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Quantile-specific heritability of total cholesterol and its pharmacogenetic and nutrigenetic implications. Int J Cardiol 2020; 327:185-192. [PMID: 33296721 DOI: 10.1016/j.ijcard.2020.11.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND "Quantile-dependent expressivity" occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g. cholesterol) is high or low relative to its distribution. We have previously shown that the effect of a 52-SNP genetic-risk score was 3-fold larger at the 90th percentile of the total cholesterol distribution than at its 10th percentile. The objective of this study is to assess quantile-dependent expressivity for total cholesterol in 7006 offspring with parents and 2112 sibships from Framingham Heart Study. METHODS Quantile-specific heritability (h2) was estimated as twice the offspring-parent regression slope as robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples. RESULTS Quantile-specific h2 increased linearly with increasing percentiles of the offspring's cholesterol distribution (P = 3.0 × 10-9), i.e. h2 = 0.38 at the 10th percentile, h2 = 0.45 at the 25th percentile, h2 = 0.52 at the 50th, h2 = 0.61 at the 75th percentile, and h2 = 0.65 at the 90th percentile of the total cholesterol distribution. Average h2 decreased from 0.55 to 0.34 in 3564 offspring who started cholesterol-lowering medications, but this was attributable to quantile-dependent expressivity and the offspring's 0.94 mmol/L average drop in total cholesterol. Quantile-dependent expressivity likely explains the reported effect of the CELSR2/PSRC1/SORT1 rs646776 and APOE rs7412 gene loci on statin efficacy. Specifically, a smaller genetic effect size at the lower (post-treatment) than higher (pre-treatment) cholesterol concentrations mandates that the trajectories of the genotypes cannot move in parallel when cholesterol is decreased pharmacologically. CONCLUSION Cholesterol concentrations exhibit quantile-dependent expressivity, which may provide an alternative interpretation to pharmacogenetic and nutrigenetic interactions.
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Kang M, Sung J. A genome-wide search for gene-by-obesity interaction loci of dyslipidemia in Koreans shows diverse genetic risk alleles. J Lipid Res 2019; 60:2090-2101. [PMID: 31662442 DOI: 10.1194/jlr.p119000226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/21/2019] [Indexed: 11/20/2022] Open
Abstract
Dyslipidemia is a well-established risk factor for CVD. Studies suggest that similar fat accumulation in a given population might result in different levels of dyslipidemia risk among individuals; for example, despite similar or leaner body composition compared with Caucasians, Asians of Korean descent experience a higher prevalence of dyslipidemia. These variations imply a possible role of gene-obesity interactions on lipid profiles. Genome-wide association studies have identified more than 500 loci regulating plasma lipids, but the interaction structure between genes and obesity traits remains unclear. We hypothesized that some loci modify the effects of obesity on dyslipidemia risk and analyzed extensive gene-environment interactions (G×Es) at genome-wide levels to search for replicated gene-obesity interactive SNPs. In four Korean cohorts (n = 18,025), we identified and replicated 20 gene-obesity interactions, including novel variants (SCN1A and SLC12A8) and known lipid-associated variants (APOA5, BUD13, ZNF259, and HMGCR). When we estimated the additional heritability of dyslipidemia by considering G×Es, the gain was substantial for triglycerides (TGs) but mild for LDL cholesterol (LDL-C) and total cholesterol (Total-C); the interaction explained up to 18.7% of TG, 2.4% of LDL-C, and 1.9% of Total-C heritability associated with waist-hip ratio. Our findings suggest that some individuals are prone to develop abnormal lipid profiles, particularly with regard to TGs, even with slight increases in obesity indices; ethnic diversities in the risk alleles might partly explain the differential dyslipidemia risk between populations. Research about these interacting variables may facilitate knowledge-based approaches to personalize health guidelines according to individual genetic profiles.
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Affiliation(s)
- Moonil Kang
- Division of Genome and Health Big Data, Department of Public Health Sciences Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Joohon Sung
- Division of Genome and Health Big Data, Department of Public Health Sciences Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea .,Institute of Health and Environment, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
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Adult onset asthma and interaction between genes and active tobacco smoking: The GABRIEL consortium. PLoS One 2017; 12:e0172716. [PMID: 28253294 PMCID: PMC5333809 DOI: 10.1371/journal.pone.0172716] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/08/2017] [Indexed: 12/03/2022] Open
Abstract
Background Genome-wide association studies have identified novel genetic associations for asthma, but without taking into account the role of active tobacco smoking. This study aimed to identify novel genes that interact with ever active tobacco smoking in adult onset asthma. Methods We performed a genome-wide interaction analysis in six studies participating in the GABRIEL consortium following two meta-analyses approaches based on 1) the overall interaction effect and 2) the genetic effect in subjects with and without smoking exposure. We performed a discovery meta-analysis including 4,057 subjects of European descent and replicated our findings in an independent cohort (LifeLines Cohort Study), including 12,475 subjects. Results First approach: 50 SNPs were selected based on an overall interaction effect at p<10−4. The most pronounced interaction effect was observed for rs9969775 on chromosome 9 (discovery meta-analysis: ORint = 0.50, p = 7.63*10−5, replication: ORint = 0.65, p = 0.02). Second approach: 35 SNPs were selected based on the overall genetic effect in exposed subjects (p <10−4). The most pronounced genetic effect was observed for rs5011804 on chromosome 12 (discovery meta-analysis ORint = 1.50, p = 1.21*10−4; replication: ORint = 1.40, p = 0.03). Conclusions Using two genome-wide interaction approaches, we identified novel polymorphisms in non-annotated intergenic regions on chromosomes 9 and 12, that showed suggestive evidence for interaction with active tobacco smoking in the onset of adult asthma.
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Lemmelä S, Solovieva S, Shiri R, Benner C, Heliövaara M, Kettunen J, Anttila V, Ripatti S, Perola M, Seppälä I, Juonala M, Kähönen M, Salomaa V, Viikari J, Raitakari OT, Lehtimäki T, Palotie A, Viikari-Juntura E, Husgafvel-Pursiainen K. Genome-Wide Meta-Analysis of Sciatica in Finnish Population. PLoS One 2016; 11:e0163877. [PMID: 27764105 PMCID: PMC5072673 DOI: 10.1371/journal.pone.0163877] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 09/15/2016] [Indexed: 12/14/2022] Open
Abstract
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6) were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p = 1.30x10-8, MAF = 0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p = 1.34x10-8, MAF = 0.06; p = 2.32x10-8, MAF = 0.07; p = 3.85x10-8, MAF = 0.06; p = 4.78x10-8, MAF = 0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p = 0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6–7%) than in other European populations (1–2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.
