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Perrino PA, Talbot L, Kirkland R, Hill A, Rendall AR, Mountford HS, Taylor J, Buscarello AN, Lahiri N, Saggar A, Fitch RH, Newbury DF. Multi-level evidence of an allelic hierarchy of USH2A variants in hearing, auditory processing and speech/language outcomes. Commun Biol 2020; 3:180. [PMID: 32313182 PMCID: PMC7170883 DOI: 10.1038/s42003-020-0885-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/11/2020] [Indexed: 11/30/2022] Open
Abstract
Language development builds upon a complex network of interacting subservient systems. It therefore follows that variations in, and subclinical disruptions of, these systems may have secondary effects on emergent language. In this paper, we consider the relationship between genetic variants, hearing, auditory processing and language development. We employ whole genome sequencing in a discovery family to target association and gene x environment interaction analyses in two large population cohorts; the Avon Longitudinal Study of Parents and Children (ALSPAC) and UK10K. These investigations indicate that USH2A variants are associated with altered low-frequency sound perception which, in turn, increases the risk of developmental language disorder. We further show that Ush2a heterozygote mice have low-level hearing impairments, persistent higher-order acoustic processing deficits and altered vocalizations. These findings provide new insights into the complexity of genetic mechanisms serving language development and disorders and the relationships between developmental auditory and neural systems. Peter Perrino et al. identify variants in USH2A linked to a dominant language disorder in a human family and find that these variants are also associated with low-frequency hearing at the population level. They investigate the function of USH2A variants in mice, showing that mutations in this gene are responsible for hearing loss.
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Affiliation(s)
- Peter A Perrino
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA.,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA
| | - Lidiya Talbot
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Rose Kirkland
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.,School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
| | - Amanda Hill
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Amanda R Rendall
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA.,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA
| | - Hayley S Mountford
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Jenny Taylor
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK.,NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
| | | | - Alexzandrea N Buscarello
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA.,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA
| | - Nayana Lahiri
- Institute of Molecular and Clinical Sciences, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, UK
| | - Anand Saggar
- Institute of Molecular and Clinical Sciences, St George's, University of London & St George's University Hospitals NHS Foundation Trust, London, UK
| | - R Holly Fitch
- Department of Psychological Science/Behavioral Neuroscience, University of Connecticut, Storrs, CT, USA. .,UConn Institute of Brain and Cognitive Sciences; UConn Murine Behavioral Neurogenetics Facility, Storrs, CT, USA.
| | - Dianne F Newbury
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK.
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Functional Analysis of Promoter Variants in Genes Involved in Sex Steroid Action, DNA Repair and Cell Cycle Control. Genes (Basel) 2019; 10:genes10030186. [PMID: 30823486 PMCID: PMC6470759 DOI: 10.3390/genes10030186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/09/2019] [Accepted: 02/21/2019] [Indexed: 01/16/2023] Open
Abstract
Genetic variants affecting the regulation of gene expression are among the main causes of human diversity. The potential importance of regulatory polymorphisms is underscored by results from Genome Wide Association Studies, which have already implicated such polymorphisms in the susceptibility to complex diseases such as breast cancer. In this study, we re-sequenced the promoter regions of 24 genes involved in pathways related to breast cancer including sex steroid action, DNA repair, and cell cycle control in 60 unrelated Caucasian individuals. We constructed haplotypes and assessed the functional impact of promoter variants using gene reporter assays and electrophoretic mobility shift assays. We identified putative functional variants within the promoter regions of estrogen receptor 1 (ESR1), ESR2, forkhead box A1 (FOXA1), ubiquitin interaction motif containing 1 (UIMC1) and cell division cycle 7 (CDC7). The functional polymorphism on CDC7, rs13447455, influences CDC7 transcriptional activity in an allele-specific manner and alters DNA–protein complex formation in breast cancer cell lines. Moreover, results from the Breast Cancer Association Consortium show a marginal association between rs13447455 and breast cancer risk (p = 9.3 × 10−5), thus warranting further investigation. Furthermore, our study has helped provide methodological solutions to some technical difficulties that were encountered with gene reporter assays, particularly regarding inter-clone variability and statistical consistency.
