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Jeon S, Choi H, Jeon Y, Choi WH, Choi H, An K, Ryu H, Bhak J, Lee H, Kwon Y, Ha S, Kim YJ, Blazyte A, Kim C, Kim Y, Kang Y, Woo YJ, Lee C, Seo J, Yoon C, Bolser D, Biro O, Shin ES, Kim BC, Kim SY, Park JH, Jeon J, Jung D, Lee S, Bhak J. Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups. Gigascience 2024; 13:giae014. [PMID: 38626723 PMCID: PMC11020240 DOI: 10.1093/gigascience/giae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 11/28/2023] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUND Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics. RESULTS Here, we present 4,157 whole genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest genomic resource of the Korean Genome Project. It encompasses most of the variants with allele frequency >0.001 in Koreans, indicating that it sufficiently covered most of the common and rare genetic variants with commonly measured phenotypes for Koreans. Korea4K provides 45,537,252 variants, and half of them were not present in Korea1K (1,094 samples). We also identified 1,356 new genotype-phenotype associations that were not found by the Korea1K dataset. Phenomics analyses further revealed 24 significant genetic correlations, 14 pleiotropic associations, and 127 causal relationships based on Mendelian randomization among 37 traits. In addition, the Korea4K imputation reference panel, the largest Korean variants reference to date, showed a superior imputation performance to Korea1K across all allele frequency categories. CONCLUSIONS Collectively, Korea4K provides not only the largest Korean genome data but also corresponding health check-up parameters and novel genome-phenome associations. The large-scale pathological whole genome-wide omics data will become a powerful set for genome-phenome level association studies to discover causal markers for the prediction and diagnosis of health conditions in future studies.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Hansol Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Whan-Hyuk Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Mathematics, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyunjoo Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungwhan An
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyojung Ryu
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Jihun Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyeonjae Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yoonsung Kwon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sukyeon Ha
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Computer Science & Engineering (CSE), College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeo Jin Kim
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
| | | | | | - Younghui Kang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | | | - Chanyoung Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jeongwoo Seo
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dan Bolser
- Geromics Ltd., Cambridge CB1 3NF, United Kingdom
| | | | - Eun-Seok Shin
- Department of Cardiology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 44033, Republic of Korea
| | | | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Ji-Hwan Park
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jongbum Jeon
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Dooyoung Jung
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
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Liang Y, Mao Y, Liang W, Liang L, Suo M, Xue J, Yang H. Association of serum alkaline phosphatase and depression in US adults: a population-based cross-sectional study. Front Psychiatry 2023; 14:1131105. [PMID: 37265554 PMCID: PMC10229779 DOI: 10.3389/fpsyt.2023.1131105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Background Depression, a serious public health disorder, is increasingly prevalent worldwide. An association between alkaline phosphatase (ALP) and neurological disorders has been reported. However, data on ALP and depression risk are scarce, which warrants attention. Methods We assessed the association between ALP and risk of depression in adults from the 2007-2014 National Health and Nutrition Examination Survey (NHANES). Depression was assessed using the Patient Health Questionnaire-9. Univariate and multivariate logistic regression were used to assess the association between ALP and risk of depression, and subgroup analyses were also performed. Results A total of 17,485 participants were included. The prevalence of depression was 9.3% (1,631/17,485) and ALP was significantly associated with the risk of depression when ALP was a categorical variable (quadratic or categorized by 79 U/L) in a multivariate logistic regression model after adjusting for confounding factors (≥79 U/L vs. <79 U/L, adjusted OR, 1.15; 95%CI, 1.02-1.29). Each 1-unit increase in ALP (log2) was associated with a 20% increase in depression prevalence (adjusted OR, 1.20; 95%CI, 1.06-1.36) when ALP was used as a continuous variable. Subgroup analysis showed that ALP was positively associated with the risk of depression with different characteristics. Conclusion Our findings suggest that higher alkaline phosphatase levels, even within the normal range, are significantly associated with a higher risk of depression in US adults. Such findings require further prospective studies to provide more evidence.