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Affiliation(s)
- Susanna Lemmelä
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Svetlana Solovieva
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Rahman Shiri
- Health and Work Ability, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
| | - Christian Benner
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Department of Public Health, 00014 University of Helsinki, Helsinki, Finland
| | - Markku Heliövaara
- Population Health Unit, National Institute for Health and Welfare, 00251 Helsinki, Finland
| | - Johannes Kettunen
- Faculty of Medicine, Institute of Health Sciences, University of Oulu, 90220 Oulu, Finland
- NMR Metabolomics Laboratory, University of Eastern Finland, Kuopio, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Verneri Anttila
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Department of Public Health, 00014 University of Helsinki, Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, 00271 Helsinki, Finland
- The Estonian Genome Center, University of Tartu, 51010 Tartu, Estonia
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Markus Juonala
- Division of Medicine, Turku University Hospital, 20521 Turku, Finland
- Department of Medicine, University of Turku, 20521 Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, 33521 Tampere, Finland
| | - Veikko Salomaa
- Department of Health, National Institute for Health and Welfare, 00251 Helsinki, Finland
| | - Jorma Viikari
- Division of Medicine, Turku University Hospital, 20521 Turku, Finland
- Department of Medicine, University of Turku, 20521 Turku, Finland
| | - Olli T. Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520 Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521 Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere School of Medicine, 33520 Tampere, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), 00014 University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States of America
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts 02114, United States of America
| | - Eira Viikari-Juntura
- Disability Prevention Centre, Finnish Institute of Occupational Health, 00250 Helsinki, Finland
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Abstract
The genome is often the conduit through which environmental exposures convey their effects on health and disease. Whilst not all diseases act by directly perturbing the genome, the phenotypic responses are often genetically determined. Hence, whilst diseases are often defined has having differing degrees of genetic determination, genetic and environmental factors are, with few exceptions, inseparable features of most diseases, not least type 2 diabetes. It follows that to optimize diabetes, prevention and treatment will require that the etiological roles of genetic and environmental risk factors be jointly considered. As we discuss here, studies focused on quantifying gene-environment and gene-treatment interactions are gathering momentum and may eventually yield data that helps guide health-related choices and medical interventions for type 2 diabetes and other complex diseases.
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Affiliation(s)
- Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Clinical Research Center, Skåne University Hospital Malmö, Lund University, Building 91, Level 10, Jan Waldenströms gata 35, 205 02, Malmö, Sweden.
- Department of Public Health and Clinical Medicine, Umeå University, 90188, Umeå, Sweden.
- Department of Nutrition, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton General Hospital Campus, DB-CVSRI, 237 Barton Street East, Room C3103, Hamilton, ON, L8L 2X2, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Department of Clinical Epidemiology and Biostatistics, Population Genomics Program, McMaster University, Hamilton, ON, Canada
- Thrombosis and Atherosclerosis Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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Okazaki M, Yamashita S. Recent Advances in Analytical Methods on Lipoprotein Subclasses: Calculation of Particle Numbers from Lipid Levels by Gel Permeation HPLC Using “Spherical Particle Model”. J Oleo Sci 2016; 65:265-82. [DOI: 10.5650/jos.ess16020] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Shizuya Yamashita
- Rinku General Medical Center
- Department of Community Medicine & Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine
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7
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Zhang J, Zhang L, Zhang Y, Yang J, Guo M, Sun L, Pan HF, Hirankarn N, Ying D, Zeng S, Lee TL, Lau CS, Chan TM, Leung AMH, Mok CC, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Garcia-Barceló MM, Cherny SS, Sham PC, Cui Y, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Gene-Based Meta-Analysis of Genome-Wide Association Study Data Identifies Independent Single-Nucleotide Polymorphisms inANXA6as Being Associated With Systemic Lupus Erythematosus in Asian Populations. Arthritis Rheumatol 2015. [PMID: 26202167 DOI: 10.1002/art.39275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jing Zhang
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and Eye and ENT Hospital of Fudan University; Shanghai China
| | - Lu Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yan Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Jing Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Mengbiao Guo
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | - Dingge Ying
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Shuai Zeng
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tsz Leung Lee
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Chak Sing Lau
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tak Mao Chan
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Chi Chiu Mok
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Sik Nin Wong
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Ka Wing Lee
- Pamela Youde Nethersole Eastern Hospital; Hong Kong China
| | - Marco Hok Kung Ho
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | - Chun Yin Chong
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Mo Yin Mok
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stacey S. Cherny
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Pak Chung Sham
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yong Cui
- Anhui Medical University; China Hefei China
| | - Sen Yang
- Anhui Medical University; China Hefei China
| | | | | | - Yu Lung Lau
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and The University of Hong Kong-Shenzhen Hospital; Shenzhen China
| | - Wanling Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
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8
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Shetty PB, Tang H, Feng T, Tayo B, Morrison AC, Kardia SLR, Hanis CL, Arnett DK, Hunt SC, Boerwinkle E, Rao DC, Cooper RS, Risch N, Zhu X. Variants for HDL-C, LDL-C, and triglycerides identified from admixture mapping and fine-mapping analysis in African American families. CIRCULATION. CARDIOVASCULAR GENETICS 2015; 8:106-13. [PMID: 25552592 PMCID: PMC4378661 DOI: 10.1161/circgenetics.114.000481] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Admixture mapping of lipids was followed-up by family-based association analysis to identify variants for cardiovascular disease in African Americans. METHODS AND RESULTS The present study conducted admixture mapping analysis for total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides. The analysis was performed in 1905 unrelated African American subjects from the National Heart, Lung and Blood Institute's Family Blood Pressure Program (FBPP). Regions showing admixture evidence were followed-up with family-based association analysis in 3556 African American subjects from the FBPP. The admixture mapping and family-based association analyses were adjusted for age, age(2), sex, body mass index, and genome-wide mean ancestry to minimize the confounding caused by population stratification. Regions that were suggestive of local ancestry association evidence were found on chromosomes 7 (low-density lipoprotein cholesterol), 8 (high-density lipoprotein cholesterol), 14 (triglycerides), and 19 (total cholesterol and triglycerides). In the fine-mapping analysis, 52 939 single-nucleotide polymorphisms (SNPs) were tested and 11 SNPs (8 independent SNPs) showed nominal significant association with high-density lipoprotein cholesterol (2 SNPs), low-density lipoprotein cholesterol (4 SNPs), and triglycerides (5 SNPs). The family data were used in the fine-mapping to identify SNPs that showed novel associations with lipids and regions, including genes with known associations for cardiovascular disease. CONCLUSIONS This study identified regions on chromosomes 7, 8, 14, and 19 and 11 SNPs from the fine-mapping analysis that were associated with high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides for further studies of cardiovascular disease in African Americans.