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Lee JH, Lee AJ, Dang LH, Pang D, Kisselev S, Krinsky-McHale SJ, Zigman WB, Luchsinger JA, Silverman W, Tycko B, Clark LN, Schupf N. Candidate gene analysis for Alzheimer's disease in adults with Down syndrome. Neurobiol Aging 2017; 56:150-158. [PMID: 28554490 DOI: 10.1016/j.neurobiolaging.2017.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 03/17/2017] [Accepted: 04/21/2017] [Indexed: 11/16/2022]
Abstract
Individuals with Down syndrome (DS) overexpress many genes on chromosome 21 due to trisomy and have high risk of dementia due to the Alzheimer's disease (AD) neuropathology. However, there is a wide range of phenotypic differences (e.g., age at onset of AD, amyloid β levels) among adults with DS, suggesting the importance of factors that modify risk within this particularly vulnerable population, including genotypic variability. Previous genetic studies in the general population have identified multiple genes that are associated with AD. This study examined the contribution of polymorphisms in these genes to the risk of AD in adults with DS ranging from 30 to 78 years of age at study entry (N = 320). We used multiple logistic regressions to estimate the likelihood of AD using single-nucleotide polymorphisms (SNPs) in candidate genes, adjusting for age, sex, race/ethnicity, level of intellectual disability and APOE genotype. This study identified multiple SNPs in APP and CST3 that were associated with AD at a gene-wise level empirical p-value of 0.05, with odds ratios in the range of 1.5-2. SNPs in MARK4 were marginally associated with AD. CST3 and MARK4 may contribute to our understanding of potential mechanisms where CST3 may contribute to the amyloid pathway by inhibiting plaque formation, and MARK4 may contribute to the regulation of the transition between stable and dynamic microtubules.
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Affiliation(s)
- Joseph H Lee
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Taub Institute, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA.
| | - Annie J Lee
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lam-Ha Dang
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA
| | - Deborah Pang
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Sergey Kisselev
- Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Sharon J Krinsky-McHale
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Warren B Zigman
- Department of Psychology, NYS Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - José A Luchsinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Tycko
- Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lorraine N Clark
- Taub Institute, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Nicole Schupf
- Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Taub Institute, College of Physicians and Surgeons, Columbia University, New York, NY, USA; Department of Epidemiology, School of Public Health, Columbia University, New York, NY, USA
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4
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Schupf N, Lee A, Park N, Dang LH, Pang D, Yale A, Oh DKT, Krinsky-McHale SJ, Jenkins EC, Luchsinger JA, Zigman WB, Silverman W, Tycko B, Kisselev S, Clark L, Lee JH. Candidate genes for Alzheimer's disease are associated with individual differences in plasma levels of beta amyloid peptides in adults with Down syndrome. Neurobiol Aging 2015; 36:2907.e1-10. [PMID: 26166206 DOI: 10.1016/j.neurobiolaging.2015.06.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 01/08/2023]
Abstract
We examined the contribution of candidates genes for Alzheimer's disease (AD) to individual differences in levels of beta amyloid peptides in adults with Down syndrom, a population at high risk for AD. Participants were 254 non-demented adults with Down syndrome, 30-78 years of age. Genomic deoxyribonucleic acid was genotyped using an Illumina GoldenGate custom array. We used linear regression to examine differences in levels of Aβ peptides associated with the number of risk alleles, adjusting for age, sex, level of intellectual disability, race and/or ethnicity, and the presence of the APOE ε4 allele. For Aβ42 levels, the strongest gene-wise association was found for a single nucleotide polymorphism (SNP) on CAHLM1; for Aβ40 levels, the strongest gene-wise associations were found for SNPs in IDE and SOD1, while the strongest gene-wise associations with levels of the Aβ42/Aβ40 ratio were found for SNPs in SORCS1. Broadly classified, variants in these genes may influence amyloid precursor protein processing (CALHM1, IDE), vesicular trafficking (SORCS1), and response to oxidative stress (SOD1).
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Affiliation(s)
- Nicole Schupf
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; G.H. Sergievsky Center, New York, NY, USA; Department of Epidemiology, Columbia University Medical Center, New York, NY, USA; Department of Psychiatry, Columbia University Medical Center, New York, NY, USA.
