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Timothy D Majarian

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Yen A, Zappala Z, Fine RS, Majarian TD, Sripakdeevong P, Altshuler D. Specificity of CRISPR-Cas9 Editing in Exagamglogene Autotemcel. N Engl J Med 2024. [PMID: 38657268 DOI: 10.1056/nejmc2313119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]

Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Huerta-Chagoya A, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Zaitlen N, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry polygenic mechanisms of type 2 diabetes. Nat Med 2024;30:1065-1074. [PMID: 38443691 DOI: 10.1038/s41591-024-02865-3] [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: 09/29/2023] [Accepted: 02/06/2024] [Indexed: 03/07/2024]

Affiliation(s)

Kirk Smith Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Aaron J Deutsch Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Carolyn McGrail Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
Hyunkyung Kim Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
Sarah Hsu Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Alicia Huerta-Chagoya Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Ravi Mandla Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Philip H Schroeder Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Kenneth E Westerman Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Lukasz Szczerbinski Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
Timothy D Majarian Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA Vertex Pharmaceuticals, Boston, MA, USA
Varinderpal Kaur Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Alice Williamson Precision Healthcare University Research Institute, Queen Mary University of London, London, UK MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
Noah Zaitlen Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
Melina Claussnitzer Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Jose C Florez Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Alisa K Manning Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Josep M Mercader Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Kyle J Gaulton Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
Miriam S Udler Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA. Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. Department of Medicine, Harvard Medical School, Boston, MA, USA.

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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity. Res Sq 2023:rs.3.rs-3399145. [PMID: 37886436 PMCID: PMC10602111 DOI: 10.21203/rs.3.rs-3399145/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]

Affiliation(s)

Kirk Smith Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Aaron J. Deutsch Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Carolyn McGrail Department of Pediatrics, University of California San Diego, San Diego, CA, USA
Hyunkyung Kim Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
Sarah Hsu Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Ravi Mandla Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Philip H. Schroeder Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Kenneth E. Westerman Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Lukasz Szczerbinski Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
Timothy D. Majarian Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Varinderpal Kaur Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Alice Williamson Precision Healthcare University Research Institute, Queen Mary University of London, London, UK MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
Melina Claussnitzer Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Jose C. Florez Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Alisa K. Manning Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Josep M. Mercader Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Kyle J. Gaulton Department of Pediatrics, University of California San Diego, San Diego, CA, USA
Miriam S. Udler Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA

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Smith K, Deutsch AJ, McGrail C, Kim H, Hsu S, Mandla R, Schroeder PH, Westerman KE, Szczerbinski L, Majarian TD, Kaur V, Williamson A, Claussnitzer M, Florez JC, Manning AK, Mercader JM, Gaulton KJ, Udler MS. Multi-ancestry Polygenic Mechanisms of Type 2 Diabetes Elucidate Disease Processes and Clinical Heterogeneity. medRxiv 2023:2023.09.28.23296294. [PMID: 37808749 PMCID: PMC10557820 DOI: 10.1101/2023.09.28.23296294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]

Affiliation(s)

Kirk Smith Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Aaron J. Deutsch Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Carolyn McGrail Department of Pediatrics, University of California San Diego, San Diego, CA, USA
Hyunkyung Kim Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, USA Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
Sarah Hsu Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Ravi Mandla Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Philip H. Schroeder Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Kenneth E. Westerman Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Lukasz Szczerbinski Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
Timothy D. Majarian Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Varinderpal Kaur Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Alice Williamson Precision Healthcare University Research Institute, Queen Mary University of London, London, UK MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
Melina Claussnitzer Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
Jose C. Florez Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Alisa K. Manning Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
Josep M. Mercader Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Kyle J. Gaulton Department of Pediatrics, University of California San Diego, San Diego, CA, USA
Miriam S. Udler Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA

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Cromer SJ, Lakhani CM, Mercader JM, Majarian TD, Schroeder P, Cole JB, Florez JC, Patel CJ, Manning AK, Burnett-Bowie SAM, Merino J, Udler MS. Association and Interaction of Genetics and Area-Level Socioeconomic Factors on the Prevalence of Type 2 Diabetes and Obesity. Diabetes Care 2023;46:944-952. [PMID: 36787958 PMCID: PMC10154653 DOI: 10.2337/dc22-1954] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/17/2022] [Indexed: 02/16/2023]

Affiliation(s)

