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Liu T, Liu S, Rui X, Cao Y, Hecker J, Guo F, Zhang Y, Gong L, Zhou Y, Yu Y, Krishnamoorthyni N, Bates S, Chun S, Boyer N, Xu S, Park JA, Perrella MA, Levy BD, Weiss ST, Mou H, Raby BA, Zhou X. Gasdermin B, an asthma-susceptibility gene, promotes MAVS-TBK1 signaling and airway inflammation. Eur Respir J 2024:2301232. [PMID: 38514093 DOI: 10.1183/13993003.01232-2023] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 12/30/2023] [Indexed: 03/23/2024]
Abstract
RATIONALE Respiratory virus-induced inflammation is the leading cause of asthma exacerbation, frequently accompanied by induction of IFN-stimulated genes (ISGs). How asthma genetic susceptible genes modulate cellular response upon viral infection through fine-tuning ISGs induction and subsequent airway inflammation in genetically susceptible asthmatics remains largely unknown. OBJECTIVES To decipher the functions of GSDMB in respiratory virus-induced lung inflammation. METHODS In two independent cohorts, we analyzed expression correlation between GSDMB and ISGs. In human bronchial epithelial cell line or primary cells, we generated GSDMB-overexpressing and -deficient cells. A series of qPCR, ELISA and co-immunoprecipitation assays were performed to determine the function and mechanism of GSDMB for ISGs induction. We also generated a novel transgenic mouse line with inducible expression of human unique GSDMB gene in airway epithelial cells and applied respiratory syncytial virus (RSV) infection to determine the role of GSDMB on RSV-induced lung inflammation in vivo. MEASUREMENTS AND MAIN RESULTS Gasdermin B encoded by GSDMB, one of the most significant asthma-susceptible genes at 17q21, acts as a novel RNA sensor, promoting MAVS-TBK1 signaling and subsequent inflammation. In airway epithelium, GSDMB is induced by respiratory viral infections. Expression of GSDMB and ISGs significantly correlated in respiratory epithelium from two independent asthma cohorts. Notably, inducible expression of human GSDMB gene in mouse airway epithelium leads to enhanced ISGs induction, increased airway inflammation with mucus hyper-secretion upon RSV infection. CONCLUSIONS GSDMB promotes ISGs expression and airway inflammation upon respiratory virus infection, thereby conferring asthma risk in risk allele carriers.
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Affiliation(s)
- Tao Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Siqi Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- These authors contributed equally
| | - Xianliang Rui
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- These authors contributed equally
| | - Ye Cao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yihan Zhang
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Lu Gong
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yihan Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Yuzhen Yu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Nandini Krishnamoorthyni
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Samuel Bates
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Sung Chun
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Nathan Boyer
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Shuang Xu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Jin-Ah Park
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Hongmei Mou
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Benjamin A Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Division of Pulmonary Medicine, Department of Pediatrics, Boston Children's Hospital and Harvard Medical School, Boston, MA
- These authors jointly conceptualized and supervised this work
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- These authors jointly conceptualized and supervised this work
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Moll M, Peljto AL, Kim JS, Xu H, Debban CL, Chen X, Menon A, Putman RK, Ghosh AJ, Saferali A, Nishino M, Hatabu H, Hobbs BD, Hecker J, McDermott G, Sparks JA, Wain LV, Allen RJ, Tobin MD, Raby BA, Chun S, Silverman EK, Zamora AC, Ortega VE, Garcia CK, Barr RG, Bleecker ER, Meyers DA, Kaner RJ, Rich SS, Manichaikul A, Rotter JI, Dupuis J, O’Connor GT, Fingerlin TE, Hunninghake GM, Schwartz DA, Cho MH. A Polygenic Risk Score for Idiopathic Pulmonary Fibrosis and Interstitial Lung Abnormalities. Am J Respir Crit Care Med 2023; 208:791-801. [PMID: 37523715 PMCID: PMC10563194 DOI: 10.1164/rccm.202212-2257oc] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Rationale: In addition to rare genetic variants and the MUC5B locus, common genetic variants contribute to idiopathic pulmonary fibrosis (IPF) risk. The predictive power of common variants outside the MUC5B locus for IPF and interstitial lung abnormalities (ILAs) is unknown. Objectives: We tested the predictive value of IPF polygenic risk scores (PRSs) with and without the MUC5B region on IPF, ILA, and ILA progression. Methods: We developed PRSs that included (PRS-M5B) and excluded (PRS-NO-M5B) the MUC5B region (500-kb window around rs35705950-T) using an IPF genome-wide association study. We assessed PRS associations with area under the receiver operating characteristic curve (AUC) metrics for IPF, ILA, and ILA progression. Measurements and Main Results: We included 14,650 participants (1,970 IPF; 1,068 ILA) from six multi-ancestry population-based and case-control cohorts. In cases excluded from genome-wide association study, the PRS-M5B (odds ratio [OR] per SD of the score, 3.1; P = 7.1 × 10-95) and PRS-NO-M5B (OR per SD, 2.8; P = 2.5 × 10-87) were associated with IPF. Participants in the top PRS-NO-M5B quintile had ∼sevenfold odds for IPF compared with those in the first quintile. A clinical model predicted IPF (AUC, 0.61); rs35705950-T and PRS-NO-M5B demonstrated higher AUCs (0.73 and 0.7, respectively), and adding both genetic predictors to a clinical model yielded the highest performance (AUC, 0.81). The PRS-NO-M5B was associated with ILA (OR, 1.25) and ILA progression (OR, 1.16) in European ancestry participants. Conclusions: A common genetic variant risk score complements the MUC5B variant to identify individuals at high risk of interstitial lung abnormalities and pulmonary fibrosis.
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Affiliation(s)
- Matthew Moll
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anna L. Peljto
- Department of Medicine and
- Department of Immunology, Division of Pulmonary Medicine, University of Colorado, Aurora, Colorado
| | - John S. Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Catherine L. Debban
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Xianfeng Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Aravind Menon
- Division of Pulmonary and Critical Care Medicine, and
| | | | - Auyon J. Ghosh
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, State University of New York Upstate Medical Center, Syracuse, New York
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mizuki Nishino
- Center for Pulmonary Functional Imaging, Department of Radiology
| | - Hiroto Hatabu
- Center for Pulmonary Functional Imaging, Department of Radiology
| | - Brian D. Hobbs
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Julian Hecker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gregory McDermott
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Jeffrey A. Sparks
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Benjamin A. Raby
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Pediatrics
- Division of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Edwin K. Silverman
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ana C. Zamora
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Victor E. Ortega
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic, Phoenix, Arizona
| | - Christine K. Garcia
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - R. Graham Barr
- Department of Medicine and
- Division of General Medicine, Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Eugene R. Bleecker
- Division of Genetics, Genomics, and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Deborah A. Meyers
- Division of Genetics, Genomics, and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona
| | - Robert J. Kaner
- Division of Pulmonary Medicine, Weill Cornell School of Medicine, New York, New York
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-University of California, Los Angeles Medical Center, Torrance, California
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, McGill University Faculty of Medicine and Health Sciences, Montreal, Quebec, Canada
| | - George T. O’Connor
- Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts; and
| | - Tasha E. Fingerlin
- The National Jewish Health Cohen Family Asthma Institute, Division of Allergy and Immunology, National Jewish Health, Denver, Colorado
| | | | - David A. Schwartz
- Department of Medicine and
- Department of Immunology, Division of Pulmonary Medicine, University of Colorado, Aurora, Colorado
| | - Michael H. Cho
- Division of Pulmonary and Critical Care Medicine, and
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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3
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Hayeck TJ, Busby GB, Chun S, Lewis AC, Roberts MC, Vilhjálmsson BJ. Polygenic Risk Scores: Genomes to Risk Prediction. Clin Chem 2023; 69:hvad049. [PMID: 37232050 PMCID: PMC10681370 DOI: 10.1093/clinchem/hvad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023]
Affiliation(s)
- Tristan J. Hayeck
- Assistant Professor, Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Assistant Professor, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - George B. Busby
- Chief Scientific Officer, Allelica Inc., New York, NY, United States
| | - Sung Chun
- Scientist, Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA, United States
- Instructor of Pediatrics, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Anna C.F. Lewis
- Research Associate, Edmond and Lily Safra Center for Ethics, Harvard University, and Division of Genetics, Brigham and Women’s Hospital, Boston, MA, United States
| | - Megan C. Roberts
- Assistant Professor and Director Implementation Science, in Precision Health & Society, Division of Pharmaceutical Outcomes and Policy, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, United States
| | - Bjarni J. Vilhjálmsson
- Professor, National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
- Professor, Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
- Professor, Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, United States
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4
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Queen K, Nguyen MN, Gilliland FD, Chun S, Raby BA, Millstein J. ACDC: a general approach for detecting phenotype or exposure associated co-expression. Front Med (Lausanne) 2023; 10:1118824. [PMID: 37275375 PMCID: PMC10235619 DOI: 10.3389/fmed.2023.1118824] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Background Existing module-based differential co-expression methods identify differences in gene-gene relationships across phenotype or exposure structures by testing for consistent changes in transcription abundance. Current methods only allow for assessment of co-expression variation across a singular, binary or categorical exposure or phenotype, limiting the information that can be obtained from these analyses. Methods Here, we propose a novel approach for detection of differential co-expression that simultaneously accommodates multiple phenotypes or exposures with binary, ordinal, or continuous data types. Results We report an application to two cohorts of asthmatic patients with varying levels of asthma control to identify associations between gene co-expression and asthma control test scores. Results suggest that both expression levels and covariances of ADORA3, ALOX15, and IDO1 are associated with asthma control. Conclusion ACDC is a flexible extension to existing methodology that can detect differential co-expression across varying external variables.