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Affiliation(s)
- Priya B Shetty
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Hua Tang
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Tao Feng
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Bamidele Tayo
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Alanna C Morrison
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Sharon L R Kardia
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Craig L Hanis
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Donna K Arnett
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Steven C Hunt
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Eric Boerwinkle
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Dabeeru C Rao
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Richard S Cooper
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Neil Risch
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.)
| | - Xiaofeng Zhu
- From the Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, OH (P.B.S., T.F., X.Z.); Department of Genetics, Stanford University School of Medicine, Stanford, CA (H.T.); Department of Public Health Sciences, Loyola University of Chicago Stritch School of Medicine, Maywood, IL (B.T., R.S.C.); Division of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston School of Public Health (A.C.M., C.L.H., E.B.); Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor (S.L.R.K.); Department of Epidemiology, University of Alabama at Birmingham School of Public Health (D.K.A.); Cardiovascular Genetics Division, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City (S.C.H.); Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO (D.C. Rao); and Department of Epidemiology and Biostatistics, University of California, San Francisco (N.R.).
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9
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The challenges of genome-wide interaction studies: lessons to learn from the analysis of HDL blood levels. PLoS One 2014; 9:e109290. [PMID: 25329471 PMCID: PMC4203717 DOI: 10.1371/journal.pone.0109290] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 08/29/2014] [Indexed: 11/23/2022] Open
Abstract
Genome-wide association studies (GWAS) have revealed 74 single nucleotide polymorphisms (SNPs) associated with high-density lipoprotein cholesterol (HDL) blood levels. This study is, to our knowledge, the first genome-wide interaction study (GWIS) to identify SNP×SNP interactions associated with HDL levels. We performed a GWIS in the Rotterdam Study (RS) cohort I (RS-I) using the GLIDE tool which leverages the massively parallel computing power of Graphics Processing Units (GPUs) to perform linear regression on all genome-wide pairs of SNPs. By performing a meta-analysis together with Rotterdam Study cohorts II and III (RS-II and RS-III), we were able to filter 181 interaction terms with a p-value<1 · 10−8 that replicated in the two independent cohorts. We were not able to replicate any of these interaction term in the AGES, ARIC, CHS, ERF, FHS and NFBC-66 cohorts (Ntotal = 30,011) when adjusting for multiple testing. Our GWIS resulted in the consistent finding of a possible interaction between rs774801 in ARMC8 (ENSG00000114098) and rs12442098 in SPATA8 (ENSG00000185594) being associated with HDL levels. However, p-values do not reach the preset Bonferroni correction of the p-values. Our study suggest that even for highly genetically determined traits such as HDL the sample sizes needed to detect SNP×SNP interactions are large and the 2-step filtering approaches do not yield a solution. Here we present our analysis plan and our reservations concerning GWIS.
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10
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Xin G, Shong L, Hui L. Effect of genetic and non-genetic factors, including aging, on waist circumference and BMI, and inter-indicator differences in risk assessment. Exp Gerontol 2014; 60:83-6. [PMID: 25305560 DOI: 10.1016/j.exger.2014.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/29/2014] [Accepted: 10/07/2014] [Indexed: 01/15/2023]
Abstract
OBJECTIVE To assess the effect of genetic and non-genetic factors on indicators derived from waist circumference (WC) and body mass index (BMI) as well as inter-indicator differences in risk assessment age-related diseases including diabetes mellitus, coronary heart disease and liver cancer. METHODS Height, weight and WC were measured in 100 families (students and their two parents), 41 subjects with regular physical exercise routines, and 170 patients with diabetes mellitus, coronary heart disease or liver cancer. The BMI, waist-height ratio (WHtR) and waist circumference density index (WCDI) were calculated for each subject. RESULTS BMI was less affected by genetic factors, while WHtR and WCDI were greatly affected by genetic factors as revealed using multiple regression analysis. BMI, WHtR and WCDI were all sensitive to physical exercise according to ROC analysis; among these factors, the most sensitive indicator was WHtR. However, ROC analysis demonstrated that WCDI was more effective than BMI and WHtR for assessing the risk of three diseases. CONCLUSIONS WCDI more accurately reflects the roles of both genetic and non-genetic factors, including aging, which can better predict disease.
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Affiliation(s)
- Ge Xin
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Liu Shong
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China
| | - Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian 116044, China.
