273 results found
Ghanbari M, Peters MJ, De Vries PS, et al., 2018, A systematic analysis highlights multiple long non-coding RNAs associated with cardiometabolic disorders, Journal of Human Genetics, Vol: 63, Pages: 431-446, ISSN: 1434-5161
Genome-wide association studies (GWAS) have identified many susceptibility loci for cardiometabolic disorders. Most of the associated variants reside in non-coding regions of the genome including long non-coding RNAs (lncRNAs), which are thought to play critical roles in diverse biological processes. Here, we leveraged data from the available GWAS meta-analyses on lipid and obesity-related traits, blood pressure, type 2 diabetes, and coronary artery disease and identified 179 associated single-nucleotide polymorphisms (SNPs) in 102 lncRNAs (p-value < 2.3 × 10-7). Of these, 55 SNPs, either the lead SNP or in strong linkage disequilibrium with the lead SNP in the related loci, were selected for further investigations. Our in silico predictions and functional annotations of the SNPs as well as expression and DNA methylation analysis of their lncRNAs demonstrated several lncRNAs that fulfilled predefined criteria for being potential functional targets. In particular, we found evidence suggesting that LOC157273 (at 8p23.1) is involved in regulating serum lipid-cholesterol. Our results showed that rs4841132 in the second exon and cg17371580 in the promoter region of LOC157273 are associated with lipids; the lncRNA is expressed in liver and associates with the expression of its nearby coding gene, PPP1R3B. Collectively, we highlight a number of loci associated with cardiometabolic disorders for which the association may act through lncRNAs.
Chaker L, Cremers LGM, Korevaar TIM, et al., 2018, Age-dependent association of thyroid function with brain morphology and microstructural organization: evidence from brain imaging., Neurobiol Aging, Vol: 61, Pages: 44-51
Thyroid hormone (TH) is crucial during neurodevelopment, but high levels of TH have been linked to neurodegenerative disorders. No data on the association of thyroid function with brain imaging in the general population are available. We therefore investigated the association of thyroid-stimulating hormone and free thyroxine (FT4) with magnetic resonance imaging (MRI)-derived total intracranial volume, brain tissue volumes, and diffusion tensor imaging measures of white matter microstructure in 4683 dementia- and stroke-free participants (mean age 60.2, range 45.6-89.9 years). Higher FT4 levels were associated with larger total intracranial volumes (β = 6.73 mL, 95% confidence interval = 2.94-9.80). Higher FT4 levels were also associated with larger total brain and white matter volumes in younger individuals, but with smaller total brain and white matter volume in older individuals (p-interaction 0.02). There was a similar interaction by age for the association of FT4 with mean diffusivity on diffusion tensor imaging (p-interaction 0.026). These results are in line with differential effects of TH during neurodevelopmental and neurodegenerative processes and can improve the understanding of the role of thyroid function in neurodegenerative disorders.
Dehghan A, 2018, Genome-Wide Association Studies., Pages: 37-49
Genetic association studies have made a major contribution to our understanding of the genetics of complex disorders over the last 10 years through genome-wide association studies (GWAS). In this chapter, we review the key concepts that underlie the GWAS approach. We will describe the "common disease, common variant" theory, and will review how we finally afforded to capture the common variance in genome to make GWAS possible. Finally, we will go over technical aspects of GWAS such as genotype imputation, epidemiologic designs, analysis methods, and considerations such as genomic inflation, multiple testing, and replication.
Richard MA, Huan T, Ligthart S, et al., 2017, DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation, AMERICAN JOURNAL OF HUMAN GENETICS, Vol: 101, Pages: 888-902, ISSN: 0002-9297
Milaneschi Y, Lamers F, Peyrot WJ, et al., 2017, Genetic Association of Major Depression With Atypical Features and Obesity-Related Immunometabolic Dysregulations., JAMA Psychiatry, Vol: 74, Pages: 1214-1225