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Affiliation(s)
- Katelyn Queen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - My-Nhi Nguyen
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Frank D. Gilliland
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - Benjamin A. Raby
- Division of Pulmonary Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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5
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Hecker J, Chun S, Samiei A, Liu C, Laurie C, Kachroo P, Lutz SM, Lee S, Smith AV, Lasky-Su J, Cho MH, Sharma S, Soto Quirós ME, Avila L, Celedón JC, Raby B, Zhou X, Silverman EK, DeMeo DL, Lange C, Weiss ST. FGF20 and PGM2 variants are associated with childhood asthma in family-based whole-genome sequencing studies. Hum Mol Genet 2023; 32:696-707. [PMID: 36255742 PMCID: PMC9896483 DOI: 10.1093/hmg/ddac258] [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: 06/24/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Asthma is a heterogeneous common respiratory disease that remains poorly understood. The established genetic associations fail to explain the high estimated heritability, and the prevalence of asthma differs between populations and geographic regions. Robust association analyses incorporating different genetic ancestries and whole-genome sequencing data may identify novel genetic associations. METHODS We performed family-based genome-wide association analyses of childhood-onset asthma based on whole-genome sequencing (WGS) data for the 'The Genetic Epidemiology of Asthma in Costa Rica' study (GACRS) and the Childhood Asthma Management Program (CAMP). Based on parent-child trios with children diagnosed with asthma, we performed a single variant analysis using an additive and a recessive genetic model and a region-based association analysis of low-frequency and rare variants. RESULTS Based on 1180 asthmatic trios (894 GACRS trios and 286 CAMP trios, a total of 3540 samples with WGS data), we identified three novel genetic loci associated with childhood-onset asthma: rs4832738 on 4p14 ($P=1.72\ast{10}^{-9}$, recessive model), rs1581479 on 8p22 ($P=1.47\ast{10}^{-8}$, additive model) and rs73367537 on 10q26 ($P=1.21\ast{10}^{-8}$, additive model in GACRS only). Integrative analyses suggested potential novel candidate genes underlying these associations: PGM2 on 4p14 and FGF20 on 8p22. CONCLUSION Our family-based whole-genome sequencing analysis identified three novel genetic loci for childhood-onset asthma. Gene expression data and integrative analyses point to PGM2 on 4p14 and FGF20 on 8p22 as linked genes. Furthermore, region-based analyses suggest independent potential low-frequency/rare variant associations on 8p22. Follow-up analyses are needed to understand the functional mechanisms and generalizability of these associations.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ahmad Samiei
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Cuining Liu
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Sharon M Lutz
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care, Boston, MA 02215, USA
| | - Sanghun Lee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, 16890, South Korea
| | - Albert V Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | | | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, 10101 San José, Costa Rica
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Benjamin Raby
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
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Connally NJ, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa CA, Sunyaev SR. The missing link between genetic association and regulatory function. eLife 2022; 11:74970. [PMID: 36515579 PMCID: PMC9842386 DOI: 10.7554/elife.74970] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The genetic basis of most traits is highly polygenic and dominated by non-coding alleles. It is widely assumed that such alleles exert small regulatory effects on the expression of cis-linked genes. However, despite the availability of gene expression and epigenomic datasets, few variant-to-gene links have emerged. It is unclear whether these sparse results are due to limitations in available data and methods, or to deficiencies in the underlying assumed model. To better distinguish between these possibilities, we identified 220 gene-trait pairs in which protein-coding variants influence a complex trait or its Mendelian cognate. Despite the presence of expression quantitative trait loci near most GWAS associations, by applying a gene-based approach we found limited evidence that the baseline expression of trait-related genes explains GWAS associations, whether using colocalization methods (8% of genes implicated), transcription-wide association (2% of genes implicated), or a combination of regulatory annotations and distance (4% of genes implicated). These results contradict the hypothesis that most complex trait-associated variants coincide with homeostatic expression QTLs, suggesting that better models are needed. The field must confront this deficit and pursue this 'missing regulation.'
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Affiliation(s)
- Noah J Connally
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Sumaiya Nazeen
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Daniel Lee
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Huwenbo Shi
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Epidemiology, Harvard T.H. Chan School of Public HealthBostonUnited States
| | | | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s HospitalBostonUnited States
| | - Chris Cotsapas
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
- Department of Neurology, Yale Medical SchoolNew HavenUnited States
- Department of Genetics, Yale Medical SchoolNew HavenUnited States
| | - Christopher A Cassa
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical SchoolBostonUnited States
- Brigham and Women’s Hospital, Division of Genetics, Harvard Medical SchoolBostonUnited States
- Program in Medical and Population Genetics, Broad Institute of MIT and HarvardCambridgeUnited States
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7
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Chun S, Akle S, Teodosiadis A, Cade BE, Wang H, Sofer T, Evans DS, Stone KL, Gharib SA, Mukherjee S, Palmer LJ, Hillman D, Rotter JI, Hanis CL, Stamatoyannopoulos JA, Redline S, Cotsapas C, Sunyaev SR. Leveraging pleiotropy to discover and interpret GWAS results for sleep-associated traits. PLoS Genet 2022; 18:e1010557. [PMID: 36574455 PMCID: PMC9829185 DOI: 10.1371/journal.pgen.1010557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/09/2023] [Accepted: 12/06/2022] [Indexed: 12/28/2022] Open
Abstract
Genetic association studies of many heritable traits resulting from physiological testing often have modest sample sizes due to the cost and burden of the required phenotyping. This reduces statistical power and limits discovery of multiple genetic associations. We present a strategy to leverage pleiotropy between traits to both discover new loci and to provide mechanistic hypotheses of the underlying pathophysiology. Specifically, we combine a colocalization test with a locus-level test of pleiotropy. In simulations, we show that this approach is highly selective for identifying true pleiotropy driven by the same causative variant, thereby improves the chance to replicate the associations in underpowered validation cohorts and leads to higher interpretability. Here, as an exemplar, we use Obstructive Sleep Apnea (OSA), a common disorder diagnosed using overnight multi-channel physiological testing. We leverage pleiotropy with relevant cellular and cardio-metabolic phenotypes and gene expression traits to map new risk loci in an underpowered OSA GWAS. We identify several pleiotropic loci harboring suggestive associations to OSA and genome-wide significant associations to other traits, and show that their OSA association replicates in independent cohorts of diverse ancestries. By investigating pleiotropic loci, our strategy allows proposing new hypotheses about OSA pathobiology across many physiological layers. For example, we identify and replicate the pleiotropy across the plateletcrit, OSA and an eQTL of DNA primase subunit 1 (PRIM1) in immune cells. We find suggestive links between OSA, a measure of lung function (FEV1/FVC), and an eQTL of matrix metallopeptidase 15 (MMP15) in lung tissue. We also link a previously known genome-wide significant peak for OSA in the hexokinase 1 (HK1) locus to hematocrit and other red blood cell related traits. Thus, the analysis of pleiotropic associations has the potential to assemble diverse phenotypes into a chain of mechanistic hypotheses that provide insight into the pathogenesis of complex human diseases.
