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Panda G, Mishra N, Sharma D, Kutum R, Bhoyar RC, Jain A, Imran M, Senthilvel V, Divakar MK, Mishra A, Garg P, Banerjee P, Sivasubbu S, Scaria V, Ray A. Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum. Front Pharmacol 2022; 13:858345. [PMID: 35865963 PMCID: PMC9294532 DOI: 10.3389/fphar.2022.858345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
India confines more than 17% of the world’s population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets. The sequence-level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas a comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network was investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveals critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.
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Affiliation(s)
- Gayatri Panda
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Neha Mishra
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Disha Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rintu Kutum
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Ashoka University, Sonipat, India
| | - Rahul C. Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhinav Jain
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mohamed Imran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vigneshwar Senthilvel
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mohit Kumar Divakar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anushree Mishra
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Parth Garg
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Priyanka Banerjee
- Institute for Physiology, Charité-University Medicine Berlin, Berlin, Germany
| | - Sridhar Sivasubbu
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Arjun Ray
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
- *Correspondence: Arjun Ray,
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Tan SC, Low TY, Mohamad Hanif EA, Sharzehan MAK, Kord-Varkaneh H, Islam MA. The rs9340799 polymorphism of the estrogen receptor alpha (ESR1) gene and its association with breast cancer susceptibility. Sci Rep 2021; 11:18619. [PMID: 34545128 PMCID: PMC8452701 DOI: 10.1038/s41598-021-97935-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
The ESR1 rs9340799 polymorphism has been frequently investigated with regard to its association with breast cancer (BC) susceptibility, but the findings have been inconclusive. In this work, we aimed to address the inconsistencies in study findings by performing a systematic review and meta-analysis. Eligible studies were identified from the Web of Science, PubMed, Scopus, China National Knowledge Infrastructure, VIP and Wanfang databases based on the predefined inclusion and exclusion criteria. The pooled odds ratio (OR) was then calculated under five genetic models: homozygous (GG vs. AA), heterozygous (AG vs. AA), dominant (AG + GG vs. AA), recessive (GG vs. AA + AG) and allele (G vs. A). Combined results from 23 studies involving 34,721 subjects indicated a lack of significant association between the polymorphism and BC susceptibility (homozygous model, OR = 1.045, 95% CI 0.887-1.231, P = 0.601; heterozygous model, OR = 0.941, 95% CI 0.861-1.030, P = 0.186; dominant model, OR = 0.957, 95% CI 0.875-1.045, P = 0.327; recessive model, OR = 1.053, 95% CI 0.908-1.222, P = 0.495; allele model, OR = 0.987, 95% CI 0.919-1.059, P = 0.709). Subgroup analyses by ethnicity, menopausal status and study quality also revealed no statistically significant association (P > 0.05). In conclusion, our results showed that the ESR1 rs9340799 polymorphism was not associated with BC susceptibility, suggesting its limited potential as a genetic marker for BC.
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Affiliation(s)
- Shing Cheng Tan
- grid.412113.40000 0004 1937 1557UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Teck Yew Low
- grid.412113.40000 0004 1937 1557UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ezanee Azlina Mohamad Hanif
- grid.412113.40000 0004 1937 1557UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Mohamad Ayub Khan Sharzehan
- grid.412113.40000 0004 1937 1557UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hamed Kord-Varkaneh
- grid.411600.2Department of Clinical Nutrition and Dietetics, Student Research Committee, Faculty of Nutrition and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Md Asiful Islam
- grid.11875.3a0000 0001 2294 3534Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
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3
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Mazuchová J, Halašová E, Mazuch J, Šarlinová M, Valentová V, Franeková M, Zelník Š, Krkošková K, Javorka K, Péč M, Grendár M. Investigation of association between genetic polymorphisms of MMP2, MMP8, MMP9 and TIMP2 and development of varicose veins in the Slovak Population - pilot study. Physiol Res 2020; 69:S443-S454. [PMID: 33471544 DOI: 10.33549/physiolres.934597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Matrix metalloproteinases (MMPs) are a family of zinc-dependent metalloendopeptidases that degrades extracellular matrix (ECM) components. MMPs are associated with venous wall remodelling, proliferation, migration, phenotypic and functional transformation of vascular smooth muscle cells and ECM organization under the physiological and pathophysiological conditions. We investigated possible association of genetic promoter polymorphisms of MMP2 (rs243866), MMP8 (rs11225395), MMP9 (rs3918242) and TIMP2 (rs8179090) to varicose veins development in the Slovak population. Genomic DNA from 276 Slovak individuals (138 cases, 138 controls) was genotyped for selected SNPs (rs243866, rs11225395, rs3918242 and rs8179090) using the PCR-RFLP analysis. The data were analysed by chi-squared (chi2) test, logistic regression, and Mann-Whitney test. The risk of varicose veins development was evaluated in dominant, codominant and recessive genetic models. The statistical evaluation of selected polymorphisms in patients in all three genetic models has not shown a significant risk of varicose veins development. Our study has not shown the association between selected polymorphisms and increased risk of varicose veins development in Slovak population. More evidence with broaden sample size is needed.
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Affiliation(s)
- J Mazuchová
- Department of Medical Biology, Jessenius Faculty of Medicine, Martin, Slovakia.
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Moazzam-Jazi M, Najd Hassan Bonab L, Zahedi AS, Daneshpour MS. High genetic burden of type 2 diabetes can promote the high prevalence of disease: a longitudinal cohort study in Iran. Sci Rep 2020; 10:14006. [PMID: 32814780 PMCID: PMC7438483 DOI: 10.1038/s41598-020-70725-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/22/2020] [Indexed: 01/08/2023] Open
Abstract
Type 2 diabetes (T2D) is emerging as one of the serious public health issues in both developed and developing counties. Here, we surveyed the worldwide population differentiation in T2D-associated variants and assessed the genetic burden of the disease in an ongoing Tehran Cardio-Metabolic Genetic Study (TCGS) cohort represented the Iranian population. We found multiple SNPs that were significantly depleted or enriched in at least one of the five populations of 1,000 Genome Project (African, American, East Asian, European, and South Asian) as well as the Iranian population. Interestingly, TCF7L2, a well-known associated gene with T2D, harbors the highest number of enriched risk alleles almost in all populations except for East Asian, where this gene embraces the largest number of significantly depleted risk alleles. The polygenic risk score (PRS) of the enriched risk alleles was calculated for 1,867 diabetic and 2,855 non-diabetic participants in the TCGS cohort, interestingly demonstrating that the risk of developing T2D was almost two times higher in top PRS quintile compared with the lowest quintile after adjusting for other known risk factors.
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Affiliation(s)
- Maryam Moazzam-Jazi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Najd Hassan Bonab
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Asiyeh Sadat Zahedi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam S Daneshpour
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Matsunaga H, Ito K, Akiyama M, Takahashi A, Koyama S, Nomura S, Ieki H, Ozaki K, Onouchi Y, Sakaue S, Suna S, Ogishima S, Yamamoto M, Hozawa A, Satoh M, Sasaki M, Yamaji T, Sawada N, Iwasaki M, Tsugane S, Tanaka K, Arisawa K, Ikezaki H, Takashima N, Naito M, Wakai K, Tanaka H, Sakata Y, Morita H, Sakata Y, Matsuda K, Murakami Y, Akazawa H, Kubo M, Kamatani Y, Komuro I. Transethnic Meta-Analysis of Genome-Wide Association Studies Identifies Three New Loci and Characterizes Population-Specific Differences for Coronary Artery Disease. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2020; 13:e002670. [PMID: 32469254 DOI: 10.1161/circgen.119.002670] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Genome-wide association studies provided many biological insights into coronary artery disease (CAD), but these studies were mainly performed in Europeans. Genome-wide association studies in diverse populations have the potential to advance our understanding of CAD. METHODS We conducted 2 genome-wide association studies for CAD in the Japanese population, which included 12 494 cases and 28 879 controls and 2808 cases and 7261 controls, respectively. Then, we performed transethnic meta-analysis using the results of the coronary artery disease genome-wide replication and meta-analysis plus the coronary artery disease 1000 Genomes meta-analysis with UK Biobank. We then explored the pathophysiological significance of these novel loci and examined the differences in CAD-susceptibility loci between Japanese and Europeans. RESULTS We identified 3 new loci on chromosome 1q21 (CTSS), 10q26 (WDR11-FGFR2), and 11q22 (RDX-FDX1). Quantitative trait locus analyses suggested the association of CTSS and RDX-FDX1 with atherosclerotic immune cells. Tissue/cell type enrichment analysis showed the involvement of arteries, adrenal glands, and fat tissues in the development of CAD. We next compared the odds ratios of lead variants for myocardial infarction at 76 genome-wide significant loci in the transethnic meta-analysis and a moderate correlation between Japanese and Europeans, where 8 loci showed a difference. Finally, we performed tissue/cell type enrichment analysis using East Asian-frequent and European-frequent variants according to the risk allele frequencies and identified significant enrichment of adrenal glands in the East Asian-frequent group while the enrichment of arteries and fat tissues was found in the European-frequent group. These findings indicate biological differences in CAD susceptibility between Japanese and Europeans. CONCLUSIONS We identified 3 new loci for CAD and highlighted the genetic differences between the Japanese and European populations. Moreover, our transethnic analyses showed both shared and unique genetic architectures between the Japanese and Europeans. While most of the underlying genetic bases for CAD are shared, further analyses in diverse populations will be needed to elucidate variations fully.