Sara J. Cromer Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
Chirag M. Lakhani Department of Biomedical Informatics, Harvard Medical School, Boston, MA
Josep M. Mercader Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
Timothy D. Majarian Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
Philip Schroeder Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
Joanne B. Cole Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Division of Endocrinology, Boston Children’s Hospital, Boston, MA Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO
Jose C. Florez Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
Chirag J. Patel Department of Biomedical Informatics, Harvard Medical School, Boston, MA
Alisa K. Manning Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Clinical and Translational Epidemiology Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA
Sherri-Ann M. Burnett-Bowie Department of Medicine, Harvard Medical School, Boston, MA Endocrine Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA
Jordi Merino Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Miriam S. Udler Diabetes Unit, Endocrine Division, Massachusetts General Hospital, Boston, MA Department of Medicine, Harvard Medical School, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA

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Deutsch AJ, Stalbow L, Majarian TD, Mercader JM, Manning AK, Florez JC, Loos RJ, Udler MS. Polygenic Scores Help Reduce Racial Disparities in Predictive Accuracy of Automated Type 1 Diabetes Classification Algorithms. Diabetes Care 2023;46:794-800. [PMID: 36745605 PMCID: PMC10090893 DOI: 10.2337/dc22-1833] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/10/2023] [Indexed: 02/07/2023]

Affiliation(s)

Aaron J. Deutsch Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Department of Medicine, Harvard Medical School, Boston, MA
Lauren Stalbow Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
Timothy D. Majarian Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
Josep M. Mercader Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Department of Medicine, Harvard Medical School, Boston, MA
Alisa K. Manning Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Department of Medicine, Harvard Medical School, Boston, MA Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA
Jose C. Florez Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Department of Medicine, Harvard Medical School, Boston, MA
Ruth J.F. Loos Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
Miriam S. Udler Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA Programs in Metabolism and Medical & Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA Department of Medicine, Harvard Medical School, Boston, MA

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Majarian TD, Bentley AR, Laville V, Brown MR, Chasman DI, de Vries PS, Feitosa MF, Franceschini N, Gauderman WJ, Marchek C, Levy D, Morrison AC, Province M, Rao DC, Schwander K, Sung YJ, Rotimi CN, Aschard H, Gu CC, Manning AK. Multi-omics insights into the biological mechanisms underlying statistical gene-by-lifestyle interactions with smoking and alcohol consumption. Front Genet 2022;13:954713. [PMID: 36544485 PMCID: PMC9760722 DOI: 10.3389/fgene.2022.954713] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open

Abstract

Though both genetic and lifestyle factors are known to influence cardiometabolic outcomes, less attention has been given to whether lifestyle exposures can alter the association between a genetic variant and these outcomes. The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium's Gene-Lifestyle Interactions Working Group has recently published investigations of genome-wide gene-environment interactions in large multi-ancestry meta-analyses with a focus on cigarette smoking and alcohol consumption as lifestyle factors and blood pressure and serum lipids as outcomes. Further description of the biological mechanisms underlying these statistical interactions would represent a significant advance in our understanding of gene-environment interactions, yet accessing and harmonizing individual-level genetic and 'omics data is challenging. Here, we demonstrate the coordinated use of summary-level data for gene-lifestyle interaction associations on up to 600,000 individuals, differential methylation data, and gene expression data for the characterization and prioritization of loci for future follow-up analyses. Using this approach, we identify 48 genes for which there are multiple sources of functional support for the identified gene-lifestyle interaction. We also identified five genes for which differential expression was observed by the same lifestyle factor for which a gene-lifestyle interaction was found. For instance, in gene-lifestyle interaction analysis, the T allele of rs6490056 (ALDH2) was associated with higher systolic blood pressure, and a larger effect was observed in smokers compared to non-smokers. In gene expression studies, this allele is associated with decreased expression of ALDH2, which is part of a major oxidative pathway. Other results show increased expression of ALDH2 among smokers. Oxidative stress is known to contribute to worsening blood pressure. Together these data support the hypothesis that rs6490056 reduces expression of ALDH2, which raises oxidative stress, leading to an increase in blood pressure, with a stronger effect among smokers, in whom the burden of oxidative stress is greater. Other genes for which the aggregation of data types suggest a potential mechanism include: GCNT4×current smoking (HDL), PTPRZ1×ever-smoking (HDL), SYN2×current smoking (pulse pressure), and TMEM116×ever-smoking (mean arterial pressure). This work demonstrates the utility of careful curation of summary-level data from a variety of sources to prioritize gene-lifestyle interaction loci for follow-up analyses.