| | - Annie Lee
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Naeun Park
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Lam-Ha Dang
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Deborah Pang
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Alexander Yale
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - David Kyung-Taek Oh
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sharon J Krinsky-McHale
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Edmund C Jenkins
- Department of Human Genetics, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - José A Luchsinger
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Warren B Zigman
- Department of Psychology, New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Benjamin Tycko
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Sergey Kisselev
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Lorraine Clark
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Joseph H Lee
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA; G.H. Sergievsky Center, New York, NY, USA; Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
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TP53 Arg72Pro polymorphism (rs1042522) and risk of endometriosis among Asian and Caucasian populations. Eur J Obstet Gynecol Reprod Biol 2015; 189:73-8. [PMID: 25889195 DOI: 10.1016/j.ejogrb.2015.03.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/23/2014] [Accepted: 03/20/2015] [Indexed: 12/20/2022]
Abstract
This study was conducted to investigate the association between TP53 Arg72Pro polymorphism (rs1042522) and risk of endometriosis. Studies were retrieved from Pubmed, Embase and HuGENet, and four models [dominant (AA+AG vs. GG), recessive (AA vs. AG+GG), co-dominant (AA vs. AG, AA vs. GG) and allele analysis (A vs. G), combined with odds ratios (OR) and 95% confidence intervals (CI)], were applied to evaluate this association. Fourteen eligible studies from eight countries were included. The pooled analysis identified a significant association between TP53 Arg72Pro polymorphism (rs1042522) and risk of endometriosis [dominant: OR 0.746, 95% CI 0.585-0.952, I(2)=59%; recessive: OR 0.650, 95% CI 0.510-0.829, I(2)=73%; co-dominant (GG vs. GC): OR 0.676, 95% CI 0.637-0.851, I(2)=67%; co-dominant (GG vs. CC): OR 0.564, 95% CI 0.395-0.806, I(2)=74%; allele analysis: OR 0.762, 95% CI 0.654-0.888, I(2)=71%]. In the subgroup analysis, the same positive associations were found among Asians. After removing studies that did not satisfy Hardy-Weinberg equilibrium, significant correlations were confirmed in both the pooled analysis and the Asian subgroup. Three bioinformatic methods (TagSNP calculations, functional prediction and linkage disequilibrium analysis) were used to determine the importance of TP53 Arg72Pro polymorphism (rs1042522), and suggested that this locus may be equally important regardless of ethnicity. In conclusion, TP53 Arg72Pro polymorphism (rs1042522) was positively associated with risk of endometriosis, particularly among Asians. However, its potential role in Caucasians should not be ignored.
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X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphism significantly associated with prostate cancer. Int J Biol Markers 2015; 30:e12-21. [PMID: 25262700 DOI: 10.5301/jbm.5000111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2014] [Indexed: 12/20/2022]
Abstract
Prostate cancer (Pca) is one of the noncutaneous cancers occurring worldwide. Its high morbidity and mortality make it a concern. X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphism (rs25487) has been reported to be related to Pca. However, the conclusions are controversial. In this study, PubMed, HuGENet and Chinese National Knowledge Infrastructure (CNKI) databases were combined with a comprehensive literature search. Four models including dominant (AA + AG vs. GG), recessive (AA vs. AG+GG), codominant (AA vs. AG, AA vs. GG) and per-allele analysis (A vs. G) were applied. Finally, 15 studies with 18 sets of data were included. A positive association was discovered in pooled results for recessive (odds ratio [OR]=1.202, 95% confidence interval [95% CI], 1.060-1.363, I2=46.20%), codominant (AA vs. AG; OR=1.258, 95% CI, 1.099-1.439, I2=38.50%; AA vs. GG; OR=1.283, 95% CI, 1.027-1.602, I2=51.70%) and allele analysis (OR=1.116, 95% CI, 1.001-1.244, I2=58.00%). In ethnicity subgroup analysis, these 4 models were also significant in the Asian subgroup. However, for whites, only 2 models seemed to be significant (AA vs. AG+GG: OR=1.525, 95% CI, 1.111-2.093, I2=52.60%; AA vs. AG: OR=1.678, 95% CI, 1.185-2.375, I2=30.70%). In further analysis, we regrouped the data based on race, in which pooled results and Asian subgroup were again shown to be positive. In the next analysis, expression quantitative trait loci (eQTL), linkage disequilibrium (LD), TagSNP and functional analysis were used. The results showed that the SNP was a tag and functional SNP with LD block in both Asians and whites. In summary, we suggest that XRCC1 Arg399Gln might be significantly associated with development of Pca.