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Affiliation(s)
- Hiroshi Matsunaga
- Laboratory for Cardiovascular Genomics & Informatics (H. Matsunaga, K.I., S.K., H. Ieki, K.O., Y.O.), Kanagawa.,Department of Cardiovascular Medicine, Graduate School of Medicine (H. Matsunaga, S.N., H. Ieki, H.M., H.A., I.K.), University of Tokyo
| | - Kaoru Ito
- Laboratory for Cardiovascular Genomics & Informatics (H. Matsunaga, K.I., S.K., H. Ieki, K.O., Y.O.), Kanagawa
| | - Masato Akiyama
- Laboratory for Statistical Analysis (M.A., A.T., S. Sakaue, Y.K.), Kanagawa
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis (M.A., A.T., S. Sakaue, Y.K.), Kanagawa.,Department of Genomic Medicine, Research Institute, National Cerebral & Cardiovascular Center, Osaka (A.T.)
| | - Satoshi Koyama
- Laboratory for Cardiovascular Genomics & Informatics (H. Matsunaga, K.I., S.K., H. Ieki, K.O., Y.O.), Kanagawa
| | - Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine (H. Matsunaga, S.N., H. Ieki, H.M., H.A., I.K.), University of Tokyo.,Genome Science Division, Research Center for Advanced Science & Technologies (S.N.), University of Tokyo
| | - Hirotaka Ieki
- Laboratory for Cardiovascular Genomics & Informatics (H. Matsunaga, K.I., S.K., H. Ieki, K.O., Y.O.), Kanagawa.,Department of Cardiovascular Medicine, Graduate School of Medicine (H. Matsunaga, S.N., H. Ieki, H.M., H.A., I.K.), University of Tokyo
| | - Kouichi Ozaki
- Laboratory for Cardiovascular Genomics & Informatics (H. Matsunaga, K.I., S.K., H. Ieki, K.O., Y.O.), Kanagawa.,Division for Genomic Medicine, Medical Genome Center, National Center for Geriatrics & Gerontology, Obu (K.O.)
| | - Yoshihiro Onouchi
- Laboratory for Cardiovascular Genomics & Informatics (H. Matsunaga, K.I., S.K., H. Ieki, K.O., Y.O.), Kanagawa.,Department of Public Health, Chiba University Graduate School of Medicine (Y.O.)
| | - Saori Sakaue
- Laboratory for Statistical Analysis (M.A., A.T., S. Sakaue, Y.K.), Kanagawa
| | - Shinichiro Suna
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita (S. Suna, Yasushi Sakata)
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization (S.O., M.Y.), Tohoku University, Sendai
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization (S.O., M.Y.), Tohoku University, Sendai
| | - Atsushi Hozawa
- Department of Preventive Medicine & Epidemiology (A.H.), Tohoku University, Sendai
| | - Mamoru Satoh
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University (M. Satoh, M. Sasaki)
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University (M. Satoh, M. Sasaki)
| | - Taiki Yamaji
- Division of Epidemiology (T.Y., N.S., M.I.), National Cancer Center, Tokyo
| | - Norie Sawada
- Division of Epidemiology (T.Y., N.S., M.I.), National Cancer Center, Tokyo
| | - Motoki Iwasaki
- Division of Epidemiology (T.Y., N.S., M.I.), National Cancer Center, Tokyo
| | - Shoichiro Tsugane
- Center for Public Health Sciences (S.T.), National Cancer Center, Tokyo
| | - Keitaro Tanaka
- Department of Preventive Medicine, Faculty of Medicine, Saga University (K.T.)
| | - Kokichi Arisawa
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School (K.A.)
| | - Hiroaki Ikezaki
- Department of Environmental Medicine & Infectious Diseases, Graduate School of Medical Sciences, Kyushu University, Fukuoka (H. Ikezaki)
| | - Naoyuki Takashima
- Department of Public Health, Shiga University of Medical Science, Otsu (N.T.)
| | - Mariko Naito
- Department of Oral Epidemiology, Graduate School of Biomedical & Health Sciences, Hiroshima University (M.N.).,Department of Preventive Medicine (M.N., K.W.), Nagoya University Graduate School of Medicine
| | - Kenji Wakai
- Department of Preventive Medicine (M.N., K.W.), Nagoya University Graduate School of Medicine
| | - Hideo Tanaka
- Department of Epidemiology (H.T.), Nagoya University Graduate School of Medicine.,Division of Epidemiology & Prevention, Aichi Cancer Center Research Institute, Nagoya (H.T.)
| | - Yasuhiko Sakata
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Sendai (Yasuhiko Sakata)
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, Graduate School of Medicine (H. Matsunaga, S.N., H. Ieki, H.M., H.A., I.K.), University of Tokyo
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita (S. Suna, Yasushi Sakata)
| | - Koichi Matsuda
- Department of Computational Biology & Medical Science, Graduate School of Frontier Sciences (K.M.), University of Tokyo
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science (Y.M.), University of Tokyo
| | - Hiroshi Akazawa
- Department of Cardiovascular Medicine, Graduate School of Medicine (H. Matsunaga, S.N., H. Ieki, H.M., H.A., I.K.), University of Tokyo
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences (M.K.), Kanagawa
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis (M.A., A.T., S. Sakaue, Y.K.), Kanagawa.,Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Japan (Y.K.)
| | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine (H. Matsunaga, S.N., H. Ieki, H.M., H.A., I.K.), University of Tokyo
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Wang D, Guo T, Guo Q, Zhang S, Zhang J, Luo J. The Association Between Schizophrenia Risk Variants and Creativity in Healthy Han Chinese Subjects. Front Psychol 2019; 10:2218. [PMID: 31649580 PMCID: PMC6792478 DOI: 10.3389/fpsyg.2019.02218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/17/2019] [Indexed: 11/14/2022] Open
Abstract
Although previous evidence has suggested that there is a genetic link between schizophrenia and creativity, the specific genetic variants that underlie the link are still largely unknown. To further explore the potential genetic link between schizophrenia and creativity, in a sample of 580 healthy Han Chinese subjects, this study aimed to (1) validate the role of Neuregulin 1 (NRG1) rs6994992 (one schizophrenia risk variant that has been previously linked to creativity in the European population) in the relationship between schizophrenia and creativity and (2) explore the associations between 10 other schizophrenia risk variants and creativity. For NRG1 rs6994992, the result validated its association with creativity measures. However, since NRG1 rs6994992 is not a schizophrenia risk variant in the Han Chinese population, the validated association suggested that ethnic difference may exist in the relationship between NRG1 rs6994992, schizophrenia and creativity. For other schizophrenia risk variants, the result only demonstrated a nominal association between ZNF536 rs2053079 and creativity measures which would not survive correction for multiple testing. No association between polygenic risk score for these 10 schizophrenia risk variants and creativity measures was observed. In conclusion, this study provides limited evidence for the associations between these schizophrenia risk variants and creativity in healthy Han Chinese subjects. Future studies are warranted to better understand the potential genetic link between schizophrenia and creativity.