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11
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Simino J, Shi G, Bis JC, Chasman DI, Ehret GB, Gu X, Guo X, Hwang SJ, Sijbrands E, Smith AV, Verwoert GC, Bragg-Gresham JL, Cadby G, Chen P, Cheng CY, Corre T, de Boer RA, Goel A, Johnson T, Khor CC, Lluís-Ganella C, Luan J, Lyytikäinen LP, Nolte IM, Sim X, Sõber S, van der Most PJ, Verweij N, Zhao JH, Amin N, Boerwinkle E, Bouchard C, Dehghan A, Eiriksdottir G, Elosua R, Franco OH, Gieger C, Harris TB, Hercberg S, Hofman A, James AL, Johnson AD, Kähönen M, Khaw KT, Kutalik Z, Larson MG, Launer LJ, Li G, Liu J, Liu K, Morrison AC, Navis G, Ong RTH, Papanicolau GJ, Penninx BW, Psaty BM, Raffel LJ, Raitakari OT, Rice K, Rivadeneira F, Rose LM, Sanna S, Scott RA, Siscovick DS, Stolk RP, Uitterlinden AG, Vaidya D, van der Klauw MM, Vasan RS, Vithana EN, Völker U, Völzke H, Watkins H, Young TL, Aung T, Bochud M, Farrall M, Hartman CA, Laan M, Lakatta EG, Lehtimäki T, Loos RJF, Lucas G, Meneton P, Palmer LJ, Rettig R, Snieder H, Tai ES, Teo YY, van der Harst P, Wareham NJ, Wijmenga C, Wong TY, Fornage M, Gudnason V, Levy D, Palmas W, Ridker PM, Rotter JI, van Duijn CM, Witteman JCM, Chakravarti A, Rao DC. Gene-age interactions in blood pressure regulation: a large-scale investigation with the CHARGE, Global BPgen, and ICBP Consortia. Am J Hum Genet 2014; 95:24-38. [PMID: 24954895 DOI: 10.1016/j.ajhg.2014.05.010] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 05/20/2014] [Indexed: 01/11/2023] Open
Abstract
Although age-dependent effects on blood pressure (BP) have been reported, they have not been systematically investigated in large-scale genome-wide association studies (GWASs). We leveraged the infrastructure of three well-established consortia (CHARGE, GBPgen, and ICBP) and a nonstandard approach (age stratification and metaregression) to conduct a genome-wide search of common variants with age-dependent effects on systolic (SBP), diastolic (DBP), mean arterial (MAP), and pulse (PP) pressure. In a two-staged design using 99,241 individuals of European ancestry, we identified 20 genome-wide significant (p ≤ 5 × 10(-8)) loci by using joint tests of the SNP main effect and SNP-age interaction. Nine of the significant loci demonstrated nominal evidence of age-dependent effects on BP by tests of the interactions alone. Index SNPs in the EHBP1L1 (DBP and MAP), CASZ1 (SBP and MAP), and GOSR2 (PP) loci exhibited the largest age interactions, with opposite directions of effect in the young versus the old. The changes in the genetic effects over time were small but nonnegligible (up to 1.58 mm Hg over 60 years). The EHBP1L1 locus was discovered through gene-age interactions only in whites but had DBP main effects replicated (p = 8.3 × 10(-4)) in 8,682 Asians from Singapore, indicating potential interethnic heterogeneity. A secondary analysis revealed 22 loci with evidence of age-specific effects (e.g., only in 20 to 29-year-olds). Age can be used to select samples with larger genetic effect sizes and more homogenous phenotypes, which may increase statistical power. Age-dependent effects identified through novel statistical approaches can provide insight into the biology and temporal regulation underlying BP associations.
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Affiliation(s)
- Jeannette Simino
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Gang Shi
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Georg B Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cardiology, Department of Specialties of Internal Medicine, Geneva University Hospitals, Geneva 1211, Switzerland
| | - Xiangjun Gu
- Research Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, MA 01702, USA; Center for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA
| | - Eric Sijbrands
- Department of Internal Medicine, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Albert V Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Germaine C Verwoert
- Department of Internal Medicine, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | | | - Gemma Cadby
- Centre for Genetic Origins of Health and Disease, University of Western Australia, Nedlands, WA 6009, Australia; Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Samuel Lunenfeld Research Institute, Toronto, ON M5T 3L9, Canada
| | - Peng Chen
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore
| | - Ching-Yu Cheng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Ophthalmology, National University Health System, Singapore 119228, Singapore; Singapore Eye Research Institute, Singapore 168751, Singapore; Centre for Quantitative Medicine, Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Tanguy Corre
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Rudolf A de Boer
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Toby Johnson
- Clinical Pharmacology, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Chiea-Chuen Khor
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore; Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Ophthalmology, National University Health System, Singapore 119228, Singapore; Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore; Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Paediatrics, National University Health System, Singapore 119074, Singapore
| | - Carla Lluís-Ganella
- Cardiovascular Epidemiology and Genetics, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 30101, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33101, Finland
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Xueling Sim
- Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Centre for Molecular Epidemiology, National University of Singapore, Singapore 119260, Singapore
| | - Siim Sõber
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Sciences Center, Houston, TX 77225, USA
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | | | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain; Epidemiology and Public Health Network (CIBERESP), 08036 Barcelona, Spain
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Tamara B Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Serge Hercberg
- U557 Institut National de la Santé et de la Recherche Médicale, U1125 Institut National de la Recherche Agronomique, Université Paris 13, 93000 Bobigny, France
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Alan L James
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia; School of Medicine and Pharmacology, University of Western Australia, Nedlands, WA 6009, Australia
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA 01702, USA; Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland; Department of Clinical Physiology, University of Tampere School of Medicine, Tampere 33521, Finland
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge CB2 2SR, UK
| | - Zoltan Kutalik
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martin G Larson
- Framingham Heart Study, Framingham, MA 01702, USA; Department of Mathematics, Boston University, Boston, MA 02215, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Guo Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Jianjun Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore; Division of Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Kiang Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alanna C Morrison
- Human Genetics Center, University of Texas Health Sciences Center, Houston, TX 77225, USA
| | - Gerjan Navis
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore
| | - George J Papanicolau
- Division of Cardiovascular Sciences, National Heart, Lung, & Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Brenda W Penninx
- Department of Psychiatry/EMGO Institute/Neuroscience Campus, VU University Medical Centre, 1081 BT Amsterdam, the Netherlands; Department of Psychiatry, Leiden University Medical Centre, 2333 ZD Leiden, the Netherlands; Department of Psychiatry, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Department of Health Services, University of Washington, Seattle, WA 98195, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA
| | - Leslie J Raffel
- Medical Genetics Institute, Cedars-Sinai Medical Center, Pacific Theatres, Los Angeles, CA 90048, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20521, Finland
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato 09042, Italy
| | - Robert A Scott
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - David S Siscovick
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Ronald P Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands; Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands; Netherland Genomics Inititiative, Netherlands Center for Healthy Aging, The Hague 2509, the Netherlands
| | - Dhananjay Vaidya
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21202, USA
| | - Melanie M van der Klauw
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA 01702, USA; Divisions of Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Eranga Nishanthie Vithana
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Ophthalmology, National University Health System, Singapore 119228, Singapore; Singapore Eye Research Institute, Singapore 168751, Singapore; Neuroscience and Behavioural Disorders (NBD) Program, Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, 17487 Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University of Greifswald, 17487 Greifswald, Germany
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Terri L Young
- Department of Ophthalmology, Duke University Medical Center, Durham, NC 27710, USA; Division of Neuroscience, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Tin Aung
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Ophthalmology, National University Health System, Singapore 119228, Singapore; Singapore Eye Research Institute, Singapore 168751, Singapore
| | - Murielle Bochud
- Institute of Social and Preventive Medicine, Lausanne University Hospital, 1010 Lausanne, Switzerland
| | - Martin Farrall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Catharina A Hartman
- Interdisciplinary Center for Pathology of Emotions, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Maris Laan