Importance: The association between major depressive disorder (MDD) and obesity may stem from shared immunometabolic mechanisms particularly evident in MDD with atypical features, characterized by increased appetite and/or weight (A/W) during an active episode. Objective: To determine whether subgroups of patients with MDD stratified according to the A/W criterion had a different degree of genetic overlap with obesity-related traits (body mass index [BMI] and levels of C-reactive protein [CRP] and leptin). Design, Setting, and Patients: This multicenter study assembled genome-wide genotypic and phenotypic measures from 14 data sets of the Psychiatric Genomics Consortium. Data sets were drawn from case-control, cohort, and population-based studies, including 26 628 participants with established psychiatric diagnoses and genome-wide genotype data. Data on BMI were available for 15 237 participants. Data were retrieved and analyzed from September 28, 2015, through May 20, 2017. Main Outcomes and Measures: Lifetime DSM-IV MDD was diagnosed using structured diagnostic instruments. Patients with MDD were stratified into subgroups according to change in the DSM-IV A/W symptoms as decreased or increased. Results: Data included 11 837 participants with MDD and 14 791 control individuals, for a total of 26 628 participants (59.1% female and 40.9% male). Among participants with MDD, 5347 (45.2%) were classified in the decreased A/W and 1871 (15.8%) in the increased A/W subgroups. Common genetic variants explained approximately 10% of the heritability in the 2 subgroups. The increased A/W subgroup showed a strong and positive genetic correlation (SE) with BMI (0.53 [0.15]; P = 6.3 × 10-4), whereas the decreased A/W subgroup showed an inverse correlation (-0.28 [0.14]; P = .06). Furthermore, the decreased A/W subgroup had a higher polygenic risk for increased BMI (odds ratio [OR], 1.18; 95% CI, 1.12-1.25; P = 1.6&thin
Brænne I, Willenborg C, Tragante V, et al., 2017, A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors, Scientific Reports, Vol: 7
© 2017 The Author(s). Cyclooxygenase-2 inhibitors (coxibs) are characterized by multiple molecular off-target effects and increased coronary artery disease (CAD) risk. Here, we systematically explored common variants of genes representing molecular targets of coxibs for association with CAD. Given a broad spectrum of pleiotropic effects of coxibs, our intention was to narrow potential mechanisms affecting CAD risk as we hypothesized that the affected genes may also display genomic signals of coronary disease risk. A Drug Gene Interaction Database search identified 47 gene products to be affected by coxibs. We traced association signals in 200-kb regions surrounding these genes in 84,813 CAD cases and 202,543 controls. Based on a threshold of 1 × 10-5 (Bonferroni correction for 3131 haplotype blocks), four gene loci yielded significant associations. The lead SNPs were rs7270354 (MMP9), rs4888383 (BCAR1), rs6905288 (VEGFA1), and rs556321 (CACNA1E). By additional genotyping, rs7270354 at MMP9 and rs4888383 at BCAR1 also reached the established GWAS threshold for genome-wide significance. The findings demonstrate overlap of genes affected by coxibs and those mediating CAD risk and points to further mechanisms, which are potentially responsible for coxib-associated CAD risk. The novel approach furthermore suggests that genetic studies may be useful to explore the clinical relevance of off-target drug effects.
Strawbridge RJ, Silveira A, Hoed MD, et al., 2017, Identification of a novel proinsulin-associated SNP and demonstration that proinsulin is unlikely to be a causal factor in subclinical vascular remodelling using Mendelian randomisation., Atherosclerosis, Vol: 266, Pages: 196-204
BACKGROUND AND AIMS: Increased proinsulin relative to insulin levels have been associated with subclinical atherosclerosis (measured by carotid intima-media thickness (cIMT)) and are predictive of future cardiovascular disease (CVD), independently of established risk factors. The mechanisms linking proinsulin to atherosclerosis and CVD are unclear. A genome-wide meta-analysis has identified nine loci associated with circulating proinsulin levels. Using proinsulin-associated SNPs, we set out to use a Mendelian randomisation approach to test the hypothesis that proinsulin plays a causal role in subclinical vascular remodelling. METHODS: We studied the high CVD-risk IMPROVE cohort (n = 3345), which has detailed biochemical phenotyping and repeated, state-of-the-art, high-resolution carotid ultrasound examinations. Genotyping was performed using Illumina Cardio-Metabo and Immuno arrays, which include reported proinsulin-associated loci. Participants with type 2 diabetes (n = 904) were omitted from the analysis. Linear regression was used to identify proinsulin-associated genetic variants. RESULTS: We identified a proinsulin locus on chromosome 15 (rs8029765) and replicated it in data from 20,003 additional individuals. An 11-SNP score, including the previously identified and the chromosome 15 proinsulin-associated loci, was significantly and negatively associated with baseline IMTmean and IMTmax (the primary cIMT phenotypes) but not with progression measures. However, MR-Eggers refuted any significant effect of the proinsulin-associated 11-SNP score, and a non-pleiotropic SNP score of three variants (including rs8029765) demonstrated no effect on baseline or progression cIMT measures. CONCLUSIONS: We identified a novel proinsulin-associated locus and demonstrated that whilst proinsulin levels are associated with cIMT measures, proinsulin per se is unlikely to have a causative effect on cIMT.
