - José L Santos
- Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bárbara Angel
- Department of Public Health Nutrition, Institute of Nutrition and Food Technology, University of Chile, Santiago, Chile
| | - Betsy Lozoff
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Venkata Saroja Voruganti
- Department of Nutrition and UNC Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Carolina Downie
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather M Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania, USA
| | - Sheila Gahagan
- Division of Academic General Pediatrics, Child Development and Community Health, University of California at San Diego, San Diego, California, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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9
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Chen HH, Shaw DM, Petty LE, Graff M, Bohlender RJ, Polikowsky HG, Zhong X, Kim D, Buchanan VL, Preuss MH, Shuey MM, Loos RJF, Huff CD, Cox NJ, Bastarache JA, Bastarache L, North KE, Below JE. Host genetic effects in pneumonia. Am J Hum Genet 2021; 108:194-201. [PMID: 33357513 PMCID: PMC7820802 DOI: 10.1016/j.ajhg.2020.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/02/2020] [Indexed: 01/05/2023] Open
Abstract
Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.
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Affiliation(s)
- Hung-Hsin Chen
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas M Shaw
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lauren E Petty
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Misa Graff
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Ryan J Bohlender
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Hannah G Polikowsky
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xue Zhong
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daeeun Kim
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Victoria L Buchanan
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan M Shuey
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Julie A Bastarache
- Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kari E North
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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