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Zhang N, Lv X, Cheng X, Wang J, Liu J, Shi J, Liu J, Hu B, Chen D, Zhang G. Risk of sudden coronary death based on genetic background in Chinese Han population. Exp Ther Med 2021; 22:1068. [PMID: 34447461 PMCID: PMC8355668 DOI: 10.3892/etm.2021.10502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022] Open
Abstract
Associations between gene variations and sudden cardiac arrest or coronary artery disease have been reported by genome-wide association studies. However, the implication of the genetic status in cases of sudden coronary death (SCD) from the Chinese Han population has remained to be investigated. The present study established a mini-sequencing system to examine putative death-causing single nucleotide polymorphisms (SNPs) using multiplex PCR, single base extension reaction and capillary electrophoresis techniques. A total of 198 samples from the Chinese Han population (age range, 34-71 years; mean age, 53.86 years) were examined using this method. Samples were classified into three groups: Coronary heart disease (CHD, n=70), SCD (n=53) and control (n=75) group. Significant associations were identified for 10, 4 and 6 SNPs in CHD, SCD and sudden death from CHD, respectively, using the χ2 test. The SNPs obtained by binary logistic regression may be used to assess and predict the risk of disease. The predictive accuracy of the SNPs in each prediction model and their area under the receiver operating characteristic curve (AUC) values were determined. The AUC of the four SNPs (rs12429889, rs10829156, rs16942421 and rs12155623) to predict CHD was 0.928, the AUC of the six SNPs (rs2389202, rs2982694, rs10183640, rs597503, rs16942421 and rs12155623) to predict SCD was 0.922 and the AUC of the four SNPs (rs16866933, rs4621553, rs10829156 and rs12155623) to predict sudden death from CHD was 0.912. The multifactor dimensionality reduction values were as follows: 0.8690 (prediction model of CHD), 0.7601 (prediction model of SCD) and 0.7628 (prediction model of sudden death from CHD). Taken together, the results of the present study suggested that these SNPs have considerable potential for application in genetic tests to predict CHD or SCD. However, further studies are required to investigate the putative functions of these SNPs.
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Affiliation(s)
- Nenghua Zhang
- Department of Clinical Laboratory and Pathology, Municipal Key-Innovative Discipline of Molecular Diagnostics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang 314001, P.R. China
| | - Xiaochun Lv
- Department of Cardiovascular Medicine, Fenyang Hospital of Shanxi Province, Fenyang Hospital Affiliated to Shanxi Medical University, Fenyang, Shanxi 032200, P.R. China
| | - Xiaojuan Cheng
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jiaqi Wang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jinding Liu
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jie Shi
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
| | - Jie Liu
- Department of Clinical Laboratory and Pathology, Municipal Key-Innovative Discipline of Molecular Diagnostics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang 314001, P.R. China
| | - Bo Hu
- Department of Clinical Laboratory and Pathology, Municipal Key-Innovative Discipline of Molecular Diagnostics, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang 314001, P.R. China
| | - Deqing Chen
- Department of Pathology, Forensic and Pathology Laboratory, Judicial Expertise Center, Jiaxing University Medical College, Jiaxing, Zhejiang 314001, P.R. China
| | - Gengqian Zhang
- Department of Forensic Biology, School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030619, P.R. China
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Keaton JM, Gao C, Guan M, Hellwege JN, Palmer ND, Pankow JS, Fornage M, Wilson JG, Correa A, Rasmussen-Torvik LJ, Rotter JI, Chen YDI, Taylor KD, Rich SS, Wagenknecht LE, Freedman BI, Ng MCY, Bowden DW. Genome-wide interaction with the insulin secretion locus MTNR1B reveals CMIP as a novel type 2 diabetes susceptibility gene in African Americans. Genet Epidemiol 2018; 42:559-570. [PMID: 29691896 PMCID: PMC6160319 DOI: 10.1002/gepi.22126] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/27/2018] [Accepted: 03/16/2018] [Indexed: 11/09/2022]
Abstract
Although type 2 diabetes (T2D) results from metabolic defects in insulin secretion and insulin sensitivity, most of the genetic risk loci identified to date relates to insulin secretion. We reported that T2D loci influencing insulin sensitivity may be identified through interactions with insulin secretion loci, thereby leading to T2D. Here, we hypothesize that joint testing of variant main effects and interaction effects with an insulin secretion locus increases power to identify genetic interactions leading to T2D. We tested this hypothesis with an intronic MTNR1B SNP, rs10830963, which is associated with acute insulin response to glucose, a dynamic measure of insulin secretion. rs10830963 was tested for interaction and joint (main + interaction) effects with genome-wide data in African Americans (2,452 cases and 3,772 controls) from five