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Affiliation(s)
- Dan Wang
- Beijing Key Laboratory of Learning and Cognition, Department of Psychology, The Collaborative Innovation Center for Capital Education Development, Capital Normal University, Beijing, China
| | - Tingting Guo
- Beijing Gese Technology Co., Ltd., Beijing, China
| | - Qi Guo
- Beijing Key Laboratory of Learning and Cognition, Department of Psychology, The Collaborative Innovation Center for Capital Education Development, Capital Normal University, Beijing, China
| | - Shun Zhang
- Department of Psychology, Shandong Normal University, Jinan, China
| | - Jinghuan Zhang
- Department of Psychology, Shandong Normal University, Jinan, China
| | - Jing Luo
- Beijing Key Laboratory of Learning and Cognition, Department of Psychology, The Collaborative Innovation Center for Capital Education Development, Capital Normal University, Beijing, China
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7
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Ahsan T, Sajib AA. Drug-response related genetic architecture of Bangladeshi population. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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8
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Whole-exome sequencing in maya indigenous families: variant in PPP1R3A is associated with type 2 diabetes. Mol Genet Genomics 2018; 293:1205-1216. [DOI: 10.1007/s00438-018-1453-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/31/2018] [Indexed: 12/11/2022]
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9
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Moravvej H, Tabatabaei-Panah PS, Ebrahimi E, Esmaeili N, Ghaderian SMH, Ludwig RJ, Akbarzadeh R. TNF-α -308G/A gene polymorphism in bullous pemphigoid and alopecia areata. Hum Antibodies 2018; 26:201-207. [PMID: 29843231 DOI: 10.3233/hab-180339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND TNF-α -308G/A polymorphism has been investigated in few studies for an association with susceptibility to bullous pemphigoid (BP) and alopecia areata (AA). Yet, these findings had so far not been independently replicated, and no data on a possible association of TNFα -308G/A polymorphism with these diseases in Iranian population were available. OBJECTIVES In the present study, a possible effect of TNF-α -308G/A variation on susceptibility to BP or AA disease was evaluated. METHODS Genomic DNA was extracted from the blood of the patients with BP and AA as well as control subjects which genotyped for the TNF-α -308 G/A polymorphism. TNF-α gene expression levels were analyzed by real-time RT-PCR. RESULTS No association was observed between the TNF-α -308 G/A variation and susceptibility to BP or AA diseases in our Iranian cohort. In contrast to AA patients, expression of TNF-α gene was significantly higher in BP patients compared to control group. TNF-α gene was found to be similarly expressed in mutant and wild-type genotypes. CONCLUSIONS TNF-α -308G/A polymorphism is not associated with the risk to develop of BP and AA in our Iranian cohort. Furthermore, this polymorphism is contributed to altering the levels of gene expression in BP disease.
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Affiliation(s)
- Hamideh Moravvej
- Skin Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Skin Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pardis-Sadat Tabatabaei-Panah
- Biology Department, East Tehran Branch, Islamic Azad University, Tehran, Iran.,Skin Research Centre, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elaheh Ebrahimi
- Biology Department, East Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Nafiseh Esmaeili
- Autoimmune Bullous Diseases Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Ralf J Ludwig
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Reza Akbarzadeh
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Institute of Anatomy, University of Lübeck, Lübeck, Germany
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10
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Li X, Li X, Luo R, Wang W, Wang T, Tang H. Detection of KIT Genotype in Pigs by TaqMan MGB Real-Time Quantitative Polymerase Chain Reaction. DNA Cell Biol 2018; 37:457-464. [DOI: 10.1089/dna.2017.4070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Xiuxiu Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, P.R. China
- College of Animal Science, Shandong Agricultural University, Tai'an, P.R. China
| | - Xiaoning Li
- Lishan College, Shandong Normal University, Jinan, P.R. China
| | - Rongrong Luo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, P.R. China
- College of Animal Science, Shandong Agricultural University, Tai'an, P.R. China
| | - Wenwen Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, P.R. China
- College of Animal Science, Shandong Agricultural University, Tai'an, P.R. China
| | - Tao Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, P.R. China
| | - Hui Tang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai'an, P.R. China
- College of Animal Science, Shandong Agricultural University, Tai'an, P.R. China
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Mattei J, Tamez M, Ríos-Bedoya CF, Xiao RS, Tucker KL, Rodríguez-Orengo JF. Health conditions and lifestyle risk factors of adults living in Puerto Rico: a cross-sectional study. BMC Public Health 2018; 18:491. [PMID: 29650018 PMCID: PMC5898045 DOI: 10.1186/s12889-018-5359-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 03/22/2018] [Indexed: 11/10/2022] Open
Abstract
Background Puerto Rico is experiencing an economic and healthcare crisis, yet there are scarce recent and comprehensive reports on the population’s health profile. We aimed to describe prevalent risk factors and health conditions of adults living in Puerto Rico and assess their interrelationship. Methods Participants (n = 380) aged 30-75y recruited from a 2015 convenience sample in primary care clinics in the San Juan, Puerto Rico metropolitan area answered cross-sectional interviewer-administered questionnaires on sociodemographic characteristics, lifestyle behaviors, self-reported medically-diagnosed diseases, health services, and psychosocial factors. Anthropometric measures were obtained. Logistic regression models assessed factors associated with having ≥2 cardiometabolic conditions or ≥ 2 chronic diseases. Results Most participants had completed ≥college education (57%), had household income <$10,000/y (60%), received government-assisted food benefits (51%), and had health insurance (93%). Nearly 20% reported smoking, 27% alcohol use, 74% light/sedentary physical activity, 51% sleeping difficulties, and 36% self-rated fair/poor diet. Social support was moderate, and 53% screened positive for depressive symptomatology. Abdominal obesity was observed in 33% of men and 76% of women (p < 0.0001). Self-reported medically-diagnosed conditions included hypertension (39%), anxiety (30%), obesity (28%), arthritis (26%), hypercholesterolemia (24%), depression (22%), respiratory problems (21%), and diabetes (21%). Higher odds of having ≥2 cardiometabolic conditions (37%) was observed among participants aged ≥50y, with sedentary physical activity, and self-rated fair/poor diet. Odds of having ≥2 chronic diseases (62%) were higher among ≥50y, sleeping difficulties, > 2 h/day television, and self-rated fair/poor diet. Participants obtained (79%) and trusted (92%) health information from physicians. While most participants with a cardiometabolic condition reported receiving medical recommendations on diet (> 73%) and physical activity (> 67%), fewer followed them (< 67% and < 53%, respectively), yet most adhered to medication treatments (> 73%). Participants following medical recommendations were more likely to report healthy vs. poor behaviors (90% vs. 75%, self-rated diet); (73% vs. 56%, physical activity). Conclusions Adults living in Puerto Rico have multiple lifestyles risk factors and high prevalence of chronic diseases, namely cardiometabolic and psychological conditions. Comprehensive epidemiological studies are needed to identify contributors to chronic disease, including lifestyle behaviors. Concerted multi-level public health and clinical programs should be prioritized to help this population improve their health.
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Affiliation(s)
- Josiemer Mattei
- Department of Nutrition, Harvard TH Chan School of Public Health, 665 Huntington Ave, Bldg. 2, Boston, MA, 02115, USA.
| | - Martha Tamez
- Department of Nutrition, Harvard TH Chan School of Public Health, 665 Huntington Ave, Bldg. 2, Boston, MA, 02115, USA
| | - Carlos F Ríos-Bedoya
- Department of Internal Medicine, Hurley Medical Center, Flint, MI, USA.,FDI Clinical Research, San Juan, PR, USA
| | - Rui S Xiao
- Department of Nutrition, Harvard TH Chan School of Public Health, 665 Huntington Ave, Bldg. 2, Boston, MA, 02115, USA
| | - Katherine L Tucker
- Department of Biochemical and Nutritional Sciences, University of Massachusetts, Lowell, MA, USA
| | - José F Rodríguez-Orengo
- FDI Clinical Research, San Juan, PR, USA.,Department of Biochemistry, School of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, USA
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12
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Sikhayeva N, Talzhanov Y, Iskakova A, Dzharmukhanov J, Nugmanova R, Zholdybaeva E, Ramanculov E. Type 2 diabetes mellitus: distribution of genetic markers in Kazakh population. Clin Interv Aging 2018; 13:377-388. [PMID: 29551892 PMCID: PMC5842777 DOI: 10.2147/cia.s156044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. Methods A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy–Weinberg equilibrium. The obtained allele frequencies were further compared to publicly available data from other ethnic populations. Allele frequencies for other (compared) populations were pooled from the haplotype map (HapMap) database. Principal component analysis (PCA), cluster analysis, and multidimensional scaling (MDS) were used for the analysis of genetic relationship between the populations. Results Comparative analysis of allele frequencies of the studied SNPs showed significant differentiation among the studied populations. The Kazakh population was grouped with Asian populations according to the cluster analysis and with the Caucasian populations according to PCA. According to MDS, results of the current study show that the Kazakh population holds an intermediate position between Caucasian and Asian populations. Conclusion A high percentage of population differentiation was observed between Kazakh and world populations. The Kazakh population was clustered with Caucasian populations, and this result may indicate a significant Caucasian component in the Kazakh gene pool.