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Affiliation(s)
- Yujiang Liang
- Department of Laboratory Medicine, Fengfeng General Hospital of North China Medical & Health Group, Han Dan, Hebei, China
| | - Yafei Mao
- Department of Laboratory Medicine, Fengfeng General Hospital of North China Medical & Health Group, Han Dan, Hebei, China
- Department of Laboratory Medicine, The First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | | | - Liping Liang
- Department of Laboratory Medicine, Fengfeng General Hospital of North China Medical & Health Group, Han Dan, Hebei, China
| | - Min Suo
- Department of Laboratory Medicine, Fengfeng General Hospital of North China Medical & Health Group, Han Dan, Hebei, China
| | - Juan Xue
- Department of Laboratory Medicine, Fengfeng General Hospital of North China Medical & Health Group, Han Dan, Hebei, China
| | - Hui Yang
- Department of Orthopaedics, Fengfeng General Hospital of North China Medical & Health Group, Han Dan, Hebei, China
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Tan LM, Wang L, Chen JJ, Li H, Luo WB. Diagnostic performance of bone metabolic indexes for the detection of stroke. Saudi Med J 2017; 38:30-35. [PMID: 28042627 PMCID: PMC5278062 DOI: 10.15537/smj.2017.1.15813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives: To explore the diagnostic performance of 25-hydroxyvitamin D (25(OH)D), parathyroid hormone (PTH), bone alkaline phosphatase (BALP), and osteocalcin (OC) in predicting stroke. Methods: This retrospective survey was conducted in The Second Affiliated Hospital to Nanchang University, Nanchang, Jiangxi Province, China. involved 121 cerebral infarction patients and 103 cerebral hemorrhage patients as the experimental groups, 100 volunteers as the healthy control group and 80 brain trauma patients as the disease control group. The 25(OH)D, PTH, BALP, and OC levels of all participants were measured by electrochemiluminescence immunoassay. Results: The serum concentration of 25(OH)D in stroke patients was appreciably lower than that of the control groups (p<0.05), and subsequently, the deficiency level of 25(OH)D in the stroke population was considerably higher than that of the control groups (p<0.05). The serum concentrations of PTH and OC in stroke patients exceeded those found in the control groups (p<0.05), and the abnormal level in the stroke patients was also higher than that of the control. Compared with the control group, BALP concentrations in cerebral infarction patients were increased significantly. Additionally, abnormal levels of BALP in stroke patients were found to be higher than those in the control groups. However, concentrations and abnormal levels of BALP in cerebral hemorrhage patients were not found to be significantly different than those found in cerebral infarction and the control groups, There were no substantial differences between the 2 control groups. Conclusion: Lack of 25(OH)D and excessive PTH, BALP, and OC could indicate a high risk of stroke.
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Affiliation(s)
- Li Ming Tan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China. E-mail.
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Sun W, Kechris K, Jacobson S, Drummond MB, Hawkins GA, Yang J, Chen TH, Quibrera PM, Anderson W, Barr RG, Basta PV, Bleecker ER, Beaty T, Casaburi R, Castaldi P, Cho MH, Comellas A, Crapo JD, Criner G, Demeo D, Christenson SA, Couper DJ, Curtis JL, Doerschuk CM, Freeman CM, Gouskova NA, Han MK, Hanania NA, Hansel NN, Hersh CP, Hoffman EA, Kaner RJ, Kanner RE, Kleerup EC, Lutz S, Martinez FJ, Meyers DA, Peters SP, Regan EA, Rennard SI, Scholand MB, Silverman EK, Woodruff PG, O’Neal WK, Bowler RP. Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD. PLoS Genet 2016; 12:e1006011. [PMID: 27532455 PMCID: PMC4988780 DOI: 10.1371/journal.pgen.1006011] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
Abstract