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Lee WT, Huang CC, Chen KC, Wong TY, Ou CY, Tsai ST, Yen CJ, Fang SY, Lo HI, Wu YH, Hsueh WT, Yang MW, Lin FC, Hsiao JR, Huang JS, Chang JY, Chang KY, Wu SY, Lin CL, Wang YH, Weng YL, Yang HC, Chang JS. Genetic polymorphisms in the prostaglandin pathway genes and risk of head and neck cancer. Oral Dis 2014; 21:207-15. [PMID: 24724948 DOI: 10.1111/odi.12244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/05/2014] [Accepted: 03/31/2014] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Previous studies examining the association between genetic variations in prostaglandin pathway and risk of head and neck cancer (HNC) have only included polymorphisms in the PTGS2 (COX2) gene. This study investigated the association between genetic polymorphisms of six prostaglandin pathway genes (PGDS, PTGDS, PTGES, PTGIS, PTGS1 and PTGS2), and risk of HNC. METHODS Interviews regarding the consumption of alcohol, betel quid, and cigarette were conducted with 222 HNC cases and 214 controls. Genotyping was performed for 48 tag and functional single-nucleotide polymorphisms (SNPs). RESULTS Two tag SNPs of PTGIS showed a significant association with HNC risk [rs522962: log-additive odds ratio (OR) = 1.42, 95% confidence interval (CI): 1.01-1.99 and dominant OR = 1.58, 95% CI: 1.02-2.47; rs6125671: log-additive OR = 1.49, 95% CI: 1.08-2.05 and dominant OR = 1.96, 95% CI: 1.16-3.32]. In addition, a region in PTGIS tagged by rs927068 and rs6019902 was significantly associated with risk of HNC (global P = 0.007). Finally, several SNPs interacted with betel quid and cigarette to influence the risk of HNC. CONCLUSIONS Genetic variations in prostaglandin pathway genes are associated with risk of HNC and may modify the relationship between use of betel quid or cigarette and development of HNC.
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Affiliation(s)
- W-T Lee
- Department of Otolaryngology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Larsen LH, Angquist L, Vimaleswaran KS, Hager J, Viguerie N, Loos RJF, Handjieva-Darlenska T, Jebb SA, Kunesova M, Larsen TM, Martinez JA, Papadaki A, Pfeiffer AFH, van Baak MA, Sørensen TI, Holst C, Langin D, Astrup A, Saris WHM. Analyses of single nucleotide polymorphisms in selected nutrient-sensitive genes in weight-regain prevention: the DIOGENES study. Am J Clin Nutr 2012; 95:1254-60. [PMID: 22492381 DOI: 10.3945/ajcn.111.016543] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Differences in the interindividual response to dietary intervention could be modified by genetic variation in nutrient-sensitive genes. OBJECTIVE This study examined single nucleotide polymorphisms (SNPs) in presumed nutrient-sensitive candidate genes for obesity and obesity-related diseases for main and dietary interaction effects on weight, waist circumference, and fat mass regain over 6 mo. DESIGN In total, 742 participants who had lost ≥ 8% of their initial body weight were randomly assigned to follow 1 of 5 different ad libitum diets with different glycemic indexes and contents of dietary protein. The SNP main and SNP-diet interaction effects were analyzed by using linear regression models, corrected for multiple testing by using Bonferroni correction and evaluated by using quantile-quantile (Q-Q) plots. RESULTS After correction for multiple testing, none of the SNPs were significantly associated with weight, waist circumference, or fat mass regain. Q-Q plots showed that ALOX5AP rs4769873 showed a higher observed than predicted P value for the association with less waist circumference regain over 6 mo (-3.1 cm/allele; 95% CI: -4.6, -1.6; P/Bonferroni-corrected P = 0.000039/0.076), independently of diet. Additional associations were identified by using Q-Q plots for SNPs in ALOX5AP, TNF, and KCNJ11 for main effects; in LPL and TUB for glycemic index interaction effects on waist circumference regain; in GHRL, CCK, MLXIPL, and LEPR on weight; in PPARC1A, PCK2, ALOX5AP, PYY, and ADRB3 on waist circumference; and in PPARD, FABP1, PLAUR, and LPIN1 on fat mass regain for dietary protein interaction. CONCLUSION The observed effects of SNP-diet interactions on weight, waist, and fat mass regain suggest that genetic variation in nutrient-sensitive genes can modify the response to diet. This trial was registered at clinicaltrials.gov as NCT00390637.
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Affiliation(s)
- Lesli H Larsen
- Department of Human Nutrition, LIFE, University of Copenhagen, Copenhagen, Denmark.