- Human Molecular Genetics Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - Edward G Lakatta
- Laboratory of Cardiovascular Science, National Institute on Aging, NIH, Bethesda, MD 21224, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 30101, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33101, Finland
| | - Ruth J F Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gavin Lucas
- Cardiovascular Epidemiology and Genetics, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
| | - Pierre Meneton
- U872 Institut National de la Santé et de la Recherche Médicale, Centre de Recherche des Cordeliers, Paris 75006, France
| | - Lyle J Palmer
- Genetic Epidemiology and Biostatistics Platform, Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Samuel Lunenfeld Research Institute, Toronto, ON M5T 3L9, Canada
| | - Rainer Rettig
- Institute of Physiology, University of Greifswald, 17495 Karlsburg, Germany
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - E Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore; Department of Medicine, National University Health System and Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Duke-National University of Singapore Graduate Medical School, Singapore 169857, Singapore
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore; Saw Swee Hock School of Public Health, National University Health System, Singapore 117597, Singapore; Life Sciences Institute, National University of Singapore, Singapore 117456, Singapore; Department of Statistics and Applied Probability, National University of Singapore, Singapore 117543, Singapore; Genome Institute of Singapore, A(∗)STAR, Singapore 138672, Singapore
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Durrer Center for Cardiogenetic Research, 3501 DG Utrecht, the Netherlands
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Tien Yin Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore; Department of Ophthalmology, National University Health System, Singapore 119228, Singapore; Singapore Eye Research Institute, Singapore 168751, Singapore
| | - Myriam Fornage
- Research Center for Human Genetics, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Sciences Center, Houston, TX 77225, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Daniel Levy
- Framingham Heart Study, Framingham, MA 01702, USA; Center for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA; Boston University School of Medicine, Boston, MA 02118, USA
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands; Netherland Genomics Inititiative, Netherlands Center for Healthy Aging, The Hague 2509, the Netherlands; Netherland Genomics Initiative, Centre for Medical Systems Biology, 2300 RC Leiden, the Netherlands
| | - Jacqueline C M Witteman
- Department of Epidemiology, Erasmus University Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Dabeeru C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA; Departments of Psychiatry, Genetics, and Mathematics, Washington University School of Medicine, St. Louis, MO 63110, USA
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12
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Zubair N, Mayer-Davis EJ, Mendez MA, Mohlke KL, North KE, Adair LS. Genetic risk score and adiposity interact to influence triglyceride levels in a cohort of Filipino women. Nutr Diabetes 2014; 4:e118. [PMID: 24932782 PMCID: PMC4079926 DOI: 10.1038/nutd.2014.16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/18/2014] [Accepted: 02/20/2014] [Indexed: 01/19/2023] Open
Abstract
Background/Objectives: Individually, genetic variants only moderately influence cardiometabolic (CM) traits, such as lipid and inflammatory markers. In this study we generated genetic risk scores from a combination of previously reported variants influencing CM traits, and used these scores to explore how adiposity levels could mediate genetic contributions to CM traits. Subjects/Methods: Participants included 1649 women from the 2005 Cebu Longitudinal Health and Nutrition Survey. Three genetic risk scores were constructed for C-reactive protein (CRP), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TGs). We used linear regression models to assess the association between each genetic risk score and its related trait. We also tested for interactions between each score and measures of adiposity. Results: Each genetic risk score explained a greater proportion of variance in trait levels than any individual genetic variant. We found an interaction between the TG genetic risk score (2.29–14.34 risk alleles) and waist circumference (WC) (Pinteraction=1.66 × 10−2). Based on model predictions, for individuals with a higher TG genetic risk score (75th percentile=12), having an elevated WC (⩾80 cm) increased TG levels from 1.32 to 1.71 mmol l−1. However, for individuals with a lower score (25th percentile=7), having an elevated WC did not significantly change TG levels. Conclusions: The TG genetic risk score interacted with adiposity to synergistically influence TG levels. For individuals with a genetic predisposition to elevated TG levels, our results suggest that reducing adiposity could possibly prevent further increases in TG levels and thereby lessen the likelihood of adverse health outcomes such as cardiovascular disease.
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Affiliation(s)
- N Zubair
- Public Health Sciences Division, Cancer Prevention, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - E J Mayer-Davis
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M A Mendez
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K L Mohlke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K E North
- Department of Epidemiology and Carolina Center for Genome Sciences, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - L S Adair
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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13
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Winkler TW, Day FR, Croteau-Chonka DC, Wood AR, Locke AE, Mägi R, Ferreira T, Fall T, Graff M, Justice AE, Luan J, Gustafsson S, Randall JC, Vedantam S, Workalemahu T, Kilpeläinen TO, Scherag A, Esko T, Kutalik Z, Heid IM, Loos RJF. Quality control and conduct of genome-wide association meta-analyses. Nat Protoc 2014; 9:1192-212. [PMID: 24762786 DOI: 10.1038/nprot.2014.071] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.
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Affiliation(s)
- Thomas W Winkler
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany
| | - Felix R Day
- Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Damien C Croteau-Chonka
- 1] Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew R Wood
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Adam E Locke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Teresa Ferreira
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tove Fall
- 1] Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jian'an Luan
- Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Sailaja Vedantam
- 1] Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Tuomas O Kilpeläinen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - André Scherag
- 1] Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany. [2] Clinical Epidemiology, Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Tonu Esko
- 1] Estonian Genome Center, University of Tartu, Tartu, Estonia. [2] Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [4] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Zoltán Kutalik
- 1] Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland. [2] Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. [3] Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Iris M Heid
- 1] Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany. [2]
| | - Ruth J F Loos
- 1] The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [3] The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [4]
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14
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Yiannakouris N, Katsoulis M, Trichopoulou A, Ordovas JM, Trichopoulos D. Additive influence of genetic predisposition and conventional risk factors in the incidence of coronary heart disease: a population-based study in Greece. BMJ Open 2014; 4:e004387. [PMID: 24500614 PMCID: PMC3918976 DOI: 10.1136/bmjopen-2013-004387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES An additive genetic risk score (GRS) for coronary heart disease (CHD) has previously been associated with incident CHD in the population-based Greek European Prospective Investigation into Cancer and nutrition (EPIC) cohort. In this study, we explore GRS-'environment' joint actions on CHD for several conventional cardiovascular risk factors (ConvRFs), including smoking, hypertension, type-2 diabetes mellitus (T2DM), body mass index (BMI), physical activity and adherence to the Mediterranean diet. DESIGN A case-control study. SETTING The general Greek population of the EPIC study. PARTICIPANTS AND OUTCOME MEASURES 477 patients with medically confirmed incident CHD and 1271 controls participated in this study. We estimated the ORs for CHD by dividing participants at higher or lower GRS and, alternatively, at higher or lower ConvRF, and calculated the relative excess risk due to interaction (RERI) as a measure of deviation from additivity. RESULTS The joint presence of higher GRS and higher risk ConvRF was in all instances associated with an increased risk of CHD, compared with the joint presence of lower GRS and lower risk ConvRF. The OR (95% CI) was 1.7 (1.2 to 2.4) for smoking, 2.7 (1.9 to 3.8) for hypertension, 4.1 (2.8 to 6.1) for T2DM, 1.9 (1.4 to 2.5) for lower physical activity, 2.0 (1.3 to 3.2) for high BMI and 1.5 (1.1 to 2.1) for poor adherence to the Mediterranean diet. In all instances, RERI values were fairly small and not statistically significant, suggesting that the GRS and the ConvRFs do not have effects beyond additivity. CONCLUSIONS Genetic predisposition to CHD, operationalised through a multilocus GRS, and ConvRFs have essentially additive effects on CHD risk.