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Affiliation(s)
- Nurgul Sikhayeva
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan.,Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan
| | - Yerkebulan Talzhanov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Aisha Iskakova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Jarkyn Dzharmukhanov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Raushan Nugmanova
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Elena Zholdybaeva
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan
| | - Erlan Ramanculov
- National Scientific Laboratory of Biotechnology, National Center for Biotechnology, Astana, Kazakhstan.,Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University, Astana, Kazakhstan.,School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
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13
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Wendt FR, Sajantila A, Budowle B. Predicted activity of UGT2B7, ABCB1, OPRM1, and COMT using full-gene haplotypes and their association with the CYP2D6-inferred metabolizer phenotype. Forensic Sci Int Genet 2018; 33:48-58. [DOI: 10.1016/j.fsigen.2017.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/01/2017] [Accepted: 11/22/2017] [Indexed: 12/20/2022]
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Hendry LM, Sahibdeen V, Choudhury A, Norris SA, Ramsay M, Lombard Z. Insights into the genetics of blood pressure in black South African individuals: the Birth to Twenty cohort. BMC Med Genomics 2018; 11:2. [PMID: 29343252 PMCID: PMC5773038 DOI: 10.1186/s12920-018-0321-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/03/2018] [Indexed: 02/08/2023] Open
Abstract
Background Cardiovascular diseases (CVDs) are the leading cause of non-communicable disease deaths globally, with hypertension being a major risk factor contributing to CVDs. Blood pressure is a heritable trait, with relatively few genetic studies having been performed in Africans. This study aimed to identify genetic variants associated with variance in systolic (SBP) and diastolic (DBP) blood pressure in black South Africans. Methods Genotyping was performed using the Metabochip in a subset of participants (mixed sex; median age 17.9) and their adult female caregivers (median age 41.0) from the Birth to Twenty cohort (n = 1947). Data were analysed as a merged dataset (all participants and caregivers together) in GEMMA (v0.94.1) using univariate linear mixed models, incorporating a centered relatedness matrix to account for the relatedness between individuals and with adjustments for age, sex, BMI and principal components of the genotype information. Results Association analysis identified regions of interest in the NOS1AP (DBP: rs112468105 - p = 7.18 × 10−5 and SBP: rs4657181 - p = 4.04 × 10−5), MYRF (SBP: rs11230796 - p = 2.16 × 10−7, rs400075 - p = 2.88 × 10−7) and POC1B (SBP: rs770373 - p = 7.05 × 10−5, rs770374 - p = 9.05 × 10−5) genes and some intergenic regions (DACH1|LOC440145 (DBP: rs17240498 - p = 4.91 × 10−6 and SBP: rs17240498 - p = 2.10 × 10−5) and INTS10|LPL (SBP: rs55830938 - p = 1.30 × 10−5, rs73599609 - p = 5.78 × 10−5, rs73667448 - p = 6.86 × 10−5)). Conclusions The study provided further insight into the contribution of genetic variants to blood pressure in black South Africans. Future functional and replication studies in larger samples are required to confirm the role of the identified loci in blood pressure regulation and whether or not these variants are African-specific. Electronic supplementary material The online version of this article (10.1186/s12920-018-0321-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liesl M Hendry
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa. .,Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Venesa Sahibdeen
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shane A Norris
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, National Health Laboratory Service & University of the Witwatersrand, Johannesburg, South Africa
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15
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Mao L, Fang Y, Campbell M, Southerland WM. Population differentiation in allele frequencies of obesity-associated SNPs. BMC Genomics 2017; 18:861. [PMID: 29126384 PMCID: PMC5681842 DOI: 10.1186/s12864-017-4262-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 11/02/2017] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Obesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms). RESULTS We collected a total of 225 obesity-associated SNPs from a public database. Their population-level allele frequencies were derived based on the genotype data from 1000 Genomes Project (phase 3). We used hypergeometric model to assess whether the effect allele at a given SNP is significantly enriched or depleted in each of the 26 populations surveyed in the 1000 Genomes Project with respect to the overall pooled population. Our results indicate that 195 out of 225 SNPs (86.7%) possess effect alleles significantly enriched or depleted in at least one of the 26 populations. Populations within the same continental group exhibit similar allele enrichment/depletion patterns whereas inter-continental populations show distinct patterns. Among the 225 SNPs, 15 SNPs cluster in the first intron region of the FTO gene, which is a major gene associated with body-mass index (BMI) and fat mass. African populations exhibit much smaller blocks of LD (linkage disequilibrium) among these15 SNPs while European and Asian populations have larger blocks. To estimate the cumulative effect of all variants associated with obesity, we developed the personal composite genetic risk score for obesity. Our results indicate that the East Asian populations have the lowest averages of the composite risk scores, whereas three European populations have the highest averages. In addition, the population-level average of composite genetic risk scores is significantly correlated (R2 = 0.35, P = 0.0060) with obesity prevalence. CONCLUSIONS We have detected substantial population differentiation in allele frequencies of obesity-associated SNPs. The results will help elucidate the genetic basis which may contribute to population disparities in obesity prevalence.
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Affiliation(s)
- Linyong Mao
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059 USA
| | - Yayin Fang
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059 USA
| | - Michael Campbell
- Department of Biology, Howard University, 415 College Street NW, Washington, 20059 DC USA
| | - William M. Southerland
- Department of Biochemistry and Molecular Biology, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059 USA
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16
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Chan DPC, Lee MP, Wong NS, Leung RKK, Naftalin CM, Lee SS. Association of immune recovery with hyperlipidaemia and apolipoprotein gene polymorphisms following highly active antiretroviral therapy in a cohort of Chinese HIV patients. BMJ Open 2016; 6:e010998. [PMID: 27067897 PMCID: PMC4838726 DOI: 10.1136/bmjopen-2015-010998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE To examine the associations between CD4 recovery, dyslipidaemia and apolipoprotein (APO) gene single nucleotide polymorphisms (SNPs) following highly active antiretroviral therapy (HAART). DESIGN Retrospective observational cohort study. SETTING A major HIV care clinic in Hong Kong. PARTICIPANTS 197 Chinese treatment-naïve HIV patients. OUTCOME MEASURES Maximum CD4 count and its rise 2-3 years after HAART initiation and their association with abnormal total cholesterol (TC), triglyceride (TG) and 8 selected APO SNP at multiple time points. RESULTS Before HAART, abnormal levels of TC, TG, high-density lipoprotein cholesterol and low-density lipoprotein cholesterol were detected in 13%, 26%, 59% and 19% of the recruited patients, respectively. APOA5 -1131T>C and c.553G>T were significantly associated with high pre-HAART TG while APOE 2198C>T was correlated with high TG at baseline and/or a rise 2-3 years following HAART initiation. Poor CD4 achievement, defined as the highest CD4 count <350/μL and a net gain of <100/μL, was associated with a low CD4 count ≤200/μL at baseline and a rise of TC beyond 5.17 mmol/L following HAART with or without the use of antilipid agents. Conversely, satisfactory CD4 achievement was associated with APOC3 3238GG genotype. Applying a linear generalised estimating equation, APOA5 -1131T>C was shown to be a predictor of a weaker temporal trend for CD4 response in the presence of a low baseline CD4≤200/μL. CONCLUSIONS Dyslipidaemia plays a predictive role in impacting immunological recovery following HAART, which could be partly explained by the APO gene SNP.
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Affiliation(s)
- Denise Pui-Chung Chan
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Man-Po Lee
- Department of Medicine, Queen Elizabeth Hospital, Kowloon, Hong Kong, People's Republic of China
| | - Ngai-Sze Wong
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Ross Ka-Kit Leung
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Claire Melinda Naftalin
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
| | - Shui-Shan Lee
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
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17
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Lu Y, Liu Y, Li Y, Zhang H, Yu M, Kanu JS, Qiao Y, Tang Y, Zhen Q, Cheng Y. Association of ATP-binding cassette transporter A1 gene polymorphisms with plasma lipid variability and coronary heart disease risk. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:13441-13449. [PMID: 26722555 PMCID: PMC4680500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
OBJECTIVE Our study aimed to investigate the association of ABCA1 polymorphisms with plasma lipid variability and CHD risk in the Chinese Han population. METHODS 754 CHD patients and 760 controls were included in this case-control study. Three SNPs (rs363717, rs4149339, and rs4149338) in ABCA1 3'UTR and one nonsynonymous SNP (rs2230808) in ABCA1 exon 35 were selected and genotyped. The analysis of genetic data was performed using the SNPstats program and the SPSS17.0 software. RESULTS Significant associations were observed between SNP rs363717 and CHD risk under different genetic models before or after Bonferroni corrections (codominant model: OR = 0.70, P = 0.003 for AG vs. AA; dominant model: OR = 0.71, P = 0.003 for GG + AG vs. AA). The nonsynonymous SNP rs2230808 was associated with higher total cholesterol levels (P = 0.047). The GCC haplotype (consisting of alleles of SNPs rs363717, rs4149339, and rs4149338) was associated with a decreased risk of CHD (OR = 0.8, P = 0.027). Three ABCA1 SNPs interacted with high triglyceride levels to increase CHD risk (P values of interactions were 0.010 for rs363717, 0.010 for rs4149339, and 0.020 for rs4149338, respectively). CONCLUSIONS Our results suggest that ABCA1 polymorphisms influence plasma lipid variability and CHD risk. ABCA1 polymorphisms could also modify the effects of plasma lipids on CHD risk.