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Affiliation(s)

Timothy D. Majarian Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, United States
Amy R. Bentley Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, United States
Vincent Laville Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
Michael R. Brown Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
Daniel I. Chasman Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
Paul S. de Vries Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
Mary F. Feitosa Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
Nora Franceschini Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
W. James Gauderman Biostatistics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA, United States
Casey Marchek Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, United States,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, United States
Daniel Levy The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MA, United States
Alanna C. Morrison Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States
Michael Province Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
Dabeeru C. Rao Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
Karen Schwander Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States,Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
Yun Ju Sung Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
Charles N. Rotimi Center for Research on Genomics and Global Health, National Human Genome Research Institute, US National Institutes of Health, Bethesda, MD, United States
Hugues Aschard Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France,Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
C. Charles Gu Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States
Alisa K. Manning Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, United States,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine and Harvard Medical School, Boston, MA, United States,*Correspondence: Alisa K. Manning,
on behalf of the CHARGE Gene-Lifestyle Interactions Working Group

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DiCorpo D, Gaynor SM, Russell EM, Westerman KE, Raffield LM, Majarian TD, Wu P, Sarnowski C, Highland HM, Jackson A, Hasbani NR, de Vries PS, Brody JA, Hidalgo B, Guo X, Perry JA, O'Connell JR, Lent S, Montasser ME, Cade BE, Jain D, Wang H, D'Oliveira Albanus R, Varshney A, Yanek LR, Lange L, Palmer ND, Almeida M, Peralta JM, Aslibekyan S, Baldridge AS, Bertoni AG, Bielak LF, Chen CS, Chen YDI, Choi WJ, Goodarzi MO, Floyd JS, Irvin MR, Kalyani RR, Kelly TN, Lee S, Liu CT, Loesch D, Manson JE, Minster RL, Naseri T, Pankow JS, Rasmussen-Torvik LJ, Reiner AP, Reupena MS, Selvin E, Smith JA, Weeks DE, Xu H, Yao J, Zhao W, Parker S, Alonso A, Arnett DK, Blangero J, Boerwinkle E, Correa A, Cupples LA, Curran JE, Duggirala R, He J, Heckbert SR, Kardia SLR, Kim RW, Kooperberg C, Liu S, Mathias RA, McGarvey ST, Mitchell BD, Morrison AC, Peyser PA, Psaty BM, Redline S, Shuldiner AR, Taylor KD, Vasan RS, Viaud-Martinez KA, Florez JC, Wilson JG, Sladek R, Rich SS, Rotter JI, Lin X, Dupuis J, Meigs JB, Wessel J, Manning AK. Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program. Commun Biol 2022;5:756. [PMID: 35902682 PMCID: PMC9334637 DOI: 10.1038/s42003-022-03702-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/06/2021] [Accepted: 07/12/2022] [Indexed: 01/04/2023] Open

Affiliation(s)