Implementing precision medicine for complex diseases such as chronic obstructive lung disease (COPD) will require extensive use of biomarkers and an in-depth understanding of how genetic, epigenetic, and environmental variations contribute to phenotypic diversity and disease progression. A meta-analysis from two large cohorts of current and former smokers with and without COPD [SPIROMICS (N = 750); COPDGene (N = 590)] was used to identify single nucleotide polymorphisms (SNPs) associated with measurement of 88 blood proteins (protein quantitative trait loci; pQTLs). PQTLs consistently replicated between the two cohorts. Features of pQTLs were compared to previously reported expression QTLs (eQTLs). Inference of causal relations of pQTL genotypes, biomarker measurements, and four clinical COPD phenotypes (airflow obstruction, emphysema, exacerbation history, and chronic bronchitis) were explored using conditional independence tests. We identified 527 highly significant (p < 8 X 10-10) pQTLs in 38 (43%) of blood proteins tested. Most pQTL SNPs were novel with low overlap to eQTL SNPs. The pQTL SNPs explained >10% of measured variation in 13 protein biomarkers, with a single SNP (rs7041; p = 10-392) explaining 71%-75% of the measured variation in vitamin D binding protein (gene = GC). Some of these pQTLs [e.g., pQTLs for VDBP, sRAGE (gene = AGER), surfactant protein D (gene = SFTPD), and TNFRSF10C] have been previously associated with COPD phenotypes. Most pQTLs were local (cis), but distant (trans) pQTL SNPs in the ABO blood group locus were the top pQTL SNPs for five proteins. The inclusion of pQTL SNPs improved the clinical predictive value for the established association of sRAGE and emphysema, and the explanation of variance (R2) for emphysema improved from 0.3 to 0.4 when the pQTL SNP was included in the model along with clinical covariates. Causal modeling provided insight into specific pQTL-disease relationships for airflow obstruction and emphysema. In conclusion, given the frequency of highly significant local pQTLs, the large amount of variance potentially explained by pQTL, and the differences observed between pQTLs and eQTLs SNPs, we recommend that protein biomarker-disease association studies take into account the potential effect of common local SNPs and that pQTLs be integrated along with eQTLs to uncover disease mechanisms. Large-scale blood biomarker studies would also benefit from close attention to the ABO blood group.
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Affiliation(s)
- Wei Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Katerina Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Sean Jacobson
- National Jewish Health, Denver, Colorado, United States of America
| | - M. Bradley Drummond
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gregory A. Hawkins
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Jenny Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ting-huei Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Pedro Miguel Quibrera
- Collaborative Studies Coordinating Center, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wayne Anderson
- Marsico Lung Institute/Cystic Fibrosis Research Center, Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States of America
| | - R. Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, New York; Department of Epidemiology, Mailman School of Public Health at Columbia University, New York, New York, United States of America
| | - Patricia V. Basta
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Eugene R. Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Terri Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University,Baltimore, Maryland, United States of America
| | - Richard Casaburi
- Division of Respiratory and Critical Care Physiology and Medicine, Harbor- University of California at Los Angeles Medical Center, Torrance, California, United States of America
| | - Peter Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Alejandro Comellas
- Division of Pulmonary and Critical Care Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - James D. Crapo
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Gerard Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Dawn Demeo
- Division of Pulmonary and Critical Care Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, Department of Medicine, University of San Francisco Medical Center, University of California San Francisco, San Francisco, California, United States of America
| | - David J. Couper
- Collaborative Studies Coordinating Center, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jeffrey L. Curtis
- Division of Pulmonary and Critical Care Medicine, University of Michigan Health System, Ann Arbor, Michigan; VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - Claire M. Doerschuk
- Marsico Lung Institute/Cystic Fibrosis Research Center, Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States of America
| | - Christine M. Freeman
- Division of Pulmonary and Critical Care Medicine, University of Michigan Health System, Ann Arbor, Michigan; VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - Natalia A. Gouskova