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Affiliation(s)
- Yuping Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Yawen Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Yong Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Huiping Zhang
- Department of Psychiatry, Yale University School of Medicine, VA Medical Center/116A2950 Campbell Avenue, West Haven, CT 06516, USA
| | - Mingxi Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Joseph Sam Kanu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Yichun Qiao
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Yuan Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Qing Zhen
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin UniversityChangchun 130021, China
| | - Yi Cheng
- The Cardiovascular Center, The First Hospital of Jilin UniversityChangchun 130021, China
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18
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Kurdistani ZK, Saberi S, Talebkhan Y, Oghalaie A, Esmaeili M, Mohajerani N, Bababeik M, Hassanpour P, Barani S, Farjaddoost A, Ebrahimzadeh F, Trejaut J, Mohammadi M. Distribution of cytokine gene single nucleotide polymorphisms among a multi-ethnic Iranian population. Adv Biomed Res 2015; 4:160. [PMID: 26436076 PMCID: PMC4581131 DOI: 10.4103/2277-9175.161809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/21/2015] [Indexed: 02/04/2023] Open
Abstract
Background: Cytokine gene single nucleotide polymorphisms (SNPs) are widely used to study susceptibility to complex diseases and as a tool for anthropological studies. Materials and Methods: To investigate cytokine SNPs in an Iranian multi-ethnic population, we have investigated 10 interleukin (IL) SNPs (IL-1β (C-511T, T-31C), IL-2 (G-384T), IL-4 (C-590T), IL-6 (G-174C), IL-8 (T-251A), IL-10 (G-1082A, C-819T, C-592A) and tumor necrosis factor-alpha (TNF-α) (G-308A) in 415 Iranian subjects comprising of 6 different ethnicities. Allelic and genotypic frequencies as well as Hardy-Weinberg equilibrium (HWE) were calculated by PyPop software. Population genetic indices including observed heterozygosity (Ho), expected heterozygosity (He), fixation index (FIS), the effective number of alleles (Ne) and polymorphism information content (PIC) were derived using Popgene 32 software. Multidimensional scaling (MDS) was constructed using Reynold's genetic distance obtained from the frequencies of cytokine gene polymorphism. Results: Genotypic distributions were consistent with the HWE assumptions, except for 3 loci (IL-4-590, IL-8-251 and IL-10-819) in Fars and 4 loci (IL-4-590, IL-6-174, IL-10-1082 and TNF-α-308) in Turks. Pairwise assessment of allelic frequencies, detected differences at the IL-4-590 locus in Gilakis versus Kurds (P = 0.028) and Lurs (P = 0.022). Mazanis and Gilakis displayed the highest (Ho= 0.50 ± 0.24) and lowest (Ho= 0.34 ± 0.16) mean observed heterozygosity, respectively. Conclusions: MDS analysis of our study population, in comparison with others, revealed that Iranian ethnicities except Kurds and Mazanis were tightly located within a single cluster with closest genetic affinity to Europeans.
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Affiliation(s)
- Zana Karimi Kurdistani
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran ; Department of Molecular Genetics, Fars Science and Research Branch, Islamic Azad University, Shiraz, Iran
| | - Samaneh Saberi
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Yeganeh Talebkhan
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Akbar Oghalaie
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Maryam Esmaeili
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Nazanin Mohajerani
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Maryam Bababeik
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Parisa Hassanpour
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Shaghik Barani
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Ameneh Farjaddoost
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | - Fatemeh Ebrahimzadeh
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
| | | | - Marjan Mohammadi
- HPGC Group, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran
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19
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Valera B, Sohani Z, Rana A, Poirier P, Anand SS. The ethnoepidemiology of obesity. Can J Cardiol 2014; 31:131-41. [PMID: 25661548 DOI: 10.1016/j.cjca.2014.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/02/2014] [Accepted: 10/06/2014] [Indexed: 12/25/2022] Open
Abstract
The prevalence of overweight and obesity varies significantly across ethnic groups and among aboriginal people in Canada and appears to be increasing overall in children and youth, which will have significant health consequences in the future. Individual health behaviours, genetic predisposition, and community-level factors all contribute to the high burden of overweight and obesity across communities in Canada. Preliminary studies indicate that individuals who live in neighbourhoods in Canada with increased walkability, fewer fast food outlets, and higher socioeconomic status have lower rates of overweight/obesity when compared with other neighbourhoods. However, more research is required to understand the impact of community level factors on overweight/obesity trends in Canadian ethnic groups, including children and youth, and aboriginal people.
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Affiliation(s)
- Beatriz Valera
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada
| | - Zahra Sohani
- Population Genomics Program, Department of Clinical Epidemiology & Biostatistics, Hamilton, Ontario, Canada; Chanchlani Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Ayesha Rana
- Population Genomics Program, Department of Clinical Epidemiology & Biostatistics, Hamilton, Ontario, Canada; Chanchlani Research Centre, McMaster University, Hamilton, Ontario, Canada
| | - Paul Poirier
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Québec, Canada; Faculté de pharmacie de l'Université Laval, Québec, Québec, Canada
| | - Sonia S Anand
- Population Genomics Program, Department of Clinical Epidemiology & Biostatistics, Hamilton, Ontario, Canada; Chanchlani Research Centre, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada.
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20
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Sohani ZN, Deng WQ, Pare G, Meyre D, Gerstein HC, Anand SS. Does genetic heterogeneity account for the divergent risk of type 2 diabetes in South Asian and white European populations? Diabetologia 2014; 57:2270-81. [PMID: 25145545 PMCID: PMC4180911 DOI: 10.1007/s00125-014-3354-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/22/2014] [Indexed: 12/16/2022]
Abstract
AIMS/HYPOTHESIS South Asians are up to four times more likely to develop type 2 diabetes than white Europeans. It is postulated that the higher prevalence results from greater genetic risk. To evaluate this hypothesis, we: (1) systematically reviewed the literature for single nucleotide polymorphisms (SNPs) predisposing to type 2 diabetes in South Asians; (2) compared risk estimates, risk alleles and risk allele frequencies of predisposing SNPs between South Asians and white Europeans; and (3) tested the association of novel SNPs discovered from South Asians in white Europeans. METHODS MEDLINE, Embase, the Cumulative Index to Nursing and Allied Health Literature (CINAHL) and the Cochrane registry were searched for studies of genetic variants associated with type 2 diabetes in South Asians. Meta-analysis estimates for common and novel bi-allelic SNPs in South Asians were compared with white Europeans from the DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) consortium. The population burden from predisposing SNPs was assessed using a genotype score. RESULTS Twenty-four SNPs from 21 loci were associated with type 2 diabetes in South Asians after meta-analysis. The majority of SNPs increase odds of the disorder by 15-35% per risk allele. No substantial differences appear to exist in risk estimates between South Asians and white Europeans from SNPs common to both groups, and the population burden also does not differ. Eight of the 24 are novel SNPs discovered from South Asian genome-wide association studies, some of which show nominal associations with type 2 diabetes in white Europeans. CONCLUSIONS/INTERPRETATION Based on current literature there is no strong evidence to indicate that South Asians possess a greater genetic risk of type 2 diabetes than white Europeans.
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Affiliation(s)
- Zahra N Sohani
- Population Genomics Program, Department of Clinical Epidemiology and Biostatistics, McMaster University, 1280 Main St W, Hamilton, ON, Canada, L8S 4L8
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21
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Li YR, Keating BJ. Trans-ethnic genome-wide association studies: advantages and challenges of mapping in diverse populations. Genome Med 2014; 6:91. [PMID: 25473427 PMCID: PMC4254423 DOI: 10.1186/s13073-014-0091-5] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies (GWASs) are the method most often used by geneticists to interrogate the human genome, and they provide a cost-effective way to identify the genetic variants underpinning complex traits and diseases. Most initial GWASs have focused on genetically homogeneous cohorts from European populations given the limited availability of ethnic minority samples and so as to limit population stratification effects. Transethnic studies have been invaluable in explaining the heritability of common quantitative traits, such as height, and in examining the genetic architecture of complex diseases, such as type 2 diabetes. They provide an opportunity for large-scale signal replication in independent populations and for cross-population meta-analyses to boost statistical power. In addition, transethnic GWASs enable prioritization of candidate genes, fine-mapping of functional variants, and potentially identification of SNPs associated with disease risk in admixed populations, by taking advantage of natural differences in genomic linkage disequilibrium across ethnically diverse populations. Recent efforts to assess the biological function of variants identified by GWAS have highlighted the need for large-scale replication, meta-analyses and fine-mapping across worldwide populations of ethnically diverse genetic ancestries. Here, we review recent advances and new approaches that are important to consider when performing, designing or interpreting transethnic GWASs, and we highlight existing challenges, such as the limited ability to handle heterogeneity in linkage disequilibrium across populations and limitations in dissecting complex architectures, such as those found in recently admixed populations.