NCD Risk Factor Collaboration NCD-RisC, 2017, Worldwide trends in body-mass index, underweight, overweight, and obesity from 1975 to 2016: a pooled analysis of 2416 population-based measurement studies in 128·9 million children, adolescents, and adults., Lancet, Vol: 390, Pages: 2627-2642, ISSN: 0140-6736
BACKGROUND: Underweight, overweight, and obesity in childhood and adolescence are associated with adverse health consequences throughout the life-course. Our aim was to estimate worldwide trends in mean body-mass index (BMI) and a comprehensive set of BMI categories that cover underweight to obesity in children and adolescents, and to compare trends with those of adults. METHODS: We pooled 2416 population-based studies with measurements of height and weight on 128·9 million participants aged 5 years and older, including 31·5 million aged 5-19 years. We used a Bayesian hierarchical model to estimate trends from 1975 to 2016 in 200 countries for mean BMI and for prevalence of BMI in the following categories for children and adolescents aged 5-19 years: more than 2 SD below the median of the WHO growth reference for children and adolescents (referred to as moderate and severe underweight hereafter), 2 SD to more than 1 SD below the median (mild underweight), 1 SD below the median to 1 SD above the median (healthy weight), more than 1 SD to 2 SD above the median (overweight but not obese), and more than 2 SD above the median (obesity). FINDINGS: Regional change in age-standardised mean BMI in girls from 1975 to 2016 ranged from virtually no change (-0·01 kg/m(2) per decade; 95% credible interval -0·42 to 0·39, posterior probability [PP] of the observed decrease being a true decrease=0·5098) in eastern Europe to an increase of 1·00 kg/m(2) per decade (0·69-1·35, PP>0·9999) in central Latin America and an increase of 0·95 kg/m(2) per decade (0·64-1·25, PP>0·9999) in Polynesia and Micronesia. The range for boys was from a non-significant increase of 0·09 kg/m(2) per decade (-0·33 to 0·49, PP=0·6926) in eastern Europe to an increase of 0·77 kg/m(2) per decade (0·50-1·06, PP>0·9999) in Polynesia and Micronesia. Tre
Ghanbari M, Iglesias AI, Springelkamp H, et al., 2017, A Genome-Wide Scan for MicroRNA-Related Genetic Variants Associated With Primary Open-Angle Glaucoma., Invest Ophthalmol Vis Sci, Vol: 58, Pages: 5368-5377
Purpose: To identify microRNAs (miRNAs) involved in primary open-angle glaucoma (POAG), using genetic data. MiRNAs are small noncoding RNAs that posttranscriptionally regulate gene expression. Genetic variants in miRNAs or miRNA-binding sites within gene 3'-untranslated regions (3'UTRs) are expected to affect miRNA function and contribute to disease risk. Methods: Data from the recent genome-wide association studies on intraocular pressure, vertical cup-to-disc ratio (VCDR), cupa area and disc area were used to investigate the association of miRNAs with POAG endophenotypes. Putative targets of the associated miRNAs were studied according to their association with POAG and tested in cell line by transfection experiments for regulation by the miRNAs. Results: Of 411 miRNA variants, rs12803915:A/G in the terminal loop of pre-miR-612 and rs2273626:A/C in the seed sequence of miR-4707 were significantly associated with VCDR and cup area (P values < 1.2 × 10-4). The first variant is demonstrated to increase the miR-612 expression. We showed that the second variant does not affect the miR-4707 biogenesis, but reduces the binding of miR-4707-3p to CARD10, a gene known to be involved in glaucoma. Moreover, of 72,052 miRNA-binding-site variants, 47 were significantly associated with four POAG endophenotypes (P value < 6.9 × 10-6). Of these, we highlighted 10 variants that are more likely to affect miRNA-mediated gene regulation in POAG. These include rs3217992 and rs1063192, which have been shown experimentally to affect miR-138-3p- and miR-323b-5p-mediated regulation of CDKN2B. Conclusions: We identified a number of miRNAs that are associated with POAG endophenotypes. The identified miRNAs and their target genes are candidates for future studies on miRNA-related therapies for POAG.
Nano J, Muka T, Ligthart S, et al., 2017, Gamma-glutamyltransferase levels, prediabetes and type 2 diabetes: a Mendelian randomization study., Int J Epidemiol, Vol: 46, Pages: 1400-1409
Background: High levels of serum gamma-glutamyltransferase (GGT) are associated with increased risk of prediabetes and type 2 diabetes in observational studies. It is unclear whether this relationship is causal, arises from residual confounding or is a consequence of reverse causation. Methods: We used data from a prospective population-based cohort study, compromising 8611 individuals without diabetes at baseline. Cox proportional hazard models were used to study the association between serum GGT levels and incident prediabetes and diabetes. A Mendelian randomization (MR) study was performed using a genetic risk score consisting of 26 GGT-related variants, based on a genome-wide association study (GWAS) on liver enzymes. Association with diabetes and glycaemic traits were investigated within the Rotterdam Study and large-scale GWAS. Results: During follow-up, 1125 cases of prediabetes (mean follow-up 5.7 years) and 811 cases of type 2 diabetes (6.9 years) were ascertained. The predicted hazard ratios per standard deviation (SD) change in GGT levels in the multivariable model were 1.10 for prediabetes [95% confidence interval (CI): 1.02-1.19] and 1.19 for type 2 diabetes (95% CI: 1.10-1.30). The genetic risk score associated with increased GGT levels (beta per SD log GGT = 0.41, 95% CI: 0.35-0.47), explaining 3.5% of the observed variation in GGT. MR analysis did not provide evidence for a causal role of GGT, with a causal relative risk for prediabetes and type 2 diabetes per SD of log GGT of 0.97 (95% CI: 0.91-1.04) and 0.96 (95% CI: 0.89-1.04), respectively. Multiple instrumental analysis using genetic associations with type 2 diabetes and glycaemic traits from previous GWA studies detected no causal effect of GGT. Conclusions: MR analyses did not support a causal role of GGT on the risk of prediabetes or diabetes. The association of GGT with diabetes in observational studies is likely to be driven by reverse causation or confounding bias. As such, t
Muka T, Asllanaj E, Avazverdi N, et al., 2017, Age at natural menopause and risk of type 2 diabetes: a prospective cohort study., Diabetologia, Vol: 60, Pages: 1951-1960
AIMS/HYPOTHESIS: In this study, we aimed to examine the association between age at natural menopause and risk of type 2 diabetes, and to assess whether this association is independent of potential mediators. METHODS: We included 3639 postmenopausal women from the prospective, population-based Rotterdam Study. Age at natural menopause was self-reported retrospectively and was treated as a continuous variable and in categories (premature, <40 years; early, 40-44 years; normal, 45-55 years; and late menopause, >55 years [reference]). Type 2 diabetes events were diagnosed on the basis of medical records and glucose measurements from Rotterdam Study visits. HRs and 95% CIs were calculated using Cox proportional hazards models, adjusted for confounding factors; in another model, they were additionally adjusted for potential mediators, including obesity, C-reactive protein, glucose and insulin, as well as for levels of total oestradiol and androgens. RESULTS: During a median follow-up of 9.2 years, we identified 348 individuals with incident type 2 diabetes. After adjustment for confounders, HRs for type 2 diabetes were 3.7 (95% CI 1.8, 7.5), 2.4 (95% CI 1.3, 4.3) and 1.60 (95% CI 1.0, 2.8) for women with premature, early and normal menopause, respectively, relative to those with late menopause (p trend <0.001). The HR for type 2 diabetes per 1 year older at menopause was 0.96 (95% CI 0.94, 0.98). Further adjustment for BMI, glycaemic traits, metabolic risk factors, C-reactive protein, endogenous sex hormone levels or shared genetic factors did not affect this association. CONCLUSIONS/INTERPRETATION: Early onset of natural menopause is an independent marker for type 2 diabetes in postmenopausal women.
van der Schaft N, Brahimaj A, Wen K-X, et al., 2017, The association between serum uric acid and the incidence of prediabetes and type 2 diabetes mellitus: The Rotterdam Study, PLoS ONE, Vol: 12, ISSN: 1932-6203
BACKGROUND: Limited evidence is available about the association between serum uric acid and sub-stages of the spectrum from normoglycaemia to type 2 diabetes mellitus. We aimed to investigate the association between serum uric acid and risk of prediabetes and type 2 diabetes mellitus. METHODS: Eligible participants of the Rotterdam Study (n = 8,367) were classified into mutually exclusive subgroups of normoglycaemia (n = 7,030) and prediabetes (n = 1,337) at baseline. These subgroups were followed up for incident prediabetes (n = 1,071) and incident type 2 diabetes mellitus (n = 407), respectively. We used Cox proportional hazard models to determine hazard ratios (HRs) for incident prediabetes among individuals with normoglycaemia and incident type 2 diabetes mellitus among individuals with prediabetes. RESULTS: The mean duration of follow-up was 7.5 years for incident prediabetes and 7.2 years for incident type 2 diabetes mellitus. A standard deviation increment in serum uric acid was significantly associated with incident prediabetes among individuals with normoglycaemia (HR 1.10, 95% confidence interval (CI) 1.01; 1.18), but not with incident type 2 diabetes mellitus among individuals with prediabetes (HR 1.07, 95% CI 0.94; 1.21). Exclusion of individuals who used diuretics or individuals with hypertension did not change our results. Serum uric acid was significantly associated with incident prediabetes among normoglycaemic women (HR 1.13, 95% CI 1.02; 1.25) but not among normoglycaemic men (HR 1.08, 95% CI 0.96; 1.21). In contrast, serum uric acid was significantly associated with incident type 2 diabetes mellitus among prediabetic men (HR 1.23, 95% CI 1.01; 1.48) but not among prediabetic women (HR 1.00, 95% CI 0.84; 1.19). CONCLUSIONS: Our findings agree with the notion that serum uric acid is more closely related to early-phase mechanisms in the development of type 2 diabetes mellitus than late-phase mechanisms.