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Affiliation(s)
- Sung Chun
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sebastian Akle
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Katie L. Stone
- California Pacific Medical Center Research Institute, San Francisco, California, United States of America
| | - Sina A. Gharib
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, Washington, United States of America
- Computational Medicine Core at Center for Lung Biology, University of Washington, Seattle, Washington, United States of America
| | - Sutapa Mukherjee
- Respiratory and Sleep Services, Southern Adelaide Local Health Network, Adelaide, South Australia, Australia
- Adelaide Institute for Sleep Health, Flinders University, Adelaide, South Australia, Australia
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - David Hillman
- Centre for Sleep Science, University of Western Australia, Perth, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, Australia
| | - 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, California, United States of America
| | - Craig L. Hanis
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - John A. Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Departments of Medicine and Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Chris Cotsapas
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
- Altius Institute for Biomedical Sciences, Seattle, Washington, United States of America
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
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Won J, Choi S, Chun S, Kim H. Abstract No. 521 Robot-assisted transarterial chemoembolization using “operation bed mounted master-slave robot system” for the treatment of hepatocellular carcinoma: pilot study to evaluate the safety and efficiency. J Vasc Interv Radiol 2022. [DOI: 10.1016/j.jvir.2022.03.503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Shin E, Lee E, Hong J, Kim H, Lee W, Chun S, Min W. W250 Accuracy evaluation of automated electrochemiluminescence immunoassay for everolimus and sirolimus compared to liquid chromatography-tandem mass spectrometry. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Hong J, Gu H, Chun S, Kim M, Sofianidis A, Klopprogge K. M041 Comparability of selected assays on COBAS pure integrated solutions under routine-like conditions. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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11
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Hong J, Cho E, Kim H, Lee W, Chun S, Min W. M104 Application and modification of reference change values for delta checks in clinical laboratory. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Shin Y, Shin E, Hong J, Kim H, Lee W, Chun S, Min W. M246 Estimated mean recovery of two LDL cholesterol homogeneous methods by non-HDL particle size distribution. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Kim S, Hong H, Hong J, Kim H, Lee W, Chun S, Min W. M109 Monitoring of the proportion of unacceptable specimen for laboratory quality improvement. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hong H, Lee E, Hong J, Kim H, Lee W, Chun S, Min W. T115 Hematocrit is a predictive marker for inaccurate interpretation of arterial blood gas analysis caused by inadequate sample mixing. Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Lam W, Wong A, Chun S, Wong T, Hung W, Lie H, Tsang C, Ho B, Ng A, Tsu J. Prostate cancer detection, tolerability and safety of transperineal prostate biopsy under local-anaesthesia versus standard transrectal biopsy in biopsy-naïve men: A pragmatic, parallel group, randomized-controlled study. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gasperi C, Chun S, Sunyaev SR, Cotsapas C. Shared associations identify causal relationships between gene expression and immune cell phenotypes. Commun Biol 2021; 4:279. [PMID: 33664438 PMCID: PMC7933159 DOI: 10.1038/s42003-021-01823-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 09/19/2020] [Accepted: 02/04/2021] [Indexed: 12/22/2022] Open
Abstract
Genetic mapping studies have identified thousands of associations between common variants and hundreds of human traits. Translating these associations into mechanisms is complicated by two factors: they fall into gene regulatory regions; and they are rarely mapped to one causal variant. One way around these limitations is to find groups of traits that share associations, using this genetic link to infer a biological connection. Here, we assess how many trait associations in the same locus are due to the same genetic variant, and thus shared; and if these shared associations are due to causal relationships between traits. We find that only a subset of traits share associations, with many due to causal relationships rather than pleiotropy. We therefore suggest that simply observing overlapping associations at a genetic locus is insufficient to infer causality; direct evidence of shared associations is required to support mechanistic hypotheses in genetic studies of complex traits.
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Affiliation(s)
- Christiane Gasperi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, Ismaninger Str. 22, Munich, Germany
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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17
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Bhak Y, Jeon Y, Jeon S, Yoon C, Kim M, Blazyte A, Kim Y, Kang Y, Kim C, Lee SY, Bae JW, Kim W, Kim YJ, Shim J, Kim N, Chun S, Kim BC, Kim BC, Lee S, Bhak J, Shin ES. Polygenic risk score validation using Korean genomes of 265 early-onset acute myocardial infarction patients and 636 healthy controls. PLoS One 2021; 16:e0246538. [PMID: 33539413 PMCID: PMC7861392 DOI: 10.1371/journal.pone.0246538] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/21/2021] [Indexed: 01/23/2023] Open
Abstract
Background The polygenic risk score (PRS) developed for coronary artery disease (CAD) is known to be effective for classifying patients with CAD and predicting subsequent events. However, the PRS was developed mainly based on the analysis of Caucasian genomes and has not been validated for East Asians. We aimed to evaluate the PRS in the genomes of Korean early-onset AMI patients (n = 265, age ≤50 years) following PCI and controls (n = 636) to examine whether the PRS improves risk prediction beyond conventional risk factors. Results The odds ratio of the PRS was 1.83 (95% confidence interval [CI]: 1.69–1.99) for early-onset AMI patients compared with the controls. For the classification of patients, the area under the curve (AUC) for the combined model with the six conventional risk factors (diabetes mellitus, family history of CAD, hypertension, body mass index, hypercholesterolemia, and current smoking) and PRS was 0.92 (95% CI: 0.90–0.94) while that for the six conventional risk factors was 0.91 (95% CI: 0.85–0.93). Although the AUC for PRS alone was 0.65 (95% CI: 0.61–0.69), adding the PRS to the six conventional risk factors significantly improved the accuracy of the prediction model (P = 0.015). Patients with the upper 50% of PRS showed a higher frequency of repeat revascularization (hazard ratio = 2.19, 95% CI: 1.47–3.26) than the others. Conclusions The PRS using 265 early-onset AMI genomes showed improvement in the identification of patients in the Korean population and showed potential for genomic screening in early life to complement conventional risk prediction.
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Affiliation(s)
- Youngjune Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Min Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Yeonkyung Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Younghui Kang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | | | - Sang Yeub Lee
- Division of Cardiology, Department of Internal Medicine, Chungbuk National University, College of Medicine, Cheongju, Republic of Korea
| | - Jang-Whan Bae
- Division of Cardiology, Department of Internal Medicine, Chungbuk National University, College of Medicine, Cheongju, Republic of Korea
| | - Weon Kim
- Division of Cardiology, Department of Internal Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Yeo Jin Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jungae Shim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Nayeong Kim
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Sung Chun
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
- Clinomics Inc, Ulsan, Republic of Korea
- Personal Genomics Institute, Genome Research Foundation, Ulsan, Republic of Korea
- * E-mail: (JB); (ESS)
| | - Eun-Seok Shin
- Personal Genomics Institute, Genome Research Foundation, Ulsan, Republic of Korea
- Division of Cardiology, Department of Internal Medicine, Ulsan Medical Center, Ulsan, Republic of Korea
- * E-mail: (JB); (ESS)
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Lin J, Li S, Pezzi T, Mohamed A, Fuller C, Chen A, Minsky B, Schwartz D, Hernandez B, Chun S. CP01.06 Veterans Affairs Insurance Disparities for Metastatic Lung Cancer in the Hawaiian Islands. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2020.10.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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Chun S, Imakaev M, Hui D, Patsopoulos NA, Neale BM, Kathiresan S, Stitziel NO, Sunyaev SR. Non-parametric Polygenic Risk Prediction via Partitioned GWAS Summary Statistics. Am J Hum Genet 2020; 107:46-59. [PMID: 32470373 PMCID: PMC7332650 DOI: 10.1016/j.ajhg.2020.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 06/15/2019] [Accepted: 05/01/2020] [Indexed: 02/07/2023] Open
Abstract
In complex trait genetics, the ability to predict phenotype from genotype is the ultimate measure of our understanding of genetic architecture underlying the heritability of a trait. A complete understanding of the genetic basis of a trait should allow for predictive methods with accuracies approaching the trait's heritability. The highly polygenic nature of quantitative traits and most common phenotypes has motivated the development of statistical strategies focused on combining myriad individually non-significant genetic effects. Now that predictive accuracies are improving, there is a growing interest in the practical utility of such methods for predicting risk of common diseases responsive to early therapeutic intervention. However, existing methods require individual-level genotypes or depend on accurately specifying the genetic architecture underlying each disease to be predicted. Here, we propose a polygenic risk prediction method that does not require explicitly modeling any underlying genetic architecture. We start with summary statistics in the form of SNP effect sizes from a large GWAS cohort. We then remove the correlation structure across summary statistics arising due to linkage disequilibrium and apply a piecewise linear interpolation on conditional mean effects. In both simulated and real datasets, this new non-parametric shrinkage (NPS) method can reliably allow for linkage disequilibrium in summary statistics of 5 million dense genome-wide markers and consistently improves prediction accuracy. We show that NPS improves the identification of groups at high risk for breast cancer, type 2 diabetes, inflammatory bowel disease, and coronary heart disease, all of which have available early intervention or prevention treatments.