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Affiliation(s)
- Yun R Li
- />The Center for Applied Genomics, 1,016 Abramson Building, The Children’s Hospital of Philadelphia, Philadelphia, 19104 PA USA
- />Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104 PA USA
| | - Brendan J Keating
- />The Center for Applied Genomics, 1,016 Abramson Building, The Children’s Hospital of Philadelphia, Philadelphia, 19104 PA USA
- />Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104 PA USA
- />Department of Surgery, Division of Transplantation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104 PA USA
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Parnell LD, Blokker BA, Dashti HS, Nesbeth PD, Cooper BE, Ma Y, Lee YC, Hou R, Lai CQ, Richardson K, Ordovás JM. CardioGxE, a catalog of gene-environment interactions for cardiometabolic traits. BioData Min 2014; 7:21. [PMID: 25368670 PMCID: PMC4217104 DOI: 10.1186/1756-0381-7-21] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/18/2014] [Indexed: 12/29/2022] Open
Abstract
Background Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions are one of these contributors and in the guise of diet and physical activity are important modulators of cardiometabolic phenotypes and ensuing diseases. Results We mined the scientific literature to collect GxE interactions from 386 publications for blood lipids, glycemic traits, obesity anthropometrics, vascular measures, inflammation and metabolic syndrome, and introduce CardioGxE, a gene-environment interaction resource. We then analyzed the genes and SNPs supporting cardiometabolic GxEs in order to demonstrate utility of GxE SNPs and to discern characteristics of these important genetic variants. We were able to draw many observations from our extensive analysis of GxEs. 1) The CardioGxE SNPs showed little overlap with variants identified by main effect GWAS, indicating the importance of environmental interactions with genetic factors on cardiometabolic traits. 2) These GxE SNPs were enriched in adaptation to climatic and geographical features, with implications on energy homeostasis and response to physical activity. 3) Comparison to gene networks responding to plasma cholesterol-lowering or regression of atherosclerotic plaques showed that GxE genes have a greater role in those responses, particularly through high-energy diets and fat intake, than do GWAS-identified genes for the same traits. Other aspects of the CardioGxE dataset were explored. Conclusions Overall, we demonstrate that SNPs supporting cardiometabolic GxE interactions often exhibit transcriptional effects or are under positive selection. Still, not all such SNPs can be assigned potential functional or regulatory roles often because data are lacking in specific cell types or from treatments that approximate the environmental factor of the GxE. With research on metabolic related complex disease risk embarking on genome-wide GxE interaction tests, CardioGxE will be a useful resource.
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Affiliation(s)
- Laurence D Parnell
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Britt A Blokker
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Hassan S Dashti
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Paula-Dene Nesbeth
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Brittany Elle Cooper
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Yiyi Ma
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Yu-Chi Lee
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Ruixue Hou
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Chao-Qiang Lai
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - Kris Richardson
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
| | - José M Ordovás
- JM-USDA Human Nutrition Research Center on Aging at Tufts University, 711 Washington Street, Boston, MA 02111, USA
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Jamal-Allial A, Griffith JL, Tucker KL. The longitudinal association of vitamin D serum concentrations & adiposity phenotype. J Steroid Biochem Mol Biol 2014; 144 Pt A:185-8. [PMID: 24333795 PMCID: PMC4055547 DOI: 10.1016/j.jsbmb.2013.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/01/2013] [Accepted: 12/04/2013] [Indexed: 11/21/2022]
Abstract
Several cross-sectional studies have reported on the association between serum 25-hydroxy vitamin D concentrations (25(OH)D) and body mass index (BMI). We examined the longitudinal effect of BMI on serum 25(OH)D concentrations among 866 Puerto Rican adults living in the Greater Boston area: 246 men and 620 women, aged 45-75 years at baseline and 2 year. Our analyses showed negative correlations at two time points between BMI and serum 25(OH)D concentrations. The multivariate analysis showed that when predicting the change of serum 25(OH)D concentrations, baseline-BMI had significant inverse association (P<0.04) controlling for age, sex, and baseline-BMI. This association remained significant after adjusting for vitamin D supplement use, smoking, miles walked/day and alcohol intake (P<0.01). In conclusion, the major findings of the present study are obesity (1) was inversely associated with 25(OH)D at baseline; (2) with the change in serum 25(OH)D at 2-year in this population of older Puerto Rican adults living in the Boston area. This article is part of a Special Issue entitled '16th Vitamin D Workshop'.
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Affiliation(s)
- Aziza Jamal-Allial
- Bouvé College of Health Sciences. Northeastern University, Boston, MA 02115, USA.
| | - John L Griffith
- Bouvé College of Health Sciences. Northeastern University, Boston, MA 02115, USA
| | - Katherine L Tucker
- Clinical Laboratory & Nutritional Sciences, University of Massachusetts Lowell, Lowell, MA, USA
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Feng X, Tucker KL, Parnell LD, Shen J, Lee YC, Ordovás JM, Ling WH, Lai CQ. Insulin receptor substrate 1 (IRS1) variants confer risk of diabetes in the Boston Puerto Rican Health Study. Asia Pac J Clin Nutr 2013; 22:150-9. [PMID: 23353623 DOI: 10.6133/apjcn.2013.22.1.09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Published data concerning associations between IRS1 variants and type 2 diabetes and related traits have been inconsistent. We examined the relationship between common variants in IRS1, type 2 diabetes, and related traits including insulin resistance, hyperglycemia and DNA damage in the Boston Puerto Rican Health Study. METHODS We genotyped six common IRS1 variants in an adult Puerto Rican population (n=1132) and tested for association with risk of type 2 diabetes and related traits. RESULTS SNPs rs934167 and rs1801123 showed significant association with fasting glucose concentrations (p = 0.005 and p = 0.016, respectively) and rs934167 showed significant association with plasma insulin levels (p = 0.005). Carriers of the rs934167 minor allele had significantly higher HOMA-IR and lower QUICKI (p = 0.001 and p = 0.001, respectively), and a 40% and 58% greater likelihood of being hyperglycaemic or hyperinsulinemic (OR = 1.40 and 1.58; p = 0.013 and 0.002, respectively). However, they exhibited only a marginally significant trend towards having type 2 diabetes (OR=1.27, p = 0.077). Furthermore, carriers of the haplotype C-T of the rs934167 and rs1801123 minor alleles showed consistent patterns of associations after correction for multiple testing. In addition, the G972R (rs1801278) minor allele was significantly associated with higher urinary 8-OHdG concentrations (p = 0.020) and plasma CRP levels (p = 0.035). CONCLUSIONS Our results support IRS1 variants associated with type 2 diabetes risk in adult Puerto Ricans. Moreover, we report the novel finding that IRS1 variant G972R (rs1801278) may contribute to oxidative DNA damage and inflammation.
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Affiliation(s)
- Xiang Feng
- Departmennt of Nutrition, School of Public Health, Sun Yat-Sen University, Guangzhou, China
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Grimsby JL, Porneala BC, Vassy JL, Yang Q, Florez JC, Dupuis J, Liu T, Yesupriya A, Chang MH, Ned RM, Dowling NF, Khoury MJ, Meigs JB. Race-ethnic differences in the association of genetic loci with HbA1c levels and mortality in U.S. adults: the third National Health and Nutrition Examination Survey (NHANES III). BMC MEDICAL GENETICS 2012; 13:30. [PMID: 22540250 PMCID: PMC3433372 DOI: 10.1186/1471-2350-13-30] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 04/27/2012] [Indexed: 12/04/2022]
Abstract
Background Hemoglobin A1c (HbA1c) levels diagnose diabetes, predict mortality and are associated with ten single nucleotide polymorphisms (SNPs) in white individuals. Genetic associations in other race groups are not known. We tested the hypotheses that there is race-ethnic variation in 1) HbA1c-associated risk allele frequencies (RAFs) for SNPs near SPTA1, HFE, ANK1, HK1, ATP11A, FN3K, TMPRSS6, G6PC2, GCK, MTNR1B; 2) association of SNPs with HbA1c and 3) association of SNPs with mortality. Methods We studied 3,041 non-diabetic individuals in the NHANES (National Health and Nutrition Examination Survey) III. We stratified the analysis by race/ethnicity (NHW: non-Hispanic white; NHB: non-Hispanic black; MA: Mexican American) to calculate RAF, calculated a genotype score by adding risk SNPs, and tested associations with SNPs and the genotype score using an additive genetic model, with type 1 error = 0.05. Results RAFs varied widely and at six loci race-ethnic differences in RAF were significant (p < 0.0002), with NHB usually the most divergent. For instance, at ATP11A, the SNP RAF was 54% in NHB, 18% in MA and 14% in NHW (p < .0001). The mean genotype score differed by race-ethnicity (NHW: 10.4, NHB: 11.0, MA: 10.7, p < .0001), and was associated with increase in HbA1c in NHW (β = 0.012 HbA1c increase per risk allele, p = 0.04) and MA (β = 0.021, p = 0.005) but not NHB (β = 0.007, p = 0.39). The genotype score was not associated with mortality in any group (NHW: OR (per risk allele increase in mortality) = 1.07, p = 0.09; NHB: OR = 1.04, p = 0.39; MA: OR = 1.03, p = 0.71). Conclusion At many HbA1c loci in NHANES III there is substantial RAF race-ethnic heterogeneity. The combined impact of common HbA1c-associated variants on HbA1c levels varied by race-ethnicity, but did not influence mortality.