Nano J, Ghanbari M, Wang W, et al., 2017, Epigenome-wide Association Study Identifies Methylation Sites Associated With Liver Enzymes and Hepatic Steatosis, Gastroenterology, Vol: 153, Pages: 1096-1106.e2, ISSN: 0016-5085
Background & aimsEpigenetic mechanisms might be involved in the regulation of liver enzyme level. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of liver enzymes and hepatic steatosis.MethodsWe conducted an epigenome-wide association study in whole blood for liver enzymes levels including gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST), among a discovery set of 731 participants of the Rotterdam Study and sought replication in a non-overlapping sample of 719 individuals. Significant DNA methylation changes were further analysed to evaluate their relation with hepatic steatosis. Expression levels of the top identified gene were measured in 9 human liver cell lines and compared with expression profiles of its potential targets associated with lipid traits. The candidate gene was subsequently knocked down in human hepatoma cells using lentiviral vectors expressing small hairpin RNAs.ResultsEight probes annotated to SLC7A11, SLC1A5, SLC43A1, PHGDH, PSORS1C1, SREBF1, ANKS3 were associated with GGT and one probe annotated to SLC7A11 was associated with ALT after Bonferroni correction (1.0 × 10-7). No probe was identified for AST levels. Four probes for GGT levels including cg06690548 (SLC7A11), cg11376147 (SLC43A1), cg22304262 (SLC1A5) and cg14476101 (PHGDH), and one for ALT cg06690548 (SLC7A11) were replicated. DNA methylation at SLC7A11 was associated with reduced risk of hepatic steatosis in participants (odds ratio, 0.69; 95% CI= (0.55 - 0.93; P-value: 2.7 × 10-3). In functional experiments, SLC7A11 was highly expressed in human liver cells; its expression is positively correlated with expression of a panel of lipid-associated genes, indicating a role of SLC7A11 in lipid metabolism.ConclusionsOur results provide new insights into epigenetic mechanisms associated with markers of liver function and hepatic steatosis, laying the groundwork for future dia
Herder C, Gala TDLH, Carstensen-Kirberg M, et al., 2017, Circulating Levels of Interleukin 1-Receptor Antagonist and Risk of Cardiovascular Disease Meta-Analysis of Six Population-Based Cohorts, ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, Vol: 37, Pages: 1222-+, ISSN: 1079-5642
Song C, Burgess S, Eicher JD, et al., 2017, Causal effect of plasminogen activator inhibitor type 1 on coronary heart disease, Journal of the American Heart Association, Vol: 6, ISSN: 2047-9980
Background--Plasminogen activator inhibitor type 1 (PAI-1) plays an essential role in the fibrinolysis system and thrombosis. Population studies have reported that blood PAI-1 levels are associated with increased risk of coronary heart disease (CHD). However, it is unclear whether the association reflects a causal influence of PAI-1 on CHD risk. Methods and Results--To evaluate the association between PAI-1 and CHD, we applied a 3-step strategy. First, we investigated the observational association between PAI-1 and CHD incidence using a systematic review based on a literature search for PAI-1 and CHD studies. Second, we explored the causal association between PAI-1 and CHD using a Mendelian randomization approach using summary statistics from large genome-wide association studies. Finally, we explored the causal effect of PAI-1 on cardiovascular risk factors including metabolic and subclinical atherosclerosis measures. In the systematic meta-analysis, the highest quantile of blood PAI-1 level was associated with higher CHD risk comparing with the lowest quantile (odds ratio=2.17; 95% CI: 1.53, 3.07) in an age- and sex-adjusted model. The effect size was reduced in studies using a multivariable-adjusted model (odds ratio=1.46; 95% CI: 1.13, 1.88). The Mendelian randomization analyses suggested a causal effect of increased PAI-1 level on CHD risk (odds ratio=1.22 per unit increase of log-transformed PAI-1; 95% CI: 1.01, 1.47). In addition, we also detected a causal effect of PAI-1 on elevating blood glucose and high-density lipoprotein cholesterol. Conclusions--Our study indicates a causal effect of elevated PAI-1 level on CHD risk, which may be mediated by glucose dysfunction.
Ghanbari M, Erkeland SJ, Xu L, et al., 2017, Genetic variants in microRNAs and their binding sites within gene 3UTRs associate with susceptibility to age-related macular degeneration, Human Mutation, Vol: 38, Pages: 827-838, ISSN: 1059-7794
Age-related macular degeneration (AMD), the leading cause of blindness in the elderly, is a complex disease that results from multiple genetic and environmental factors. MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate target mRNAs and are frequently implicated in human diseases. Here, we investigated the association of genetic variants in miRNAs and miRNA-binding sites within gene 3′-untranslated regions (3′UTRs) with AMD using data from the largest AMD genome-wide association study. First, we identified three variants in miRNAs significantly associated with AMD. These include rs2168518:G>A in the miR-4513 seed sequence, rs41292412:C>T in pre-miR-122/miR-3591, and rs4351242:C>T in the terminal-loop of pre-miR-3135b. We demonstrated that these variants reduce expression levels of the mature miRNAs in vitro and pointed the target genes that may mediate downstream effects of these miRNAs in AMD. Second, we identified 54 variants (in 31 genes) in miRNA-binding sites associated with AMD. Based on stringent prioritization criteria, we highlighted the variants that are more likely to have an impact on the miRNA-target interactions. Further, we selected rs4151672:C>T within the CFB 3′UTR and experimentally showed that while miR-210-5p downregulates expression of CFB, the variant decreases miR-210-5p-mediated repression of CFB. Together, our findings support the notion that miRNAs may play a role in AMD.
Saleheen D, Zhao W, Young R, et al., 2017, Loss of Cardioprotective Effects at the ADAMTS7 Locus as a Result of Gene-Smoking Interactions, CIRCULATION, Vol: 135, Pages: 2336-+, ISSN: 0009-7322
Gorski M, Most PJVD, Teumer A, et al., 2017, Corrigendum: 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function., Sci Rep, Vol: 7, Pages: 46835-46835
This corrects the article DOI: 10.1038/srep45040.