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Affiliation(s)
- Nikos Yiannakouris
- Hellenic Health Foundation, Athens, Greece
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens, Greece
| | | | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece
- Department of Hygiene, Epidemiology and Medical Statistics, WHO Collaborating Center for Food and Nutrition Policies, University of Athens Medical School, Athens, Greece
| | - Jose M Ordovas
- Nutrition and Genomics Laboratory, Jean Mayer—US Department of Agriculture, Human Nutrition Research Center on Aging (HNRCA) at Tufts University, Boston, Massachusetts, USA
- Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Instituto Madrileño de Estudios Avanzados (IMDEA) Alimentacion, Madrid, Spain
| | - Dimitrios Trichopoulos
- Hellenic Health Foundation, Athens, Greece
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Bureau of Epidemiologic Research, Academy of Athens, Athens, Greece
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15
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Whitfield JB. Genetic insights into cardiometabolic risk factors. Clin Biochem Rev 2014; 35:15-36. [PMID: 24659834 PMCID: PMC3961996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Many biochemical traits are recognised as risk factors, which contribute to or predict the development of disease. Only a few are in widespread use, usually to assist with treatment decisions and motivate behavioural change. The greatest effort has gone into evaluation of risk factors for cardiovascular disease and/or diabetes, with substantial overlap as 'cardiometabolic' risk. Over the past few years many genome-wide association studies (GWAS) have sought to account for variation in risk factors, with the expectation that identifying relevant polymorphisms would improve our understanding or prediction of disease; others have taken the direct approach of genomic case-control studies for the corresponding diseases. Large GWAS have been published for coronary heart disease and Type 2 diabetes, and also for associated biomarkers or risk factors including body mass index, lipids, C-reactive protein, urate, liver function tests, glucose and insulin. Results are not encouraging for personal risk prediction based on genotyping, mainly because known risk loci only account for a small proportion of risk. Overlap of allelic associations between disease and marker, as found for low density lipoprotein cholesterol and heart disease, supports a causal association, but in other cases genetic studies have cast doubt on accepted risk factors. Some loci show unexpected effects on multiple markers or diseases. An intriguing feature of risk factors is the blurring of categories shown by the correlation between them and the genetic overlap between diseases previously thought of as distinct. GWAS can provide insight into relationships between risk factors, biomarkers and diseases, with potential for new approaches to disease classification.
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16
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Wu Y, Marvelle AF, Li J, Croteau-Chonka DC, Feranil AB, Kuzawa CW, Li Y, Adair LS, Mohlke KL. Genetic association with lipids in Filipinos: waist circumference modifies an APOA5 effect on triglyceride levels. J Lipid Res 2013; 54:3198-205. [PMID: 24023260 DOI: 10.1194/jlr.p042077] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Blood levels of lipoprotein cholesterol and triglycerides (TGs) are highly heritable and are major risk factors for cardiovascular disease (CVD). Approximately 100 lipid-associated loci have been identified in populations of European ancestry. We performed a genome-wide association study of lipid traits in 1,782 Filipino women from the Cebu Longitudinal Health and Nutrition Survey, and tested for evidence of interactions with waist circumference. We conducted additional association and interaction analyses in 1,719 of their young adult offspring. Genome-wide significant associations (P < 5 × 10⁻⁸) were detected at APOE for low density lipoprotein cholesterol and total cholesterol, and at APOA5 for TGs. Suggestive associations (P < 10⁻⁶) were detected at GCKR for TGs, and at CETP and TOM1 for high density lipoprotein cholesterol. Our data also supported the existence of allelic heterogeneity at APOA5, CETP, LIPC, and APOE. The secondary signal (Gly185Cys) at APOA5 exhibited a single nucleotide polymorphism (SNP)-by-waist circumference interaction affecting TGs (Pinteraction = 1.6 × 10⁻⁴), manifested by stronger SNP effects as waist circumference increased. These findings provide the first evidence that central obesity may accentuate the effect of the TG-increasing allele of the APOA5 signal, emphasizing that CVD risk could be reduced by central obesity control.