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Affiliation(s)
- Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Maxim Imakaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - Daniel Hui
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Nikolaos A Patsopoulos
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Benjamin M Neale
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sekar Kathiresan
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nathan O Stitziel
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA; McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA.
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Hung W, Chun S, Wong T, Tsang C, Ho B, Ng A, Tsu H, Lam W. Transrectal vs. transperineal prostate biopsy under local anaesthesia: Prospective comparative analysis of cancer detection, safety and tolerability using patient-reported outcome measures at a single centre. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)34175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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21
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Chun S, Pezzi T, Schwartz D, Pisters K, Mohamed A, Welsh J, Chang J, Liao Z, Gandhi S, Byers L, Minsky B, Hahn S, Fuller C. PD01.20 Medicaid Outcome Inequalities in Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Park J, Shin D, Han K, Chun S. Association between kidney function, proteinuria and the risk of kidney cancer: A nationwide cohort study involving 10 million participants. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Chun S, Liao Z, Jeter M, Chang J, Lin S, Komaki R, Guerrero T, Mayo R, Korah B, Koshy S, Heymach J, Koong A, Skinner H. P1.20 Metabolic Responses to Metformin in Early-Stage NSCLC Treated with Definitive Radiotherapy: Results of a Phase II Trial. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.09.077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kim J, Kim S, Kang J, Chun S, Kim SY. Clinical implication of multiplex IHC and serologic biomarkers on hyperprogression in NSCLC patients receiving immune checkpoint blockers in real world. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz260.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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25
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Oh E, Kim D, Cha Y, Chun S, Chie E, Kim K, Park J, Kim J, Yu J, Kim S, Nam T, Kim J. Evaluation of the New AJCC Staging System (8th edition) in Anal Cancer Patients Treated with Curative Chemoradiotherapy (KROG 18-05). Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Lee E, Kim H, Ahn S, Lee W, Kim H, Chun S, Min W. Performance evaluation of a novel automated chemiluminescence immunoassay for the concentration of everolimus and sirolimus. Clin Chim Acta 2019. [DOI: 10.1016/j.cca.2019.03.1581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Lee W, Kim A, Kim H, An S, Hong Y, Lim S, Byeon J, Chun S, Min W. Identification of a novel splice site variant of APC gene in a patient with familial adenomatous polyposis. Clin Chim Acta 2019. [DOI: 10.1016/j.cca.2019.03.434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Chun S, Meloche J, Woo A, Yu E. COMPETENCE IN ADULT ECHOCARDIOGRAPHY OF GRADUATING CARDIOLOGY TRAINEES: TWO-YEAR STUDY. Can J Cardiol 2018. [DOI: 10.1016/j.cjca.2018.07.276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Chun S. PO-0719: Risk factors influencing survival after re-Op plus re-RT for recurrent high-grade gliomas. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31029-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Chen H, Cade BE, Gleason KJ, Bjonnes AC, Stilp AM, Sofer T, Conomos MP, Ancoli-Israel S, Arens R, Azarbarzin A, Bell GI, Below JE, Chun S, Evans DS, Ewert R, Frazier-Wood AC, Gharib SA, Haba-Rubio J, Hagen EW, Heinzer R, Hillman DR, Johnson WC, Kutalik Z, Lane JM, Larkin EK, Lee SK, Liang J, Loredo JS, Mukherjee S, Palmer LJ, Papanicolaou GJ, Penzel T, Peppard PE, Post WS, Ramos AR, Rice K, Rotter JI, Sands SA, Shah NA, Shin C, Stone KL, Stubbe B, Sul JH, Tafti M, Taylor KD, Teumer A, Thornton TA, Tranah GJ, Wang C, Wang H, Warby SC, Wellman DA, Zee PC, Hanis CL, Laurie CC, Gottlieb DJ, Patel SR, Zhu X, Sunyaev SR, Saxena R, Lin X, Redline S. Multiethnic Meta-Analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea-related Quantitative Trait Locus in Men. Am J Respir Cell Mol Biol 2018; 58:391-401. [PMID: 29077507 PMCID: PMC5854957 DOI: 10.1165/rcmb.2017-0237oc] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [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: 06/30/2017] [Accepted: 10/24/2017] [Indexed: 12/19/2022] Open
Abstract
Obstructive sleep apnea (OSA) is a common heritable disorder displaying marked sexual dimorphism in disease prevalence and progression. Previous genetic association studies have identified a few genetic loci associated with OSA and related quantitative traits, but they have only focused on single ethnic groups, and a large proportion of the heritability remains unexplained. The apnea-hypopnea index (AHI) is a commonly used quantitative measure characterizing OSA severity. Because OSA differs by sex, and the pathophysiology of obstructive events differ in rapid eye movement (REM) and non-REM (NREM) sleep, we hypothesized that additional genetic association signals would be identified by analyzing the NREM/REM-specific AHI and by conducting sex-specific analyses in multiethnic samples. We performed genome-wide association tests for up to 19,733 participants of African, Asian, European, and Hispanic/Latino American ancestry in 7 studies. We identified rs12936587 on chromosome 17 as a possible quantitative trait locus for NREM AHI in men (N = 6,737; P = 1.7 × 10-8) but not in women (P = 0.77). The association with NREM AHI was replicated in a physiological research study (N = 67; P = 0.047). This locus overlapping the RAI1 gene and encompassing genes PEMT1, SREBF1, and RASD1 was previously reported to be associated with coronary artery disease, lipid metabolism, and implicated in Potocki-Lupski syndrome and Smith-Magenis syndrome, which are characterized by abnormal sleep phenotypes. We also identified gene-by-sex interactions in suggestive association regions, suggesting that genetic variants for AHI appear to vary by sex, consistent with the clinical observations of strong sexual dimorphism.