Gorski M, van der Most PJ, Teumer A, et al., 2017, 1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function., Sci Rep, Vol: 7
HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data. We identified 10 novel loci with p-value < 5 × 10-8 previously missed by HapMap-based GWAS. Six of these loci (HOXD8, ARL15, PIK3R1, EYA4, ASTN2, and EPB41L3) are tagged by common SNPs unique to the 1000 Genomes reference panel. Using pathway analysis, we identified 39 significant (FDR < 0.05) genes and 127 significantly (FDR < 0.05) enriched gene sets, which were missed by our previous analyses. Among those, the 10 identified novel genes are part of pathways of kidney development, carbohydrate metabolism, cardiac septum development and glucose metabolism. These results highlight the utility of re-imputing from denser reference panels, until whole-genome sequencing becomes feasible in large samples.
Stringa N, Brahimaj A, Zaciragic A, et al., 2017, Relation of antioxidant capacity of diet and markers of oxidative status with C-reactive protein and adipocytokines: a prospective study, Metabolism: clinical and experimental, Vol: 71, Pages: 171-181, ISSN: 0026-0495
BackgroundThe role of dietary antioxidants and plasma oxidant-antioxidant status in low-grade chronic inflammation and adipocytokine levels is not established yet.ObjectivesWe aimed to evaluate whether total dietary antioxidant capacity (assessed by dietary ferric reducing antioxidant potential (FRAP)), serum uric acid (UA) and gamma glutamyltransferase (GGT) were associated with low-grade chronic inflammation and circulating adipocytokines.MethodsData of 4506 participants aged ≥ 55 years from the Rotterdam Study were analyzed. Baseline (1990–1993) FRAP score was assessed by a food frequency questionnaire. Baseline UA and GGT levels were assessed in non-fasting serum samples. Serum high sensitivity C-reactive protein (hs-CRP) was measured at baseline and 10 years later. Plasma leptin, adiponectin, plasminogen activator inhibitor-1 (PAI-1) and resistin levels were assessed 10 years later.ResultsA high FRAP score was associated with lower levels of UA and GGT. Overall, no association was found between FRAP and hs-CRP levels. FRAP score was associated with lower levels of leptin and PAI-1, higher levels of adiponectin, and no difference in resistin levels. Increased levels of UA were associated with higher levels of hs-CRP, PAI-1 and leptin; lower levels of adiponectin and no difference in resistin levels. Similarly, GGT was associated with higher levels of hs-CRP whereas no association was observed between GGT and adipocytokines.ConclusionThese findings suggest that overall antioxidant capacity of diet and low levels of UA are associated with circulating adipocytokines whereas no consistent association was found with hs-CRP.
Böger CA, Gorski M, McMahon GM, et al., 2017, NFAT5 and SLC4A10 Loci Associate with Plasma Osmolality., Journal of the American Society of Nephrology, Vol: 28, ISSN: 1533-3450
Disorders of water balance, an excess or deficit of total body water relative to body electrolyte content, are common and ascertained by plasma hypo- or hypernatremia, respectively. We performed a two-stage genome-wide association study meta-analysis on plasma sodium concentration in 45,889 individuals of European descent (stage 1 discovery) and 17,637 additional individuals of European descent (stage 2 replication), and a transethnic meta-analysis of replicated single-nucleotide polymorphisms in 79,506 individuals (63,526 individuals of European descent, 8765 individuals of Asian Indian descent, and 7215 individuals of African descent). In stage 1, we identified eight loci associated with plasma sodium concentration at P<5.0 × 10(-6) Of these, rs9980 at NFAT5 replicated in stage 2 meta-analysis (P=3.1 × 10(-5)), with combined stages 1 and 2 genome-wide significance of P=5.6 × 10(-10) Transethnic meta-analysis further supported the association at rs9980 (P=5.9 × 10(-12)). Additionally, rs16846053 at SLC4A10 showed nominally, but not genome-wide, significant association in combined stages 1 and 2 meta-analysis (P=6.7 × 10(-8)). NFAT5 encodes a ubiquitously expressed transcription factor that coordinates the intracellular response to hypertonic stress but was not previously implicated in the regulation of systemic water balance. SLC4A10 encodes a sodium bicarbonate transporter with a brain-restricted expression pattern, and variant rs16846053 affects a putative intronic NFAT5 DNA binding motif. The lead variants for NFAT5 and SLC4A10 are cis expression quantitative trait loci in tissues of the central nervous system and relevant to transcriptional regulation. Thus, genetic variation in NFAT5 and SLC4A10 expression and function in the central nervous system may affect the regulation of systemic water balance.