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Affiliation(s)
- Ying Wu
- Departments of Genetics, University of North Carolina, Chapel Hill, NC 27599
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17
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Chen CP, Lee MJ, Chern SR, Wu PS, Su JW, Chen YT, Lee MS, Wang W. Prenatal diagnosis and molecular cytogenetic characterization of a de novo proximal interstitial deletion of chromosome 4p (4p15.2→p14). Gene 2013; 529:351-6. [PMID: 23948085 DOI: 10.1016/j.gene.2013.07.063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/13/2013] [Accepted: 07/16/2013] [Indexed: 02/03/2023]
Abstract
We present prenatal diagnosis of de novo proximal interstitial deletion of chromosome 4p (4p15.2→p14) and molecular cytogenetic characterization of the deletion using uncultured amniocytes. We review the phenotypic abnormalities of previously reported patients with similar proximal interstitial 4p deletions, and we discuss the functions of the genes of RBPJ, CCKAR, STIM2, PCDH7 and ARAP2 that are deleted within this region.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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18
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Mallol R, Rodriguez MA, Brezmes J, Masana L, Correig X. Human serum/plasma lipoprotein analysis by NMR: application to the study of diabetic dyslipidemia. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 70:1-24. [PMID: 23540574 DOI: 10.1016/j.pnmrs.2012.09.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/26/2012] [Indexed: 06/02/2023]
Affiliation(s)
- Roger Mallol
- Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
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19
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Laurila PP, Surakka I, Sarin AP, Yetukuri L, Hyötyläinen T, Söderlund S, Naukkarinen J, Tang J, Kettunen J, Mirel DB, Soronen J, Lehtimäki T, Ruokonen A, Ehnholm C, Eriksson JG, Salomaa V, Jula A, Raitakari OT, Järvelin MR, Palotie A, Peltonen L, Orešič M, Jauhiainen M, Taskinen MR, Ripatti S. Genomic, Transcriptomic, and Lipidomic Profiling Highlights the Role of Inflammation in Individuals With Low High-density Lipoprotein Cholesterol. Arterioscler Thromb Vasc Biol 2013; 33:847-57. [DOI: 10.1161/atvbaha.112.300733] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective—
Low high-density lipoprotein cholesterol (HDL-C) is associated with cardiometabolic pathologies. In this study, we investigate the biological pathways and individual genes behind low HDL-C by integrating results from 3 high-throughput data sources: adipose tissue transcriptomics, HDL lipidomics, and dense marker genotypes from Finnish individuals with low or high HDL-C (n=450).
Approach and Results—
In the pathway analysis of genetic data, we demonstrate that genetic variants within inflammatory pathways were enriched among low HDL-C associated single-nucleotide polymorphisms, and the expression of these pathways upregulated in the adipose tissue of low HDL-C subjects. The lipidomic analysis highlighted the change in HDL particle quality toward putatively more inflammatory and less vasoprotective state in subjects with low HDL-C, as evidenced by their decreased antioxidative plasmalogen contents. We show that the focal point of these inflammatory pathways seems to be the
HLA
region with its low HDL-associated alleles also associating with more abundant local transcript levels in adipose tissue, increased plasma vascular cell adhesion molecule 1 (VCAM1) levels, and decreased HDL particle plasmalogen contents, markers of adipose tissue inflammation, vascular inflammation, and HDL antioxidative potential, respectively. In a population-based look-up of the inflammatory pathway single-nucleotide polymorphisms in a large Finnish cohorts (n=11 211), no association of the
HLA
region was detected for HDL-C as quantitative trait, but with extreme HDL-C phenotypes, implying the presence of low or high HDL genes in addition to the population-genomewide association studies–identified HDL genes.
Conclusions—
Our study highlights the role of inflammation with a genetic component in subjects with low HDL-C and identifies novel
cis
-expression quantitative trait loci (
cis
-eQTL) variants in
HLA
region to be associated with low HDL-C.
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Affiliation(s)
- Pirkka-Pekka Laurila
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Ida Surakka
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Antti-Pekka Sarin
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Laxman Yetukuri
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Tuulia Hyötyläinen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Sanni Söderlund
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Jussi Naukkarinen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Jing Tang
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Johannes Kettunen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Daniel B. Mirel
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Jarkko Soronen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Terho Lehtimäki
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Aimo Ruokonen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Christian Ehnholm
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Johan G. Eriksson
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Veikko Salomaa
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Antti Jula
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Olli T. Raitakari
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Marjo-Riitta Järvelin
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Aarno Palotie
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Leena Peltonen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Matej Orešič
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Matti Jauhiainen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Marja-Riitta Taskinen
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
| | - Samuli Ripatti
- From the Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland (P-P.L., I.S., A-P.S., J.K., A.P., S.R.); Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland (P-P.L., I.S., A-P.S., J.N., J.K., J.S., C.E., M.J., S.R.); Department of Medical Genetics, University of Helsinki, Helsinki, Finland (P-P.L., A.P.); VTT Technical Research Centre of Finland, Espoo, Finland (L.Y., T.H., J.T., M.O.); Department of Medicine, Helsinki University
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Surakka I, Whitfield JB, Perola M, Visscher PM, Montgomery GW, Falchi M, Willemsen G, de Geus EJC, Magnusson PKE, Christensen K, Sørensen TIA, Pietiläinen KH, Rantanen T, Silander K, Widen E, Muilu J, Rahman I, Liljedahl U, Syvänen AC, Palotie A, Kaprio J, Kyvik KO, Pedersen NL, Boomsma DI, Spector T, Martin NG, Ripatti S, Peltonen L. A genome-wide association study of monozygotic twin-pairs suggests a locus related to variability of serum high-density lipoprotein cholesterol. Twin Res Hum Genet 2012; 15:691-9. [PMID: 23031429 PMCID: PMC4333218 DOI: 10.1017/thg.2012.63] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Genome-wide association analysis on monozygotic twin-pairs offers a route to discovery of gene environment interactions through testing for variability loci associated with sensitivity to individual environment/lifestyle. We present a genome-wide scan of loci associated with intra-pair differences in serum lipid and apolipoprotein levels. We report data for 1,720 monozygotic female twin-pairs from GenomEUtwin project with 2.5 million SNPs, imputed or genotyped, and measured serum lipid fractions for both twins. We found one locus associated with intra-pair differences in high-density lipoprotein cholesterol, rs2483058 in an intron of SRGAP2, where twins carrying the C allele are more sensitive to environmental factors(P=3.98 x 10-8). We followed up the association in further genotyped monozygotic twins (N= 1,261),which showed a moderate association for the variant (P= 0.200, same direction of an effect). In addition,we report a new association on the level of apolipoprotein A-ll (P= 4.03 x 1 o-8).