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Affiliation(s)
- Han Chen
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health and
- Center for Precision Health, School of Public Health & School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Brian E. Cade
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
| | - Kevin J. Gleason
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois
| | - Andrew C. Bjonnes
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Matthew P. Conomos
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Sonia Ancoli-Israel
- Departments of Medicine and Psychiatry, University of California, San Diego, California
| | - Raanan Arens
- the Children’s Hospital at Montefiore, Division of Respiratory and Sleep Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Ali Azarbarzin
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
| | - Graeme I. Bell
- Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, the University of Chicago, Chicago, Illinois
| | - Jennifer E. Below
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health and
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sung Chun
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Ralf Ewert
- Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | | | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington Medicine Sleep Center, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Washington, Seattle, Washington
| | - José Haba-Rubio
- Center of Investigation and Research on Sleep, Lausanne University Hospital, Lausanne, Switzerland
| | - Erika W. Hagen
- Department of Population Health Sciences, University of Wisconsin, Madison, Wisconsin
| | - Raphael Heinzer
- Center of Investigation and Research on Sleep, Lausanne University Hospital, Lausanne, Switzerland
| | - David R. Hillman
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Zoltan Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jacqueline M. Lane
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Emma K. Larkin
- Department of Medicine, Division of Allergy, Pulmonary, and Critical Care, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Seung Ku Lee
- Institute of Human Genomic Study, College of Medicine, Korea University Ansan Hospital, Jeokgum-ro, Danwon-gu, Ansan-si, Gyeonggi-Do, Republic of Korea
| | - Jingjing Liang
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Jose S. Loredo
- Division of Pulmonary Critical Care and Sleep Medicine, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California
| | - Sutapa Mukherjee
- Adelaide Institute for Sleep Health, Flinders Centre of Research Excellence, Flinders University, Adelaide, South Australia, Australia
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, South Australia, Australia
| | - George J. Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, Maryland
| | - Thomas Penzel
- University Hospital Charité Berlin, Sleep Center, Berlin, Germany
| | - Paul E. Peppard
- Department of Population Health Sciences, University of Wisconsin, Madison, Wisconsin
| | - Wendy S. Post
- Division of Cardiology, Johns Hopkins University, Baltimore, Maryland
| | - Alberto R. Ramos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor–University of California Los Angeles Medical Center, Torrance, California
| | - Scott A. Sands
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
| | - Neomi A. Shah
- Division of Pulmonary, Critical Care, and Sleep, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Chol Shin
- Department of Pulmonary, Sleep, and Critical Care Medicine, College of Medicine, Korea University Ansan Hospital, Jeokgum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, Republic of Korea
| | - Katie L. Stone
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, Germany
| | - Jae Hoon Sul
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California
| | - Mehdi Tafti
- Center of Investigation and Research on Sleep, Lausanne University Hospital, Lausanne, Switzerland
- Department of Physiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute and Department of Pediatrics at Harbor–University of California Los Angeles Medical Center, Torrance, California
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | | | - Gregory J. Tranah
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Chaolong Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Simon C. Warby
- Department of Psychiatry, University of Montreal, Montreal, Quebec, Canada
| | - D. Andrew Wellman
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
| | - Phyllis C. Zee
- Department of Neurology and Sleep Medicine Center, Northwestern University, Chicago, Illinois
| | - Craig L. Hanis
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health and
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Daniel J. Gottlieb
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Veterans Affairs Boston Healthcare System, Boston, Massachusetts
| | - Sanjay R. Patel
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts; and
| | - Richa Saxena
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Center for Genomic Medicine and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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31
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Chun S, Chan K, McCallion P, Ferretti L, Shi J. IMPACT OF DISABILITY ON ACCESS TO DIABETES CARE AMONG OLDER ADULTS WITH DIABETES. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.1744] [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] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- S. Chun
- University at Albany SUNY, Cambridge, Massachusetts
| | - K. Chan
- University at Albany SUNY, Cambridge, Massachusetts
| | - P. McCallion
- University at Albany SUNY, Cambridge, Massachusetts
| | - L. Ferretti
- University at Albany SUNY, Cambridge, Massachusetts
| | - J. Shi
- University at Albany SUNY, Cambridge, Massachusetts
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32
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Chun S, Eom K, Kim H. EP-1294: Interfractional motion of vaginal cuff after hysterectomy in gynecologic cancer. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)31729-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Oh CM, Chun S, Lee JE, Lee JS, Park S, Gee HY, Kim SW. A novel missense mutation in NR0B1 causes delayed-onset primary adrenal insufficiency in adults. Clin Genet 2017; 92:344-346. [PMID: 28075027 DOI: 10.1111/cge.12966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 01/09/2017] [Accepted: 01/09/2017] [Indexed: 11/28/2022]
Abstract
A novel missense mutation (c.775T>C; p.ser259Pro) in the NROBI gene cause a late-onset adrenal insufficiency without hypogonadism.
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Affiliation(s)
- C-M Oh
- Department of Internal Medicine, CHA Bundang Medical Center, School of Medicine CHA University, Seongnam, Korea
| | - S Chun
- Department of Internal Medicine, CHA Bundang Medical Center, School of Medicine CHA University, Seongnam, Korea
| | - J-E Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul, Korea
| | - J S Lee
- Department of Pharmacology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - S Park
- Department of Biochemistry, College of Medicine, Catholic Kwandong University, Gangneung, Korea
| | - H Y Gee
- Department of Pharmacology, Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul, Korea
| | - S W Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Internal Medicine, Boramae Medical Center, Seoul, Korea
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34
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Seo MH, Won EJ, Hong YJ, Chun S, Kwon JR, Choi YS, Kim JN, Lee SA, Lim AH, Kim SH, Park KU, Cho D. An effective diagnostic strategy for accurate detection of RhD variants including Asian DEL type in apparently RhD-negative blood donors in Korea. Vox Sang 2016; 111:425-430. [PMID: 27864976 DOI: 10.1111/vox.12450] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 04/03/2016] [Revised: 08/16/2016] [Accepted: 08/17/2016] [Indexed: 01/26/2023]
Abstract
BACKGROUND AND OBJECTIVES The purpose of this study was to provide an effective RHD genotyping strategy for the East Asian blood donors. MATERIAL AND METHODS RhD phenotyping, weak D testing and RhCE phenotyping were performed on 110 samples from members of the RhD-negative club, private organization composed of RhD-negative blood donors, in the GwangJu-Chonnam region of Korea. The RHD promoter, intron 4, and exons 7 and 10 were analysed by real-time PCR. Two nucleotide changes (c.1227 G>A, and c.1222 T>C) in exon 9 were analysed by sequencing. RESULTS Of 110 RhD-negative club members, 79 (71·8%) showed complete deletion of the RHD gene, 10 (9·1%) showed results consistent with RHD-CE-D hybrid, and 21 (19·1%) showed amplification of RHD promoter, intron 4, and exons 7 and 10. Of the latter group, 16 (14·5%) were in the DEL blood group including c.1227 G>A (N = 14) and c.1222 T>C (N = 2), 2 (1·8%) were weak D, 1(0·9%) was partial D, and 2 (1·8%) were undetermined. The RhD-negative phenotype samples consisted of 58 C-E-c+e+, 19 C-E+c+e+, 3 C-E+c+e-, 21 C+E-c+e-, 6 C+E-c+e+ and 3 C+E-c-e + . Notably, all 58 samples with the C-E-c+e+ phenotype were revealed to have complete deletion of the RHD gene. The C-E-c+e+ phenotype showed 100% positive predictive value for detecting D-negative cases. CONCLUSIONS RHD genotyping is not required in half of D-negative cases. We suggest here an effective RHD genotyping strategy for accurate detection of RhD variants in apparently RhD-negative blood donors in East Asia.
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Affiliation(s)
- M H Seo
- Department of Biomedical Sciences, Chonnam National University, Gwangju, Korea
| | - E J Won
- Department of Laboratory Medicine, Chonnam National University Hospital, Gwangju, Korea
| | - Y J Hong
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - S Chun
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunwan University School of Medicine, Seoul, Korea
| | - J R Kwon
- The Division of Human Blood Safety Surveillance, Korea Centers for Disease Control and Prevention, Cheongwon, Korea
| | - Y S Choi
- The Division of Human Blood Safety Surveillance, Korea Centers for Disease Control and Prevention, Cheongwon, Korea
| | - J N Kim
- The Division of Human Blood Safety Surveillance, Korea Centers for Disease Control and Prevention, Cheongwon, Korea
| | - S A Lee
- Blood Transfusion Research Institute, Korean Red Cross, Wonju, Korea
| | - A H Lim
- Blood Transfusion Research Institute, Korean Red Cross, Wonju, Korea
| | - S H Kim
- Department of Laboratory Medicine, Chonnam National University Hwasun Hospital, Chonnam National University School of Medicine, Gwangju, Korea
| | - K U Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - D Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunwan University School of Medicine, Seoul, Korea.,Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Korea
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Cade BE, Chen H, Stilp AM, Gleason KJ, Sofer T, Ancoli-Israel S, Arens R, Bell GI, Below JE, Bjonnes AC, Chun S, Conomos MP, Evans DS, Johnson WC, Frazier-Wood AC, Lane JM, Larkin EK, Loredo JS, Post WS, Ramos AR, Rice K, Rotter JI, Shah NA, Stone KL, Taylor KD, Thornton TA, Tranah GJ, Wang C, Zee PC, Hanis CL, Sunyaev SR, Patel SR, Laurie CC, Zhu X, Saxena R, Lin X, Redline S. Genetic Associations with Obstructive Sleep Apnea Traits in Hispanic/Latino Americans. Am J Respir Crit Care Med 2016; 194:886-897. [PMID: 26977737 PMCID: PMC5074655 DOI: 10.1164/rccm.201512-2431oc] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/14/2016] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Obstructive sleep apnea is a common disorder associated with increased risk for cardiovascular disease, diabetes, and premature mortality. Although there is strong clinical and epidemiologic evidence supporting the importance of genetic factors in influencing obstructive sleep apnea, its genetic basis is still largely unknown. Prior genetic studies focused on traits defined using the apnea-hypopnea index, which contains limited information on potentially important genetically determined physiologic factors, such as propensity for hypoxemia and respiratory arousability. OBJECTIVES To define novel obstructive sleep apnea genetic risk loci for obstructive sleep apnea, we conducted genome-wide association studies of quantitative traits in Hispanic/Latino Americans from three cohorts. METHODS Genome-wide data from as many as 12,558 participants in the Hispanic Community Health Study/Study of Latinos, Multi-Ethnic Study of Atherosclerosis, and Starr County Health Studies population-based cohorts were metaanalyzed for association with the apnea-hypopnea index, average oxygen saturation during sleep, and average respiratory event duration. MEASUREMENTS AND MAIN RESULTS Two novel loci were identified at genome-level significance (rs11691765, GPR83, P = 1.90 × 10-8 for the apnea-hypopnea index, and rs35424364; C6ORF183/CCDC162P, P = 4.88 × 10-8 for respiratory event duration) and seven additional loci were identified with suggestive significance (P < 5 × 10-7). Secondary sex-stratified analyses also identified one significant and several suggestive associations. Multiple loci overlapped genes with biologic plausibility. CONCLUSIONS These are the first genome-level significant findings reported for obstructive sleep apnea-related physiologic traits in any population. These findings identify novel associations in inflammatory, hypoxia signaling, and sleep pathways.