Brahimaj A, Ligthart S, Ghanbari M, et al., 2017, Novel inflammatory markers for incident pre-diabetes and type 2 diabetes: the Rotterdam Study, European Journal of Epidemiology, Vol: 32, Pages: 217-226, ISSN: 0393-2990
The immune response involved in each phase oftype 2 diabetes (T2D) development might be different. Weaimed to identify novel inflammatory markers that predictprogression from normoglycemia to pre-diabetes, incidentT2D and insulin therapy. We used plasma levels of 26inflammatory markers in 971 subjects from the RotterdamStudy. Among them 17 are novel and 9 previously studied.Cox regression models were built to perform survivalanalysis. Main Outcome Measures: During a follow-up ofup to 14.7 years (between April 1, 1997, and Jan 1, 2012)139 cases of pre-diabetes, 110 cases of T2D and 26 cases ofinsulin initiation were identified. In age and sex adjustedCox models, IL13 (HR = 0.78), EN-RAGE (1.30), CFH(1.24), IL18 (1.22) and CRP (1.32) were associated withincident pre-diabetes. IL13 (0.62), IL17 (0.75), EN-RAGE(1.25), complement 3 (1.44), IL18 (1.35), TNFRII (1.27),IL1ra (1.24) and CRP (1.64) were associated with incidentT2D. In multivariate models, IL13 (0.77), EN-RAGE(1.23) and CRP (1.26) remained associated with pre-diabetes.IL13 (0.67), IL17 (0.76) and CRP (1.32) remainedassociated with T2D. IL13 (0.55) was the only markerassociated with initiation of insulin therapy in diabetics.Various inflammatory markers are associated with progressionfrom normoglycemia to pre-diabetes (IL13, ENRAGE,CRP), T2D (IL13, IL17, CRP) or insulin therapystart (IL13). Among them, EN-RAGE is a novel inflammatorymarker for pre-diabetes, IL17 for incident T2D andIL13 for pre-diabetes, incident T2D and insulin therapystart.
Brahimaj A, Ligthart S, Ikram MA, et al., 2017, Serum Levels of Apolipoproteins and Incident Type 2 Diabetes: A Prospective Cohort Study, DIABETES CARE, Vol: 40, Pages: 346-351, ISSN: 0149-5992
Muka T, Nano J, Jaspers L, et al., 2017, Associations of Steroid Sex Hormones and Sex Hormone-Binding Globulin With the Risk of Type 2 Diabetes in Women: A Population-Based Cohort Study and Meta-analysis, DIABETES, Vol: 66, Pages: 577-586, ISSN: 0012-1797
Li M, Li Y, Weeks O, et al., 2017, SOS2 and ACP1 Loci Identified through Large-Scale Exome Chip Analysis Regulate Kidney Development and Function., J Am Soc Nephrol, Vol: 28, Pages: 981-994
Genome-wide association studies have identified >50 common variants associated with kidney function, but these variants do not fully explain the variation in eGFR. We performed a two-stage meta-analysis of associations between genotypes from the Illumina exome array and eGFR on the basis of serum creatinine (eGFRcrea) among participants of European ancestry from the CKDGen Consortium (nStage1: 111,666; nStage2: 48,343). In single-variant analyses, we identified single nucleotide polymorphisms at seven new loci associated with eGFRcrea (PPM1J, EDEM3, ACP1, SPEG, EYA4, CYP1A1, and ATXN2L; PStage1<3.7×10-7), of which most were common and annotated as nonsynonymous variants. Gene-based analysis identified associations of functional rare variants in three genes with eGFRcrea, including a novel association with the SOS Ras/Rho guanine nucleotide exchange factor 2 gene, SOS2 (P=5.4×10-8 by sequence kernel association test). Experimental follow-up in zebrafish embryos revealed changes in glomerular gene expression and renal tubule morphology in the embryonic kidney of acp1- and sos2-knockdowns. These developmental abnormalities associated with altered blood clearance rate and heightened prevalence of edema. This study expands the number of loci associated with kidney function and identifies novel genes with potential roles in kidney formation.
Kieboom BCT, Ligthart S, Dehghan A, et al., 2017, Serum magnesium and the risk of prediabetes: a population-based cohort study, Diabetologia, Vol: 60, Pages: 843-853, ISSN: 0012-186X
Aims/hypothesis: Previous studies have found an association between serum magnesium and incident diabetes; however, this association may be due to reverse causation, whereby diabetes may induce urinary magnesium loss. In contrast, in prediabetes (defined as impaired fasting glucose), serum glucose levels are below the threshold for urinary magnesium wasting and, hence, unlikely to influence serum magnesium levels. Thus, to study the directionality of the association between serum magnesium levels and diabetes, we investigated its association with prediabetes. We also investigated whether magnesium-regulating genes influence diabetes risk through serum magnesium levels. Additionally, we quantified the effect of insulin resistance in the association between serum magnesium levels and diabetes risk. Methods: Within the population-based Rotterdam Study, we used Cox models, adjusted for age, sex, lifestyle factors, comorbidities, kidney function, serum levels of electrolytes and diuretic use, to study the association between serum magnesium and prediabetes/diabetes. In addition, we performed two mediation analyses: (1) to study if common genetic variation in eight magnesium-regulating genes influence diabetes risk through serum magnesium levels; and (2) to quantify the proportion of the effect of serum magnesium levels on diabetes that is mediated through insulin resistance (quantified by HOMA-IR). Results: A total of 8555 participants (mean age, 64.7 years; median follow-up, 5.7 years) with normal glucose levels (mean ± SD: 5.46 ± 0.58 mmol/l) at baseline were included. A 0.1 mmol/l decrease in serum magnesium level was associated with an increase in diabetes risk (HR 1.18 [95% CI 1.04, 1.33]), confirming findings from previous studies. Of interest, a similar association was found between serum magnesium levels and prediabetes risk (HR 1.12 [95% CI 1.01, 1.25] ). Genetic variation in CLDN19, CNNM2, FXYD2, SLC41A2, and TRPM6 significantl