- Collaborative Studies Coordinating Center, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - MeiLan K. Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan Health System, Ann Arbor, Michigan, United States of America
| | - Nicola A. Hanania
- Section of Pulmonary and Critical Care Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nadia N. Hansel
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Craig P. Hersh
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Eric A. Hoffman
- Department of Radiology, Division of Physiologic Imaging, University of Iowa Hospitals and Clinics, Iowa City, Iowa, United States of America
| | - Robert J. Kaner
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Richard E. Kanner
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Eric C. Kleerup
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sharon Lutz
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Fernando J. Martinez
- Department of Medicine, Weill Cornell Medical College, New York-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York, United States of America
| | - Deborah A. Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Stephen P. Peters
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Immunologic Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Elizabeth A. Regan
- Department of Medicine, National Jewish Health, Denver, Colorado United States of America
| | - Stephen I. Rennard
- Division of Pulmonary and Critical Care Medicine, University of Nebraska, Omaha, Nebraska, United States of America
| | - Mary Beth Scholand
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine and Cardiovascular Research Institute, University of California San Francisco School of Medicine, San Francisco, California, United States of America
| | - Wanda K. O’Neal
- Marsico Lung Institute/Cystic Fibrosis Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States of America
| | - Russell P. Bowler
- Department of Medicine, Division of Pulmonary Medicine, National Jewish Health, Denver, Colorado, United States of America
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5
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McLachlan S, Giambartolomei C, White J, Charoen P, Wong A, Finan C, Engmann J, Shah T, Hersch M, Podmore C, Cavadino A, Jefferis BJ, Dale CE, Hypponen E, Morris RW, Casas JP, Kumari M, Ben-Shlomo Y, Gaunt TR, Drenos F, Langenberg C, Kuh D, Kivimaki M, Rueedi R, Waeber G, Hingorani AD, Price JF, Walker AP. Replication and Characterization of Association between ABO SNPs and Red Blood Cell Traits by Meta-Analysis in Europeans. PLoS One 2016; 11:e0156914. [PMID: 27280446 PMCID: PMC4900668 DOI: 10.1371/journal.pone.0156914] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/20/2016] [Indexed: 01/07/2023] Open
Abstract
Red blood cell (RBC) traits are routinely measured in clinical practice as important markers of health. Deviations from the physiological ranges are usually a sign of disease, although variation between healthy individuals also occurs, at least partly due to genetic factors. Recent large scale genetic studies identified loci associated with one or more of these traits; further characterization of known loci and identification of new loci is necessary to better understand their role in health and disease and to identify potential molecular mechanisms. We performed meta-analysis of Metabochip association results for six RBC traits—hemoglobin concentration (Hb), hematocrit (Hct), mean corpuscular hemoglobin (MCH), mean corpuscular hemoglobin concentration (MCHC), mean corpuscular volume (MCV) and red blood cell count (RCC)—in 11 093 Europeans from seven studies of the UCL-LSHTM-Edinburgh-Bristol (UCLEB) Consortium. We identified 394 non-overlapping SNPs in five loci at genome-wide significance: 6p22.1-6p21.33 (with HFE among others), 6q23.2 (with HBS1L among others), 6q23.3 (contains no genes), 9q34.3 (only ABO gene) and 22q13.1 (with TMPRSS6 among others), replicating previous findings of association with RBC traits at these loci and extending them by imputation to 1000 Genomes. We further characterized associations between ABO SNPs and three traits: hemoglobin, hematocrit and red blood cell count, replicating them in an independent cohort. Conditional analyses indicated the independent association of each of these traits with ABO SNPs and a role for blood group O in mediating the association. The 15 most significant RBC-associated ABO SNPs were also associated with five cardiometabolic traits, with discordance in the direction of effect between groups of traits, suggesting that ABO may act through more than one mechanism to influence cardiometabolic risk.