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Affiliation(s)
- Brian E. Cade
- Division of Sleep and Circadian Disorders and
- Division of Sleep Medicine and
| | - Han Chen
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, Washington
| | | | - Tamar Sofer
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Sonia Ancoli-Israel
- Department of Medicine and
- Department of Psychiatry, University of California, San Diego, California
- Department of Veterans Affairs San Diego Center of Excellence for Stress and Mental Health, San Diego, California
| | - Raanan Arens
- The Children’s Hospital at Montefiore, Division of Respiratory and Sleep Medicine, Albert Einstein College of Medicine, Bronx, New York
| | - Graeme I. Bell
- Section of Adult and Pediatric Endocrinology, Diabetes, and Metabolism, The University of Chicago, Chicago, Illinois
| | - Jennifer E. Below
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Andrew C. Bjonnes
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Sung Chun
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Matthew P. Conomos
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, California
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, Washington
| | | | - Jacqueline M. Lane
- Division of Sleep and Circadian Disorders and
- Division of Sleep Medicine and
- Center for Human Genetic Research and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Emma K. Larkin
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jose S. Loredo
- Division of Pulmonary Critical Care and Sleep Medicine, Department of Medicine, UC San Diego School of Medicine, La Jolla, California
| | - Wendy S. Post
- Division of Cardiology, Johns Hopkins University, Baltimore, Maryland
| | - Alberto R. Ramos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida
| | - Ken Rice
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Neomi A. Shah
- Department of Medicine, Montefiore Medical Center, Bronx, New York
| | - Katie L. Stone
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California
| | | | - Gregory J. Tranah
- California Pacific Medical Center Research Institute, San Francisco, California
| | - Chaolong Wang
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Genome Institute of Singapore, Singapore
| | - Phyllis C. Zee
- Department of Neurology and Sleep Medicine Center, Northwestern University, Chicago, Illinois
| | - Craig L. Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Medical Sciences, Harvard Medical School, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Sanjay R. Patel
- Division of Sleep and Circadian Disorders and
- Division of Sleep Medicine and
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts; and
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Richa Saxena
- Division of Sleep and Circadian Disorders and
- Center for Human Genetic Research and Department of Anesthesia, Pain, and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Susan Redline
- Division of Sleep and Circadian Disorders and
- Division of Sleep Medicine and
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts; and
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Phan J, Frank S, Chun S, Zhu X, Tung S, Wang C, Zhang X, Crawford C, Garden A, Rosenthal D, Gunn G, Nguyen Q, Fuller C, Wang H. Evaluation of Intensity Modulated Proton Therapy for Stereotactic Ablative Radiation Therapy of Recurrent Skull Base Tumors: A Comparative Treatment Planning Study With Volumetric Modulated Arc Therapy. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.2323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Lee HS, Choi KM, Won EJ, Thi Phan MT, Lee SY, Shin DJ, Chun S, Park G, Kim SK, Lee KB, Lee HJ, Cho D. Protein stability changes of the novel p.Arg180Cys mutant A glycosyltransferase resulted in a weak A phenotype. Vox Sang 2016; 111:441-444. [PMID: 27538125 DOI: 10.1111/vox.12440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 04/12/2016] [Revised: 06/30/2016] [Accepted: 06/01/2016] [Indexed: 11/27/2022]
Abstract
A novel A subgroup allele (c.538C>T p.Arg180Cys) showing weak A phenotype was found in a 30-year-old Korean woman with ABO discrepancy. Using 3D structural analysis, protein stability prediction and flow cytometric analysis of ABO antigen expression on HeLa cells transfected with plasmids containing the p.Arg180Cys mutant, we found that the Arg180 residue in the loop region of the A glycosyltransferases (GTA) structure plays significant role in stabilizing its closed conformation, which is required for substrate binding and catalysis study.
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Affiliation(s)
- H-S Lee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - K-M Choi
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.,Department of Biological Engineering, Graduate School of Konkuk University, Seoul, South Korea
| | - E J Won
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea
| | - M-T Thi Phan
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, South Korea.,Center for Creative Biomedical Scientists, Chonnam National University, Gwangju, South Korea
| | - S Y Lee
- Department of Medical System Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, South Korea
| | - D-J Shin
- Department of Companion & Laboratory Animal Science, Kongju National University, Yesan, South Korea
| | - S Chun
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - G Park
- Department of Laboratory Medicine, Chosun University College of Medicine, Gwangju, South Korea
| | - S-K Kim
- Department of Companion & Laboratory Animal Science, Kongju National University, Yesan, South Korea
| | - K-B Lee
- Advanced Analysis Center and Green City Technology Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - H-J Lee
- Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - D Cho
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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Lim Y, Chun S, Lee JH, Baek KH, Lee WK, Yim HW, Kang MI. Association of bone mineral density and diabetic retinopathy in diabetic subjects: the 2008-2011 Korea National Health and Nutrition Examination Survey. Osteoporos Int 2016; 27:2249-2257. [PMID: 26883444 DOI: 10.1007/s00198-016-3527-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/04/2016] [Indexed: 12/27/2022]
Abstract
UNLABELLED Because diabetic retinopathy increases fracture risk, we studied the association between bone mineral density (BMD) and diabetic retinopathy in a nationally representative sample. A significant association between the presence of diabetic retinopathy and low BMD was observed. Therefore, diabetic retinopathy might be considered as a marker of low BMD. INTRODUCTION Several diabetic complications, including nephropathy, retinopathy, and peripheral neuropathy, are associated with a higher fracture risk in diabetic subjects. However, in contrast to diabetic nephropathy and peripheral neuropathy, which are associated with low bone mineral density (BMD), little is known about the association between BMD and diabetic retinopathy. The aim of the present study was to determine whether the prevalence of diabetic retinopathy is associated with BMD. METHODS This cross-sectional study included a nationally representative sample consisting of 4357 men aged 50 years and older and 4392 postmenopausal women who participated in the Korea National Health and Nutritional Examination Survey (KNHANES) from 2008 to 2011 and underwent BMD measurement by dual-energy X-ray absorptiometry (DXA) and diabetic retinopathy assessments using seven standard gradable photographs. RESULTS The diabetic women with retinopathy had lower mean BMD at all measured sites than those without retinopathy, although the BMD difference between the two groups was small (3-5 %). In addition, the diabetic women with retinopathy were 2.27 times more likely to have osteoporosis following adjustments for all clinically relevant covariates. However, the prevalence of diabetes mellitus (DM) or diabetic retinopathy was not associated with the prevalence of osteoporosis in men. CONCLUSIONS This study has shown that the presence of diabetic retinopathy is significantly associated with a reduced BMD and increased prevalence of osteoporosis in diabetic women.
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Affiliation(s)
- Y Lim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, 137-701, Seoul, Korea
| | - S Chun
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, Republic of Korea
| | - J H Lee
- Department of Ophthalmology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, Republic of Korea
| | - K H Baek
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, 137-701, Seoul, Korea
| | - W K Lee
- Department of Ophthalmology, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, Republic of Korea
| | - H-W Yim
- Department of Preventive Medicine, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 137-701, Republic of Korea
| | - M-I Kang
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, 137-701, Seoul, Korea.