Braun KVE, Dhana K, de Vries PS, et al., 2017, Epigenome-wide association study (EWAS) on lipids: the Rotterdam Study, Clinical Epigenetics, Vol: 9, ISSN: 1868-7083
BackgroundDNA methylation is a key epigenetic mechanism that is suggested to be associated with blood lipid levels. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of triglycerides, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and total cholesterol in 725 participants of the Rotterdam Study, a population-based cohort study. Subsequently, we sought replication in a non-overlapping set of 760 participants.ResultsGenome-wide methylation levels were measured in whole blood using the Illumina Methylation 450 array. Associations between lipid levels and DNA methylation beta values were examined using linear mixed-effect models. All models were adjusted for sex, age, smoking, white blood cell proportions, array number, and position on array. A Bonferroni-corrected p value lower than 1.08 × 10−7 was considered statistically significant. Five CpG sites annotated to genes including DHCR24, CPT1A, ABCG1, and SREBF1 were identified and replicated. Four CpG sites were associated with triglycerides, including CpG sites annotated to CPT1A (cg00574958 and cg17058475), ABCG1 (cg06500161), and SREBF1 (cg11024682). Two CpG sites were associated with HDL-C, including ABCG1 (cg06500161) and DHCR24 (cg17901584). No significant associations were observed with LDL-C or total cholesterol.ConclusionsWe report an association of HDL-C levels with methylation of a CpG site near DHCR24, a protein-coding gene involved in cholesterol biosynthesis, which has previously been reported to be associated with other metabolic traits. Furthermore, we confirmed previously reported associations of methylation of CpG sites within CPT1A, ABCG1, and SREBF1 and lipids. These results provide insight in the mechanisms that are involved in lipid metabolism.
de Vries PS, Sabater-Lleal M, Chasman DI, et al., 2017, Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study, PLoS ONE, Vol: 12, ISSN: 1932-6203
An increasing number of genome-wide association (GWA) studies are now using the higherresolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectationthat 1000G imputation will lead to the discovery of additional associated loci when comparedto HapMap imputation. In order to assess the improvement of 1000G over HapMapimputation in identifying associated loci, we compared the results of GWA studies of circulatingfibrinogen based on the two reference panels. Using both HapMap and 1000G imputationwe performed a meta-analysis of 22 studies comprising the same 91,953 individuals.We identified six additional signals using 1000G imputation, while 29 loci were associatedusing both HapMap and 1000G imputation. One locus identified using HapMap imputationwas not significant using 1000G imputation. The genome-wide significance threshold of5×10−8 is based on the number of independent statistical tests using HapMap imputation,and 1000G imputation may lead to further independent tests that should be corrected for.When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10−8),the number of loci significant only using HapMap imputation increased to 4 while the numberof loci significant only using 1000G decreased to 5. In conclusion, 1000G imputationenabled the identification of 20% more loci than HapMap imputation, although the advantageof 1000G imputation became less clear when a stricter Bonferroni correction was used.More generally, our results provide insights that are applicable to the implementation ofother dense reference panels that are under development.
van Rooij FJA, Qayyum R, Smith AV, et al., 2017, Genome-wide Trans-ethnic Meta-analysis Identifies Seven Genetic Loci Influencing Erythrocyte Traits and a Role for RBPMS in Erythropoiesis, AMERICAN JOURNAL OF HUMAN GENETICS, Vol: 100, Pages: 51-63, ISSN: 0002-9297
Brænne I, Zeng L, Willenborg C, et al., 2017, Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk., PLoS One, Vol: 12
Glatiramer acetate is used therapeutically in multiple sclerosis but also known for adverse effects including elevated coronary artery disease (CAD) risk. The mechanisms underlying the cardiovascular side effects of the medication are unclear. Here, we made use of the chromosomal variation in the genes that are known to be affected by glatiramer treatment. Focusing on genes and gene products reported by drug-gene interaction database to interact with glatiramer acetate we explored a large meta-analysis on CAD genome-wide association studies aiming firstly, to investigate whether variants in these genes also affect cardiovascular risk and secondly, to identify new CAD risk genes. We traced association signals in a 200-kb region around genomic positions of genes interacting with glatiramer in up to 60 801 CAD cases and 123 504 controls. We validated the identified association in additional 21 934 CAD cases and 76 087 controls. We identified three new CAD risk alleles within the TGFB1 region on chromosome 19 that independently affect CAD risk. The lead SNP rs12459996 was genome-wide significantly associated with CAD in the extended meta-analysis (odds ratio 1.09, p = 1.58×10-12). The other two SNPs at the locus were not in linkage disequilibrium with the lead SNP and by a conditional analysis showed p-values of 4.05 × 10-10 and 2.21 × 10-6. Thus, studying genes reported to interact with glatiramer acetate we identified genetic variants that concordantly with the drug increase the risk of CAD. Of these, TGFB1 displayed signal for association. Indeed, the gene has been associated with CAD previously in both in vivo and in vitro studies. Here we establish genome-wide significant association with CAD in large human samples.
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