cohorts. Genome-wide genotype data (Affymetrix Human Genome 6.0 array) was imputed to a 1000 Genomes Project reference panel. T2D risk was modeled using logistic regression with rs10830963 dosage, age, sex, and principal component as predictors. Joint effects were captured using the Kraft two degrees of freedom test. Genome-wide significant (P < 5 × 10-8 ) interaction with MTNR1B and joint effects were detected for CMIP intronic SNP rs17197883 (Pinteraction = 1.43 × 10-8 ; Pjoint = 4.70 × 10-8 ). CMIP variants have been nominally associated with T2D, fasting glucose, and adiponectin in individuals of East Asian ancestry, with high-density lipoprotein, and with waist-to-hip ratio adjusted for body mass index in Europeans. These data support the hypothesis that additional genetic factors contributing to T2D risk, including insulin sensitivity loci, can be identified through interactions with insulin secretion loci.
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Affiliation(s)
- Jacob M. Keaton
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Chuan Gao
- Molecular Genetics and Genomics Program, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Meijian Guan
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Jacklyn N. Hellwege
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
| | - Nicholette D. Palmer
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC
| | - James S. Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX
| | | | - Adolfo Correa
- University of Mississippi Medical Center, Jackson, MS
| | | | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Yii-Der I. Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Lynne E. Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Barry I. Freedman
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Internal Medicine - Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Maggie C. Y. Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
| | - Donald W. Bowden
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC
- Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC
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3
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Tabb KL, Hellwege JN, Palmer ND, Dimitrov L, Sajuthi S, Taylor KD, Ng MCY, Hawkins GA, Chen YDI, Brown WM, McWilliams D, Williams A, Lorenzo C, Norris JM, Long J, Rotter JI, Curran JE, Blangero J, Wagenknecht LE, Langefeld CD, Bowden DW. Analysis of Whole Exome Sequencing with Cardiometabolic Traits Using Family-Based Linkage and Association in the IRAS Family Study. Ann Hum Genet 2017; 81:49-58. [PMID: 28067407 DOI: 10.1111/ahg.12184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023]
Abstract
Family-based methods are a potentially powerful tool to identify trait-defining genetic variants in extended families, particularly when used to complement conventional association analysis. We utilized two-point linkage analysis and single variant association analysis to evaluate whole exome sequencing (WES) data from 1205 Hispanic Americans (78 families) from the Insulin Resistance Atherosclerosis Family Study. WES identified 211,612 variants above the minor allele frequency threshold of ≥0.005. These variants were tested for linkage and/or association with 50 cardiometabolic traits after quality control checks. Two-point linkage analysis yielded 10,580,600 logarithm of the odds (LOD) scores with 1148 LOD scores ≥3, 183 LOD scores ≥4, and 29 LOD scores ≥5. The maximal novel LOD score was 5.50 for rs2289043:T>C, in UNC5C with subcutaneous adipose tissue volume. Association analysis identified 13 variants attaining genome-wide significance (P < 5 × 10-08 ), with the strongest association between rs651821:C>T in APOA5 and triglyceride levels (P = 3.67 × 10-10 ). Overall, there was a 5.2-fold increase in the number of informative variants detected by WES compared to exome chip analysis in this population, nearly 30% of which were novel variants relative to the Database of Single Nucleotide Polymorphisms (dbSNP) build 138. Thus, integration of results from two-point linkage and single-variant association analysis from WES data enabled identification of novel signals potentially contributing to cardiometabolic traits.
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Affiliation(s)
- Keri L Tabb
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Latchezar Dimitrov
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Satria Sajuthi
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Maggie C Y Ng
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yii-der Ida Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W Mark Brown
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - David McWilliams
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Adrienne Williams
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carlos Lorenzo
- Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Jill M Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E Curran
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Lynne E Wagenknecht
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Center for Public Health Genomics, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
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