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Akle S, Chun S, Jordan DM, Cassa CA. Mitigating false-positive associations in rare disease gene discovery. Hum Mutat 2016; 36:998-1003. [PMID: 26378430 DOI: 10.1002/humu.22847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 04/23/2015] [Accepted: 07/19/2015] [Indexed: 11/09/2022]
Abstract
Clinical sequencing is expanding, but causal variants are still not identified in the majority of cases. These unsolved cases can aid in gene discovery when individuals with similar phenotypes are identified in systems such as the Matchmaker Exchange. We describe risks for gene discovery in this growing set of unsolved cases. In a set of rare disease cases with the same phenotype, it is not difficult to find two individuals with the same phenotype that carry variants in the same gene. We quantify the risk of false-positive association in a cohort of individuals with the same phenotype, using the prior probability of observing a variant in each gene from over 60,000 individuals (Exome Aggregation Consortium). Based on the number of individuals with a genic variant, cohort size, specific gene, and mode of inheritance, we calculate a P value that the match represents a true association. A match in two of 10 patients in MECP2 is statistically significant (P = 0.0014), whereas a match in TTN would not reach significance, as expected (P > 0.999). Finally, we analyze the probability of matching in clinical exome cases to estimate the number of cases needed to identify genes related to different disorders. We offer Rare Disease Match, an online tool to mitigate the uncertainty of false-positive associations.
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Affiliation(s)
- Sebastian Akle
- Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA.,Division of Genetics, Brigham and Women's Hospital, Boston, MA
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
| | - Daniel M Jordan
- Division of Genetics, Brigham and Women's Hospital, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
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40
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Cassa CA, Smith SE, Docken W, Hoffman E, McLaughlin H, Chun S, Leshchiner I, Miraoui H, Raychaudhuri S, Frank NY, Wilson BJ, Sunyaev SR, Maas RL, Vuzman D. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. Rheumatology (Oxford) 2016; 55:586-9. [PMID: 26493744 PMCID: PMC5009447 DOI: 10.1093/rheumatology/kev367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/03/2015] [Indexed: 01/12/2023] Open
Affiliation(s)
- Christopher A. Cassa
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - Stacy E. Smith
- Division of Musculoskeletal Imaging and Intervention, Brigham and Women’s Hospital
- Department of Radiology, Harvard Medical School
| | - William Docken
- Department of Medicine, Harvard Medical School
- Division of Rheumatology, Brigham and Women’s Hospital, Boston
| | - Erin Hoffman
- Division of Genetics, Brigham and Women’s Hospital
| | - Heather McLaughlin
- Partners Healthcare Center for Personalized Medicine, Cambridge
- Department of Pathology, Harvard Medical School
| | - Sung Chun
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - Ignaty Leshchiner
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - Hichem Miraoui
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - Soumya Raychaudhuri
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - Natasha Y. Frank
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
- Department of Medicine, Boston Children’s Hospital and
- Department of Medicine, VA Boston Healthcare System, Boston, MA, USA
| | | | - Shamil R. Sunyaev
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - Richard L. Maas
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
| | - the Brigham Genomic Medicine
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
- Division of Musculoskeletal Imaging and Intervention, Brigham and Women’s Hospital
- Department of Radiology, Harvard Medical School
- Division of Rheumatology, Brigham and Women’s Hospital, Boston
- Partners Healthcare Center for Personalized Medicine, Cambridge
- Department of Pathology, Harvard Medical School
- Department of Medicine, Boston Children’s Hospital and
- Department of Medicine, VA Boston Healthcare System, Boston, MA, USA
| | - Dana Vuzman
- Division of Genetics, Brigham and Women’s Hospital
- Department of Medicine, Harvard Medical School
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41
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Chun S, Song JS, Yu S, Kim JS, Kwon OJ, Kang ES. Identification of a novel HLA-C*03 variant allele, C*03:280 by sequence-based typing. ACTA ACUST UNITED AC 2015; 86:455-6. [PMID: 26514239 DOI: 10.1111/tan.12685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 07/22/2015] [Revised: 08/31/2015] [Accepted: 09/22/2015] [Indexed: 11/29/2022]
Abstract
The new allele, HLA-C*03:280 differs from C*03:04:01 by one nucleotide substitution at codon 35 (CGG→CAG).
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Affiliation(s)
- S Chun
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J S Song
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - S Yu
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J S Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - O J Kwon
- Biowithus Life Science Institute, Seoul, Korea
| | - E S Kang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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42
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Nikolskiy I, Conrad DF, Chun S, Fay JC, Cheverud JM, Lawson HA. Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides. BMC Genomics 2015; 16:415. [PMID: 26016481 PMCID: PMC4445795 DOI: 10.1186/s12864-015-1592-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 04/28/2015] [Indexed: 12/04/2022] Open
Abstract
Background The laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity. Results We identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F16 generation) and developmental (41 QTL identified in an F34 generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length. Conclusions We show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1592-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Igor Nikolskiy
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | - Donald F Conrad
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Justin C Fay
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
| | | | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, Campus Box 8108, 660 S Euclid Ave, St Louis, MO, 63110, USA.
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43
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Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev SR. Genome-wide patterns and properties of de novo mutations in humans. Nat Genet 2015; 47:822-826. [PMID: 25985141 PMCID: PMC4485564 DOI: 10.1038/ng.3292] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 04/07/2015] [Indexed: 12/12/2022]
Abstract
Mutations create variation in the population, fuel evolution, and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect 1–10. Here, we analyze 11,020 de novo mutations from whole-genomes of 250 families. We show that de novo mutations in offspring of older fathers are not only more numerous 11–13 but also occur more frequently in early-replicating, genic regions. Functional regions exhibit higher mutation rates due to CpG dinucleotides and reveal signatures of transcription-coupled repair, while mutation clusters with a unique signature point to a novel mutational mechanism. Mutation and recombination rates independently associate with nucleotide diversity, and regional variation in human-chimpanzee divergence is only partly explained by mutation rate heterogeneity. Finally, we provide a genome-wide mutation rate map for medical and population genetics applications. Our results reveal novel insights and refine long-standing hypotheses about human mutagenesis.
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Affiliation(s)
- Laurent C Francioli
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paz P Polak
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Androniki Menelaou
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ivo Renkens
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Morris Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Gertjan van Ommen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Kai Ye
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands.,The Genome Institute, Washington University, St. Louis, MO, USA
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Peter F Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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44
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Chun S, Yun JW, Huh HJ, Lee NY. Clinical characteristics of Raoultella ornithinolytica bacteremia. Infection 2014; 43:59-64. [PMID: 25367410 DOI: 10.1007/s15010-014-0696-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 10/20/2014] [Indexed: 01/04/2023]
Abstract
PURPOSE Raoultella ornithinolytica is not well known as a clinical pathogen. We performed a retrospective review of R. ornithinolytica bacteremia to investigate its clinical features, antimicrobial susceptibility, and overall patient outcomes. METHODS R. ornithinolytica bacteremia cases were collected from an electronic database of all cases of bacteremia over a 10-year period. Medical records were retrospectively reviewed. Demographic data, clinical information, the presence of underlying comorbidities, the results of antimicrobial susceptibility testing, and the antimicrobial regimen administered were investigated. RESULTS R. ornithinolytica was isolated from blood culture specimens in 16 cases. The majority of these patients had an underlying malignant condition of advanced stage (15 patients, 94 %). Seven of these patients had a solid tumor with lesions or metastases that extended to the bile duct or biliary tract. Neutropenic fever following hematologic stem cell transplantation was found in three cases. No resistance to piperacillin/tazobactam or imipenem was found. Four cases showed resistance to cefoxitin, while one of these cases showed resistance to multiple cephalosporins. In overall outcomes, seven patients (44 %) did not recover from the infection and subsequently expired. CONCLUSIONS R. ornithinolytica bacteremia occurs mainly in patients with underlying malignancies. The overall outcome was not favorable, despite favorable antimicrobial susceptibility test results. The findings of this study contradict those of other studies that demonstrated that infection from Raoultella species have good prognoses.