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Affiliation(s)
- Jonna L Grimsby
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
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CARPENTER SL, MICHAEL SOUCIE J, STERNER S, PRESLEY R. Increased prevalence of inhibitors in Hispanic patients with severe haemophilia A enrolled in the Universal Data Collection database. Haemophilia 2012; 18:e260-5. [DOI: 10.1111/j.1365-2516.2011.02739.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mattei J, Demissie S, Tucker KL, Ordovas JM. The APOA1/C3/A4/A5 cluster and markers of allostatic load in the Boston Puerto Rican Health Study. Nutr Metab Cardiovasc Dis 2011; 21:862-870. [PMID: 20674306 PMCID: PMC3004022 DOI: 10.1016/j.numecd.2010.02.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 02/08/2010] [Accepted: 02/15/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND AIMS The APOA1/C3/A4/A5 cluster encodes key regulators of plasma lipids. Interactions between dietary factors and single nucleotide polymorphisms (SNPs) in the cluster have been reported. Allostatic load, or physiological dysregulation in response to stress, has been implicated in shaping health disparities in ethnic groups. We aimed to determine the association between polymorphisms in the APOA1/C3/A4/A5 cluster with allostatic load parameters, alone, and in interaction with dietary fat intake in Puerto Ricans adults. METHODS AND RESULTS Data on demographic and anthropometric measures, lifestyle behaviors, and medication use, as well as blood and urine samples for biomarker analysis, were obtained from participants of the Boston Puerto Rican Health Study (n=821, age 45-75 y). The 12 polymorphisms analyzed were not associated with allostatic load parameters. Significant interactions were observed between dietary fat intake and APOA1-75 in association with waist circumference (WC), (P=0.005), APOC3-640 with diastolic blood pressure (DBP), (P=0.003), and APOA4 N147S and APOA5 S19W with systolic blood pressure (SBP), (P=0.001 and P=0.002, respectively). Puerto Ricans homozygous for the common allele of APOA1-75, APOA4 N147S and APOA5 S19W had lower WC and SBP when consuming <31% of total fat from energy, than participants with the minor allele. Participants heterozygous for APOC3-640 had lower DBP at total fat intake ≥31% from energy. CONCLUSION SNPs in APOA1/C3/A4/A5, as modulated by dietary fat intake, appear to influence allostatic load parameters in Puerto Ricans.
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Affiliation(s)
- J Mattei
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA, 02111 USA
- Friedman School of Nutrition Science and Policy at Tufts University, Boston, MA, 02111 USA
| | - S Demissie
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, 02108 USA
| | - KL Tucker
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA, 02111 USA
- Friedman School of Nutrition Science and Policy at Tufts University, Boston, MA, 02111 USA
| | - JM Ordovas
- Jean Mayer US Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA, 02111 USA
- Friedman School of Nutrition Science and Policy at Tufts University, Boston, MA, 02111 USA
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Genotype and ancestry modulate brain's DAT availability in healthy humans. PLoS One 2011; 6:e22754. [PMID: 21826203 PMCID: PMC3149615 DOI: 10.1371/journal.pone.0022754] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/30/2011] [Indexed: 12/18/2022] Open
Abstract
The dopamine transporter (DAT) is a principal regulator of dopaminergic neurotransmission and its gene (the SLC6A3) is a strong biological candidate gene for various behavioral- and neurological disorders. Intense investigation of the link between the SLC6A3 polymorphisms and behavioral phenotypes yielded inconsistent and even contradictory results. Reliance on objective brain phenotype measures, for example, those afforded by brain imaging, might critically improve detection of DAT genotype-phenotype association. Here, we tested the relationship between the DAT brain availability and the SLC6A3 genotypes using an aggregate sample of 95 healthy participants of several imaging studies. These studies employed positron emission tomography (PET) with [¹¹C]cocaine wherein the DAT availability was estimated as Bmax/Kd; while the genotype values were obtained on two repeat polymorphisms--3-UTR- and intron 8--VNTRs. The main findings are the following: 1) both polymorphisms analyzed as single genetic markers and in combination (haplotype) modulate DAT density in midbrain; 2) ethnic background and age influence the strength of these associations; and 3) age-related changes in DAT availability differ in the 3-UTR and intron 8--genotype groups.
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Oxenkrug G, Tucker KL, Requintina P, Summergrad P. Neopterin, a Marker of Interferon-Gamma-Inducible Inflammation, Correlates with Pyridoxal-5'-Phosphate, Waist Circumference, HDL-Cholesterol, Insulin Resistance and Mortality Risk in Adult Boston Community Dwellers of Puerto Rican Origin. ACTA ACUST UNITED AC 2011; 3:48-52. [PMID: 22308202 DOI: 10.1166/ajnn.2011.1024] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Interferon-gamma (IFNG), a pro-inflammatory cytokine, increases concentrations of neopterin, a stable pteridine derivative, due to IFNG-induced transcriptional activation of the rate-limiting enzyme of pteridines biosynthesis. Neopterin concentrations were reported to correlate with metabolic syndrome (MetS), the cause of increased mortality risk, in subjects of European ancestry. We were interested to assessed neopterin correlations with clinical markers of MetS and mortality risk in population with a different genetic background, i.e., Puerto Ricans residents of Boston. Since inflammation is associated with pyridoxal-5'-phosphate (PLP) deficiency, we assessed correlations of neopterin with PLP. Plasma neopterin concentrations were evaluated in 592 adult (45-75 years of age) participants of Boston Puerto Rican Health Study. Neopterin concentrations correlated with abdominal obesity (waist circumference, r = 0.085, p < 0.038), HDL cholesterol (r = -0.15, p < 0.0001), insulin resistance (HOMA-IR, r = 0.08, P < 0.03), and plasma pyridoxal-5'-phosphate (PLP (r = -0.13, P = 0.002). Neopterin concentrations of >16 nmol/L at baseline were associated with the increased risk of mortality in 113 subjects followed for 6 years. The present results together with previously reported data in European subjects suggest a similar pattern of neopterin correlations with MetS and mortality risk in population with different genetic backgrounds. PLP is a cofactor of IFNG-induced key enzymes of tryptophan-kynurenine metabolism. Since PLP deficiency is associated with the increased production of diabetogenic kynurenine derivative, xanthurenic acid, our results suggest that up-regulated IFNG production might contribute to the development of insulin resistance. Assessment of neopterin concentrations might help to monitor the activity of IFNG-inducible inflammation associated with aging-associated medical and psychiatric disorders.
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Affiliation(s)
- G Oxenkrug
- Psychiatry and Inflammation Program, Department of Psychiatry, Tufts University/Tufts Medical Center, Boston, MA 02111, USA
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Abstract
PURPOSE OF REVIEW Cachexia is a progressive deterioration of body habitus associated with chronic diseases. The finding that only a proportion of patients with chronic disease develop cachexia has prompted studies looking for genetic polymorphisms that may underlie differential susceptibility. The aim of this review is to explore how inflammation and gene polymorphisms influence susceptibility to cachexia. RECENT FINDINGS There has been evidence that certain cytokine gene polymorphisms are associated with cachexia. However, only the IL10 -1082 G allele, which is associated with an increased risk of developing cachexia has been replicated in more than one study. Variation in genes outwith inflammation pathways (e.g. genes involved in protein metabolism) is also likely to contribute the susceptibility of developing cachexia. The insertion/deletion angiotensin converting enzyme (ACE) gene polymorphism has recently been linked with lower lean body mass in cancer patients with cachexia. SUMMARY Although there is an increasing body of evidence of genetic susceptibility to cachexia, most studies so far have only focussed on a small number of polymorphisms and have small sample sizes. Large-scale candidate gene studies or genome-wide association studies are required to further elucidate the link between genotype and cachexia.