Daniel DiCorpo Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
Sheila M Gaynor Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
Emily M Russell Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
Kenneth E Westerman Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, 02114, USA Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
Laura M Raffield Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
Timothy D Majarian Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
Peitao Wu Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
Chloé Sarnowski Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
Heather M Highland Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
Anne Jackson Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
Natalie R Hasbani Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
Paul S de Vries Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
Jennifer A Brody Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA Department of Medicine, University of Washington, Seattle, WA, 98101, USA
Bertha Hidalgo Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, 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
James A Perry Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
Jeffrey R O'Connell Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
Samantha Lent Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
May E Montasser Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
Brian E Cade Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
Deepti Jain Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
Heming Wang Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA
Ricardo D'Oliveira Albanus Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
Arushi Varshney Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
Lisa R Yanek GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
Leslie Lange Department of Medicine, Anschutz Medical Campus, University of Colorado Denver, Aurora, CO, 80045, USA
Nicholette D Palmer Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
Marcio Almeida Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
Juan M Peralta Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
Stella Aslibekyan 23andMe, Sunnyvale, CA, 94086, USA
Abigail S Baldridge Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
Alain G Bertoni Department of Epidemiology & Prevention, Wake Forest School of Medicine, Winston-, Salem, NC, 27157, USA
Lawrence F Bielak Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
Chung-Shiuan Chen Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, 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
Won Jung Choi Psomagen, Inc, Rockville, MD, 20850, USA
Mark O Goodarzi Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
James S Floyd Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA Department of Medicine, University of Washington, Seattle, WA, 98195, USA
Marguerite R Irvin Ryals School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
Rita R Kalyani GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
Tanika N Kelly Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
Seonwook Lee Psomagen, Inc, Rockville, MD, 20850, USA
Ching-Ti Liu Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
Douglas Loesch Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
JoAnn E Manson Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA Brigham and Women's Hospital, Boston, MA, 02115, USA
Ryan L Minster Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
Take Naseri Ministry of Health, Government of Samoa, Apia, Samoa
James S Pankow Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, 55454, USA
Laura J Rasmussen-Torvik Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
Alexander P Reiner Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
Muagututi'a Sefuiva Reupena Lutia i Puava 'ae Mapu i Fagalele, Apia, Samoa
Elizabeth Selvin Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21287, USA
Jennifer A Smith Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
Daniel E Weeks Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
Huichun Xu Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, 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
Wei Zhao Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
Stephen Parker Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
Alvaro Alonso Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
Donna K Arnett College of Public Health, University of Kentucky, Lexington, KY, 40506, USA
John Blangero Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
Eric Boerwinkle Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
Adolfo Correa Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39211, USA
L Adrienne Cupples Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA National Heart Lung and Blood Institute and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
Joanne E Curran Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
Ravindranath Duggirala Department of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville and Edinburg, TX, 78539, USA
Jiang He Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
Susan R Heckbert Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98195, USA Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA
Sharon L R Kardia Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
Ryan W Kim Psomagen, Inc, Rockville, MD, 20850, USA
Charles Kooperberg Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
Simin Liu Center for Global Cardiometabolic Health (CGCH), Boston, MA, 02215, USA
Rasika A Mathias GeneSTAR Research Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
Stephen T McGarvey International Health Institute and Department of Epidemiology, Brown University School of Public Health, Providence, RI, 02912, USA
Braxton D Mitchell Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, 21201, USA
Alanna C Morrison Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
Patricia A Peyser Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, 48109, USA
Bruce M Psaty Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA Department of Medicine, University of Washington, Seattle, WA, 98101, USA Department of Epidemiology, University of Washington, Seattle, WA, 98195, USA Department of Health Services, University of Washington, Seattle, WA, 98101, USA
Susan Redline Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA Division of Sleep Medicine, Harvard Medical School, Boston, MA, 02115, USA Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
Alan R Shuldiner Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21231, 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
Ramachandran S Vasan National Heart Lung and Blood Institute and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA Evans Department of Medicine, Section of Preventive Medicine and Epidemiology, Boston University School of Medicine, Boston, MA, 02118, USA Evans Department of Medicine, Whitaker Cardiovascular Institute and Cardiology Section, Boston University School of Medicine, Boston, MA, 02118, USA
Karine A Viaud-Martinez Illumina Laboratory Services, Illumina, Inc, San Diego, CA, 92122, USA
Jose C Florez Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
James G Wilson Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02115, USA
Robert Sladek Department of Human Genetics, McGill University, Montreal, Montreal, Quebec, H3A 0G1, Canada Department of Medicine, McGill University, Montreal, Montreal, Quebec, H3A 0G1, Canada
Stephen S Rich Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
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
Xihong Lin Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
Josée Dupuis Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
James B Meigs Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
Jennifer Wessel Department of Epidemiology, Fairbanks School of Public Health, Indiana University, IN, 46202, USA. Department of Medicine, School of Medicine, Indiana University, IN, 46202, USA. Diabetes Translational Research Center, Indiana University, IN, 46202, USA.
Alisa K Manning Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, 02114, USA. Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, 02124, USA. Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.

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Westerman KE, Majarian TD, Giulianini F, Jang DK, Miao J, Florez JC, Chen H, Chasman DI, Udler MS, Manning AK, Cole JB. Variance-quantitative trait loci enable systematic discovery of gene-environment interactions for cardiometabolic serum biomarkers. Nat Commun 2022;13:3993. [PMID: 35810165 PMCID: PMC9271055 DOI: 10.1038/s41467-022-31625-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/15/2021] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open

Affiliation(s)

Kenneth E Westerman Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA. Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. Department of Medicine, Harvard Medical School, Boston, MA, USA.
Timothy D Majarian Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
Franco Giulianini Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
Dong-Keun Jang Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
Jenkai Miao Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
Jose C Florez Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
Han Chen Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
Daniel I Chasman Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA Division of Genetics, Brigham and Women's Hospital, Boston, MA, 02115, USA Medical and Population Genetics Program, Broad Institute, Cambridge, MA, USA Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
Miriam S Udler Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
Alisa K Manning Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA Department of Medicine, Harvard Medical School, Boston, MA, USA
Joanne B Cole Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA. Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA. Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.

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Johnson GR, Kangas JD, Dovzhenko A, Trojok R, Voigt K, Majarian TD, Palme K, Murphy RF. A method for characterizing phenotypic changes in highly variable cell populations and its application to high content screening of Arabidopsis thaliana protoplasts. Cytometry A 2017;91:326-335. [PMID: 28245335 DOI: 10.1002/cyto.a.23067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/22/2016] [Accepted: 01/19/2017] [Indexed: 11/08/2022]

Li Y, Majarian TD, Naik AW, Johnson GR, Murphy RF. Point process models for localization and interdependence of punctate cellular structures. Cytometry A 2016;89:633-43. [PMID: 27327612 DOI: 10.1002/cyto.a.22873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 03/09/2016] [Accepted: 04/29/2016] [Indexed: 11/08/2022]

Abstract

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry.

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