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Affiliation(s)
- S Chun
- Department of Laboratory Medicine & Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Ilwon-Dong, Kangnam-Gu, Seoul, 135-710, Korea
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45
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Kim KR, Kim HK, Chun EK, Chun S, Min WK. Urinary concentrations of bisphenol a and their association with indicators of implantation in IVF couples. Fertil Steril 2014. [DOI: 10.1016/j.fertnstert.2014.07.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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46
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Setton J, Morrow M, Lok B, Krause K, Chun S, Pei X, McCormick B, Powell S, Ho A. Impact of Approximated Biological Subtype on Locoregional Recurrence in Women With Node-Negative Breast Cancer Treated With Mastectomy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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47
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Chun S, Ji YI. RETRACTED: Bone mineral density of lumbar spine and femur in patients with gynecologic cancer. Climacteric 2013:1-7. [PMID: 24228804 DOI: 10.3109/13697137.2013.861815] [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: 11/13/2022]
Abstract
Objective To compare the bone mineral density (BMD) of the lumbar spine and femur in postmenopausal women with cervical and endometrial cancer without bone metastasis with that in normal control postmenopausal women Methods We retrospectively analyzed the BMD of the lumbar spine and femur using dual-energy X-ray absorptiometry in 130 patients with cervical cancer, 68 patients with endometrial cancer, and 225 healthy controls. Results The serum levels of calcium, phosphorus, osteocalcin, total alkaline phosphatase and urine deoxypyridinoline were measured in all participants. Age, body mass index, parity and time since menopause were not significantly different between the three groups. The T-scores of basal BMD at the fourth lumbar vertebra (L4) were significantly lower in patients with cervical cancer (- 0.68 ± 0.10) compared to those in the other two groups. Additionally, the incidence of osteoporosis at L4 according to the basal status of bone mass was significantly higher in patients with cervical cancer (10.0%) compared to that in controls (0.4%). Urine deoxypyridinoline levels were significantly higher in patients with cervical cancer compared to those in controls. No differences in basal BMD of the lumbar spine and femur were observed between patients with endometrial cancer and controls, and no significant differences in biochemical markers were detected between patients with endometrial cancer and controls. Conclusion Our results suggest that postmenopausal women with cervical cancer have a lower BMD and are at increased risk of osteoporosis in the lumbar spine before receiving anticancer treatment compared with postmenopausal women with endometrial cancer.
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Affiliation(s)
- S Chun
- Department of Obstetrics and Gynecology, Inje University Haeundae Paik Hospital , Busan , Korea
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48
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Yim HS, Cho YS, Guang X, Kang SG, Jeong JY, Cha SS, Oh HM, Lee JH, Yang EC, Kwon KK, Kim YJ, Kim TW, Kim W, Jeon JH, Kim SJ, Choi DH, Jho S, Kim HM, Ko J, Kim H, Shin YA, Jung HJ, Zheng Y, Wang Z, Chen Y, Chen M, Jiang A, Li E, Zhang S, Hou H, Kim TH, Yu L, Liu S, Ahn K, Cooper J, Park SG, Hong CP, Jin W, Kim HS, Park C, Lee K, Chun S, Morin PA, O'Brien SJ, Lee H, Kimura J, Moon DY, Manica A, Edwards J, Kim BC, Kim S, Wang J, Bhak J, Lee HS, Lee JH. Minke whale genome and aquatic adaptation in cetaceans. Nat Genet 2013; 46:88-92. [PMID: 24270359 DOI: 10.1038/ng.2835] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/01/2013] [Indexed: 01/14/2023]
Abstract
The shift from terrestrial to aquatic life by whales was a substantial evolutionary event. Here we report the whole-genome sequencing and de novo assembly of the minke whale genome, as well as the whole-genome sequences of three minke whales, a fin whale, a bottlenose dolphin and a finless porpoise. Our comparative genomic analysis identified an expansion in the whale lineage of gene families associated with stress-responsive proteins and anaerobic metabolism, whereas gene families related to body hair and sensory receptors were contracted. Our analysis also identified whale-specific mutations in genes encoding antioxidants and enzymes controlling blood pressure and salt concentration. Overall the whale-genome sequences exhibited distinct features that are associated with the physiological and morphological changes needed for life in an aquatic environment, marked by resistance to physiological stresses caused by a lack of oxygen, increased amounts of reactive oxygen species and high salt levels.
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Affiliation(s)
- Hyung-Soon Yim
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2]
| | - Yun Sung Cho
- 1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. [2]
| | - Xuanmin Guang
- 1] Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. [2]
| | - Sung Gyun Kang
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jae-Yeon Jeong
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Sun-Shin Cha
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea. [3] Ocean Science and Technology School, Korea Maritime University, Busan, Republic of Korea
| | - Hyun-Myung Oh
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jae-Hak Lee
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Eun Chan Yang
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Kae Kyoung Kwon
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Yun Jae Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Tae Wan Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Wonduck Kim
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Jeong Ho Jeon
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sang-Jin Kim
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Dong Han Choi
- Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Hak-Min Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Junsu Ko
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Hyunmin Kim
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Young-Ah Shin
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Hyun-Ju Jung
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Yuan Zheng
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Zhuo Wang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Yan Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Ming Chen
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Awei Jiang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Erli Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Shu Zhang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Haolong Hou
- Shaanxi Yulin Energy Group Co. Ltd., Yulin, Shaanxi, China
| | - Tae Hyung Kim
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Lili Yu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Sha Liu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Kung Ahn
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Jesse Cooper
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Sin-Gi Park
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Chang Pyo Hong
- Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea
| | - Wook Jin
- Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, Republic of Korea
| | - Chankyu Park
- Laboratory of Genome Biology, Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Kyooyeol Lee
- Laboratory of Genome Biology, Department of Animal Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sung Chun
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Phillip A Morin
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, California, USA
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Hang Lee
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jumpei Kimura
- Department of Anatomy and Cell Biology, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dae Yeon Moon
- Marine Biodiversity Institute of Korea (MABIK), Ministry of Ocean and Fisheries, Sejong, Republic of Korea
| | - Andrea Manica
- Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeremy Edwards
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Byung Chul Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea
| | - Sangsoo Kim
- School of Systems Biomedical Science, Soongsil University, Seoul, Republic of Korea
| | - Jun Wang
- 1] Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China. [2] Department of Biology, University of Copenhagen, Copenhagen, Denmark. [3] King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jong Bhak
- 1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea. [2] Theragen BiO Institute, TheragenEtex, Suwon, Republic of Korea. [3] Program in Nano Science and Technology, Department of Transdisciplinary Studies, Seoul National University, Suwon, Republic of Korea. [4] Advanced Institutes of Convergence Technology Nano Science and Technology, Suwon, Republic of Korea
| | - Hyun Sook Lee
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Jung-Hyun Lee
- 1] Korea Institute of Ocean Science and Technology, Ansan, Republic of Korea. [2] Department of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
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Chun S, Plunkett J, Teramo K, Muglia LJ, Fay JC. Fine-mapping an association of FSHR with preterm birth in a Finnish population. PLoS One 2013; 8:e78032. [PMID: 24205076 PMCID: PMC3812121 DOI: 10.1371/journal.pone.0078032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/09/2013] [Indexed: 12/18/2022] Open
Abstract
Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, follicle-stimulating hormone receptor (FSHR), has been associated with preterm birth in Finnish and African American mothers but not other populations. To refine the genetic association of FSHR with preterm birth we conducted a fine-mapping study at the FSHR locus in a Finnish cohort. We sequenced a total of 44 kb, including protein-coding and conserved non-coding regions, in 127 preterm and 135 term mothers. Overall, we identified 288 single nucleotide variants and 65 insertion/deletions of 1-2 bp across all subjects. While no common SNPs in protein-coding regions were associated with preterm birth, including one previously associated with timing of fertilization, multiple SNPs spanning the first and second intron showed the strongest associations. Analysis of the associated SNPs revealed that they form both a protective (OR = 0.50, 95% CI = 0.25-0.93) as well as a risk (OR = 1.89, 95% CI = 1.08-3.39) haplotype with independent effects. In these haplotypes, two SNPs, rs12052281 and rs72822025, were predicted to disrupt ZEB1 and ELF3 transcription factor binding sites, respectively. Our results show that multiple haplotypes at FSHR are associated with preterm birth and we discuss the frequency and structure of these haplotypes outside of the Finnish population as a potential explanation for the absence of FSHR associations in some populations.
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Affiliation(s)
- Sung Chun
- Computational and Systems Biology Program, Washington University, St. Louis, Missouri, United States of America
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Chun S, Sadeghi M, Wong B, Wijeysundera H. Improving Coronary Intensive Care Unit Performance on Meeting Canadian Quality Indicators on Acute Coronary Syndrome and Congestive Heart Failure. Can J Cardiol 2013. [DOI: 10.1016/j.cjca.2013.07.458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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