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Casto AM, Feldman MW. Genome-wide association study SNPs in the human genome diversity project populations: does selection affect unlinked SNPs with shared trait associations? PLoS Genet 2011; 7:e1001266. [PMID: 21253569 PMCID: PMC3017115 DOI: 10.1371/journal.pgen.1001266] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 12/02/2010] [Indexed: 01/11/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human fitness, including many immunological, metabolic, cardiovascular, and behavioral phenotypes. Given the polygenic nature of complex traits, selection may exert its influence on them by altering allele frequencies at many associated loci, a possibility which has yet to be explored empirically. Here we use 38 different measures of allele frequency variation and 8 iHS scores to characterize over 1,300 GWAS SNPs in 53 globally distributed human populations. We apply these same techniques to evaluate SNPs grouped by trait association. We find that groups of SNPs associated with pigmentation, blood pressure, infectious disease, and autoimmune disease traits exhibit unusual allele frequency patterns and elevated iHS scores in certain geographical locations. We also find that GWAS SNPs have generally elevated scores for measures of allele frequency variation and for iHS in Eurasia and East Asia. Overall, we believe that our results provide evidence for selection on several complex traits that has caused changes in allele frequencies and/or elevated iHS scores at a number of associated loci. Since GWAS SNPs collectively exhibit elevated allele frequency measures and iHS scores, selection on complex traits may be quite widespread. Our findings are most consistent with this selection being either positive or negative, although the relative contributions of the two are difficult to discern. Our results also suggest that trait-SNP associations identified in Eurasian samples may not be present in Africa, Oceania, and the Americas, possibly due to differences in linkage disequilibrium patterns. This observation suggests that non-Eurasian and non-East Asian sample populations should be included in future GWAS.
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Affiliation(s)
- Amanda M Casto
- Department of Genetics, Stanford University, Stanford, California, United States of America.
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Oxenkrug GF. Interferon-gamma-inducible kynurenines/pteridines inflammation cascade: implications for aging and aging-associated psychiatric and medical disorders. J Neural Transm (Vienna) 2011; 118:75-85. [PMID: 20811799 PMCID: PMC3026891 DOI: 10.1007/s00702-010-0475-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 08/23/2010] [Indexed: 12/20/2022]
Abstract
This review of literature and our data suggests that up-regulated production of interferon-gamma (IFNG) in periphery and brain triggers a merger of tryptophan (TRY)-kynurenine (KYN) and guanine-tetrahydrobiopterin (BH4) metabolic pathways into inflammation cascade involved in aging and aging-associated medical and psychiatric disorders (AAMPD) (metabolic syndrome, depression, vascular cognitive impairment). IFNG-inducible KYN/pteridines inflammation cascade is characterized by up-regulation of nitric oxide synthase (NOS) activity (induced by KYN) and decreased formation of NOS cofactor, BH4, that results in uncoupling of NOS that shifting arginine from NO to superoxide anion production. Superoxide anion and free radicals among KYN derivatives trigger phospholipase A2-arachidonic acid cascade associated with AAMPD. IFNG-induced up-regulation of indoleamine 2,3-dioxygenase (IDO), rate-limiting enzyme of TRY-KYN pathway, decreases TRY conversion into serotonin (substrate of antidepressant effect) and increases production of KYN associated with diabetes [xanthurenic acid (XA)], anxiety (KYN), psychoses and cognitive impairment (kynurenic acid). IFNG-inducible KYN/pteridines inflammation cascade is impacted by IFNG (+874) T/A genotypes, encoding cytokine production. In addition to literature data on KYN/TRY ratio (IDO activity index), we observe neopterin levels (index of activity of rate-limiting enzyme of guanine-BH4 pathway) to be higher in carriers of high (T) than of low (A) producers alleles; and to correlate with AAMPD markers (e.g., insulin resistance, body mass index, mortality risk), and with IFN-alpha-induced depression in hepatitis C patients. IFNG-inducible cascade is influenced by environmental factors (e.g., vitamin B6 deficiency increases XA formation) and by pharmacological agents; and might offer new approaches for anti-aging and anti-AAMPD interventions.
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Affiliation(s)
- Gregory F Oxenkrug
- Psychiatry and Inflammation Program, Department of Psychiatry, Tufts University/Tufts Medical Center, Boston, MA, USA.
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Current World Literature. Curr Opin Support Palliat Care 2010; 4:293-304. [DOI: 10.1097/spc.0b013e328340e983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Tucker KL, Mattei J, Noel SE, Collado BM, Mendez J, Nelson J, Griffith J, Ordovas JM, Falcon LM. The Boston Puerto Rican Health Study, a longitudinal cohort study on health disparities in Puerto Rican adults: challenges and opportunities. BMC Public Health 2010; 10:107. [PMID: 20193082 PMCID: PMC2848197 DOI: 10.1186/1471-2458-10-107] [Citation(s) in RCA: 178] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 03/01/2010] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The Boston Puerto Rican Health Study is an ongoing longitudinal cohort study designed to examine the role of psychosocial stress on presence and development of allostatic load and health outcomes in Puerto Ricans, and potential modification by nutritional status, genetic variation, and social support. METHODS Self-identified Puerto Ricans, aged 45-75 years and residing in the Boston, MA metro area, were recruited through door-to-door enumeration and community approaches. Participants completed a comprehensive set of questionnaires and tests. Blood, urine and salivary samples were extracted for biomarker and genetic analysis. Measurements are repeated at a two-year follow-up. RESULTS A total of 1500 eligible participants completed baseline measurements, with nearly 80% two-year follow-up retention. The majority of the cohort is female (70%), and many have less than 8th grade education (48%), and fall below the poverty level (59%). Baseline prevalence of health conditions is high for this age range: considerable physical (26%) and cognitive (7%) impairment, obesity (57%), type 2 diabetes (40%), hypertension (69%), arthritis (50%) and depressive symptomatology (60%). CONCLUSIONS The enrollment of minority groups presents unique challenges. This report highlights approaches to working with difficult to reach populations, and describes some of the health issues and needs of Puerto Rican older adults. These results may inform future studies and interventions aiming to improve the health of this and similar communities.
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Affiliation(s)
- Katherine L Tucker
- USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
- Northeastern University, Boston, Massachusetts, USA
| | - Josiemer Mattei
- USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, USA
| | - Sabrina E Noel
- USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, USA
| | - Bridgette M Collado
- USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Jackie Mendez
- USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Jason Nelson
- Tufts Medical Center, Boston, Massachusetts, USA
| | | | - Jose M Ordovas
- USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, Massachusetts, USA
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Mattei J, Demissie S, Tucker KL, Ordovas JM. Apolipoprotein A5 polymorphisms interact with total dietary fat intake in association with markers of metabolic syndrome in Puerto Rican older adults. J Nutr 2009; 139:2301-8. [PMID: 19828688 PMCID: PMC2777477 DOI: 10.3945/jn.109.109900] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
APOA5 -1131T > C and S19W single nucleotide polymorphisms (SNP) have been consistently associated with plasma lipid concentration and metabolic syndrome (MetS), alone and in modulation by dietary factors. Puerto Ricans have a high prevalence of metabolic conditions and high minor allele frequency for these SNP, suggesting a possible role in disease for this population. We aimed to determine the association of APOA5 -1131T > C and S19W with plasma lipids and markers of MetS, alone and in interaction with total fat intake, as a percent of total energy intake, in Puerto Ricans. Anthropometric and demographic data, FFQ, and blood samples were collected at baseline from participants in the Boston Puerto Rican Health Study (n = 802, 45-75 y). APOA5 S19W was associated with plasma HDL cholesterol (HDL-C) (P = 0.044); minor allele carriers had lower HDL-C [1.12 +/- 0.03 (mean +/- SE)] than those with the common variant (1.18 +/- 0.01 mmol/L), even after adjustment for plasma triglycerides (TG) (P = 0.012). Neither polymorphism was associated with TG or other lipids. Interaction of the -1131T > C SNP with total fat energy intake was observed for plasma TG (P = 0.032) and total cholesterol (P = 0.034). APOA5 S19W interacted with total fat intake in association with systolic (P = 0.002) and diastolic (P = 0.007) blood pressure. Neither SNP was associated with MetS in the overall analysis or after stratifying by total energy intake as fat. In conclusion, Puerto Ricans present a distinctive lipid profile in association with APOA5 polymorphisms. Dietary fat intake seems to modulate these associations. The results contribute to the understanding of health disparities in this population.
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Affiliation(s)
- Josiemer Mattei
- Jean Mayer USDA Human Nutrition Research Center on Aging and Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111; and Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118
| | - Serkalem Demissie
- Jean Mayer USDA Human Nutrition Research Center on Aging and Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111; and Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118
| | - Katherine L. Tucker
- Jean Mayer USDA Human Nutrition Research Center on Aging and Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111; and Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118
| | - Jose M. Ordovas
- Jean Mayer USDA Human Nutrition Research Center on Aging and Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111; and Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118,To whom correspondence should be addressed. E-mail:
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