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Affiliation(s)
- Stela McLachlan
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Claudia Giambartolomei
- Department of Psychiatry, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, The Leon and Norma Hess Center for Science and Medicine, New York, New York, United States of America
| | - Jon White
- University College London Genetics Institute, Department of Genetics, Environment and Evolution, London, United Kingdom
| | - Pimphen Charoen
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, London, United Kingdom
| | - Chris Finan
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Jorgen Engmann
- Genetic Epidemiology Group, Institute of Cardiovascular Science, University College London, London, United Kingdom
- Farr Institute of Health Informatics Research, Department of Epidemiology & Public Health, University College London, London, United Kingdom
| | - Tina Shah
- Genetic Epidemiology Group, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Micha Hersch
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Clara Podmore
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Alana Cavadino
- Centre for Environmental and Preventive Medicine, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, United Kingdom
| | - Barbara J. Jefferis
- Department of Primary Care & Population Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
| | - Caroline E. Dale
- Farr Institute of Health Informatics Research, Department of Epidemiology & Public Health, University College London, London, United Kingdom
| | - Elina Hypponen
- Population, Policy and Practice, UCL Institute of Child Health, University College London, London, United Kingdom
- Centre for Population Health Research, School of Health Sciences and Sansom Institute of Health Research, University of South Australia, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Richard W. Morris
- Department of Primary Care & Population Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Juan P. Casas
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, United Kingdom
- Department of Epidemiology & Public Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
| | - Yoav Ben-Shlomo
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Fotios Drenos
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at UCL, London, United Kingdom
| | - Mika Kivimaki
- Department of Epidemiology & Public Health, UCL Institute of Epidemiology & Health Care, University College London, London, United Kingdom
| | - Rico Rueedi
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Aroon D. Hingorani
- Institute of Cardiovascular Science, University College London, London, United Kingdom
- Farr Institute of Health Informatics Research, Department of Epidemiology & Public Health, University College London, London, United Kingdom
| | - Jacqueline F. Price
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Ann P. Walker
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
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6
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Zhang YP, Zhang YY, Duan DD. From Genome-Wide Association Study to Phenome-Wide Association Study: New Paradigms in Obesity Research. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 140:185-231. [PMID: 27288830 DOI: 10.1016/bs.pmbts.2016.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Obesity is a condition in which excess body fat has accumulated over an extent that increases the risk of many chronic diseases. The current clinical classification of obesity is based on measurement of body mass index (BMI), waist-hip ratio, and body fat percentage. However, these measurements do not account for the wide individual variations in fat distribution, degree of fatness or health risks, and genetic variants identified in the genome-wide association studies (GWAS). In this review, we will address this important issue with the introduction of phenome, phenomics, and phenome-wide association study (PheWAS). We will discuss the new paradigm shift from GWAS to PheWAS in obesity research. In the era of precision medicine, phenomics and PheWAS provide the required approaches to better definition and classification of obesity according to the association of obese phenome with their unique molecular makeup, lifestyle, and environmental impact.
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Affiliation(s)
- Y-P Zhang
- Pediatric Heart Center, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Y-Y Zhang
- Department of Cardiology, Changzhou Second People's Hospital, Changzhou, Jiangsu, China
| | - D D Duan
- Laboratory of Cardiovascular Phenomics, Center for Cardiovascular Research, Department of Pharmacology, and Center for Molecular Medicine, University of Nevada School of Medicine, Reno, NV, United States.
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7
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Interaction of genetic markers associated with serum alkaline phosphatase levels in the Japanese population. Hum Genome Var 2015; 2:15019. [PMID: 27081532 PMCID: PMC4785570 DOI: 10.1038/hgv.2015.19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 04/26/2015] [Accepted: 05/04/2015] [Indexed: 11/28/2022] Open
Abstract
In the present genome-wide association study of 2,994 Japanese subjects, rs2071699 (35C>T) in the fucosyltransferase 1 (FUT1) gene was identified as a marker associated with serum alkaline phosphatase (ALP) levels. This gene encodes α(1,2)-fucosyltransferase, which is responsible for the synthesis of H antigens. In a linear regression model incorporating genetic markers, rs550057 (C>T), which is located within an intron of the ABO blood group (ABO) locus, rs2071699 in FUT1 and a gene–gene interaction between these loci accounted for 12.4, 0.9 and 0.3% of the total variability in the serum ALP level, respectively. Further association analysis using imputed genotypes detected rs1047781 in FUT2. rs1047781 is well known in this association with serum ALP levels and showed a moderate linkage with rs2071699 in FUT1. An interaction analysis using rs1047781 in FUT2 also suggested that the interaction with rs550057 in ABO is significant and contributes to the interindividual variance of serum ALP levels as well as rs2071699 in the FUT1 gene. Thus, there is evidence of interactions between ABO and FUT1/FUT2 on serum ALP levels, regardless of the possibility that rs2071699 in FUT1 is a proxy of rs1047781 in FUT2 in the Japanese population.
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