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Affiliation(s)
- Ida Surakka
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
| | - John B. Whitfield
- Queensland Institute of Medical Research, Locked Bag 2000, Royal Brisbane Hospital, Queensland 4029, Australia
| | - Markus Perola
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- The Estonian Genome Center and the Center of Translational Genomics of the University of Tartu, Tartu, Estonia
| | - Peter M. Visscher
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Grant W. Montgomery
- Queensland Institute of Medical Research, Locked Bag 2000, Royal Brisbane Hospital, Queensland 4029, Australia
| | - Mario Falchi
- Genomic Medicine, Hammersmith Hospital, Imperial College London, London, U.K
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Eco JC de Geus
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kaare Christensen
- The Danish Twin Registry, University of Southern Denmark, Odense C, Denmark; and Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | | | - Kirsi H. Pietiläinen
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
- Obesity Research Unit, Department of Medicine, Division of Endocrinology, Helsinki University Central Hospital and University of Helsinki, Finland
| | - Taina Rantanen
- Department of Health Sciences, Gerontology Research Centre, University of Jyväskylä, Finland
| | - Kaisa Silander
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
| | - Elisabeth Widen
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
| | - Juha Muilu
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
| | - Iffat Rahman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Aarno Palotie
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Department of Medical Genetics, Haartman Institute, University of Helsinki and Helsinki University Central Hospital, Finland
- The Broad Institute, Massachusetts Institute of Technology, USA
| | - Jaakko Kaprio
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
- Faculty of Medicine, Department of Public Health, FI-00014 University of Helsinki, Finland
- Unit for Child and Adolescent Mental Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Kirsten O. Kyvik
- Institute of Regional Health Services Research, University of Southern Denmark, Denmark
- Odense Patient Data Explorative Network (OPEN), Odense University Hospital, Odense, Denmark
| | - Nancy L. Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, UK
| | - Nicholas G. Martin
- Queensland Institute of Medical Research, Locked Bag 2000, Royal Brisbane Hospital, Queensland 4029, Australia
| | - Samuli Ripatti
- FIMM, Institute for Molecular Medicine, Finland, Biomedicum, FI-00014 University of Helsinki, Finland
- Public Health Genomics Unit, National Institute for Health and Welfare, FI-00271 Helsinki, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Lamina C, Forer L, Schönherr S, Kollerits B, Ried JS, Gieger C, Peters A, Wichmann HE, Kronenberg F. Evaluation of gene–obesity interaction effects on cholesterol levels: A genetic predisposition score on HDL-cholesterol is modified by obesity. Atherosclerosis 2012; 225:363-9. [DOI: 10.1016/j.atherosclerosis.2012.09.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 09/14/2012] [Accepted: 09/14/2012] [Indexed: 01/19/2023]
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Nutrition, Genetics, and Cardiovascular Disease. Curr Nutr Rep 2012. [DOI: 10.1007/s13668-012-0008-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Abstract
PURPOSE OF REVIEW To discuss if and how the combined analysis of large-scale datasets from multiple independent sources benefits the mapping of novel genetic elements with relevance to lipoprotein metabolism and allows for conclusions on underlying molecular mechanisms. RECENT FINDINGS Genome-wide association studies (GWAS) have identified numerous genomic loci associated with plasma lipid levels and cardiovascular disease. Yet, despite being highly successful in mapping novel loci the GWAS approach falls short to systematically extract functional information from genomic data. With the aim to complement GWAS for a better insight into disease mechanisms and identification of the most promising targets for drug development, a number of high-throughput functional genomics strategies have now been applied. These include computational approaches, consideration of gene-gene and gene-environment interactions, as well as unbiased gene-expression analyses in relevant tissues. For a limited number of loci, mechanistic insight has been gained through in-vitro and in-vivo studies by knockdown and overexpression of candidate genes. SUMMARY The integration of GWAS data with existing functional genomics strategies has contributed to ascertain the relevance of a number of novel factors for lipoprotein biology and disease. However, technologies are warranted that provide a more systematic insight into the molecular function and pathogenic relevance of promising candidate genes.
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Affiliation(s)
- Heiko Runz
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.
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Yan TT, Yin RX, Li Q, Huang P, Zeng XN, Huang KK, Aung LHH, Wu DF, Liu CW, Pan SL. Sex-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels in the Mulao and Han populations. Lipids Health Dis 2011; 10:248. [PMID: 22208664 PMCID: PMC3274493 DOI: 10.1186/1476-511x-10-248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Accepted: 12/31/2011] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The association of rs16996148 single nucleotide polymorphism (SNP) in NCAN/CILP2/PBX4 and serum lipid levels is inconsistent. Furthermore, little is known about the association of rs16996148 SNP and serum lipid levels in the Chinese population. We therefore aimed to detect the association of rs16996148 SNP and several environmental factors with serum lipid levels in the Guangxi Mulao and Han populations. METHOD A total of 712 subjects of Mulao nationality and 736 participants of Han nationality were randomly selected from our stratified randomized cluster samples. Genotyping of the rs16996148 SNP was performed by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing. RESULTS The levels of apolipoprotein (Apo) B were higher in Mulao than in Han (P < 0.001). The frequencies of G and T alleles were 87.2% and 12.8% in Mulao, and 89.9% and 10.1% in Han (P <0.05); respectively. The frequencies of GG, GT and TT genotypes were 76.0%, 22.5% and 1.5% in Mulao, and 81.2%, 17.4% and 1.4% in Han (P <0.05); respectively. There were no significant differences in the genotypic and allelic frequencies between males and females in both ethnic groups. The levels of HDL-C, ApoAI, and the ratio of ApoAI to ApoB in Mulao were different between the GG and GT/TT genotypes in males but not in females (P < 0.01 for all), the subjects with GT/TT genotypes had higher serum levels of HDL-C, ApoAI, and the ratio of ApoAI to ApoB than the subjects with GG genotype. The levels of TC, TG, LDL-C, ApoAI, and ApoB in Han were different between the GG and GT/TT genotypes in males but not in females (P < 0.05-0.001), the T allele carriers had higher serum levels of TC, TG, LDL-C, ApoAI, and ApoB than the T allele noncarriers. The levels of HDL-C, ApoAI, and the ratio of ApoAI to ApoB in Mulao were correlated with the genotypes in males (P < 0.05-0.01) but not in females. The levels of TC, TG, HDL-C, LDL-C, ApoAI and ApoB in Han were associated with the genotypes in males (P < 0.05-0.001) but not in females. Serum lipid parameters were also correlated with several enviromental factors in both ethnic groups (P < 0.05-0.001). CONCLUSIONS The genotypic and allelic frequencies of rs16996148 SNP and the associations of the SNP and serum lipid levels are different in the Mulao and Han populations. Sex (male)-specific association of rs16996148 SNP in the NCAN/CILP2/PBX4 and serum lipid levels is also observed in the both ethnic groups.
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Affiliation(s)
- Ting-Ting Yan
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Rui-Xing Yin
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Qing Li
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Ping Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiao-Na Zeng
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Ke-Ke Huang
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Lynn Htet Htet Aung
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Dong-Feng Wu
- Department of Cardiology, Institute of Cardiovascular Diseases, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Cheng-Wu Liu
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Premedical Sciences, Guangxi Medical University, Nanning 530021, Guangxi, People's Republic of China
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