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Ignatovica V, Latkovskis G, Peculis R, Megnis K, Schioth HB, Vaivade I, Fridmanis D, Pirags V, Erglis A, Klovins J. Single nucleotide polymorphisms of the purinergic 1 receptor are not associated with myocardial infarction in a Latvian population. Mol Biol Rep 2011; 39:1917-25. [PMID: 21643756 DOI: 10.1007/s11033-011-0938-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/25/2011] [Indexed: 01/11/2023]
Abstract
The purinergic 1 receptor (P2RY1) has been implicated in development of heart disease and in individual pharmacodynamic response to anticoagulant therapies. However, the association of polymorphisms in the P2RY1 gene with myocardial infarction (MI), and its associated conditions, has yet to be reported in the literature. We evaluated seven known SNPs in P2RY1 for association with MI in a Latvian population. Seven independent parameters that are related to MI [body mass index (BMI), type 2 diabetes (T2D), angina pectoris, hypertension, hyperlipidemia, atrial fibrillation and heart failure] were investigated. No significant association with MI was observed for any of the polymorphisms. Those SNPs for which the P value was close to significance were located in coding or promoter regions. Intriguingly, carriers of the minor allele in the P2RY1 gene locus showed a tendency towards higher onset age for MI, suggesting a possible protective effect of these SNPs against MI or their contribution in progression as opposed to onset. Finally, a linkage disequilibrium (LD) plot was generated for these polymorphisms in the Latvian population. The results of this study suggest that the role of P2RY1 in individuals from Latvian population is likely to be principally involved in platelet aggregation and thromboembolic diseases, and not as a significant contributing factor to the global metabolic syndrome.
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Affiliation(s)
- Vita Ignatovica
- Latvian Biomedical Research and Study Centre, Ratsupites str. 1, Riga 1067, Latvia.
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Chu AY, Coresh J, Arking DE, Pankow JS, Tomaselli GF, Chakravarti A, Post WS, Spooner PH, Boerwinkle E, Kao WHL. NOS1AP variant associated with incidence of type 2 diabetes in calcium channel blocker users in the Atherosclerosis Risk in Communities (ARIC) study. Diabetologia 2010; 53:510-6. [PMID: 19943157 PMCID: PMC3039128 DOI: 10.1007/s00125-009-1608-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 10/26/2009] [Indexed: 01/04/2023]
Abstract
AIMS/HYPOTHESIS To validate the reported association between rs10494366 in NOS1AP (the gene encoding nitric oxide synthase-1 adaptor protein) and the incidence of type 2 diabetes in calcium channel blocker (CCB) users and to identify additional NOS1AP variants associated with type 2 diabetes risk. METHODS Data from 9 years of follow-up in 9,221 middle-aged white and 2,724 African-American adults free of diabetes at baseline from the Atherosclerosis Risk in Communities study were analysed. Nineteen NOS1AP variants were examined for associations with incident diabetes and fasting glucose levels stratified by baseline CCB use. RESULTS Prevalence of CCB use at baseline was 2.7% (n = 247) in whites and 2.3% (n = 72) in African-Americans. Among white CCB users, the G allele of rs10494366 was associated with lower diabetes incidence (HR 0.57, 95% CI 0.35-0.92, p = 0.016). The association was marginally significant after adjusting for age, sex, obesity, smoking, alcohol use, physical activity, hypertension, heart rate and electrocardiographic QT interval (HR 0.63, 95% CI 0.38-1.04, p = 0.052). rs10494366 was associated with lower average fasting glucose during follow-up (p = 0.037). No other variants were associated with diabetes risk in CCB users after multiple-testing correction. No associations were observed between any NOS1AP variant and diabetes development in non-CCB users. NOS1AP variants were not associated with diabetes risk in either African-American CCB users or non-CCB users. CONCLUSIONS/INTERPRETATION We have independently replicated the association between rs10494366 in NOS1AP and incident diabetes among white CCB users. Further exploration of NOS1AP variants and type 2 diabetes and functional studies of NOS1AP in type 2 diabetes pathology is warranted.
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Affiliation(s)
- A Y Chu
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD, USA.
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McGeachie M, Ramoni RLB, Mychaleckyj JC, Furie KL, Dreyfuss JM, Liu Y, Herrington D, Guo X, Lima JA, Post W, Rotter JI, Rich S, Sale M, Ramoni MF. Integrative predictive model of coronary artery calcification in atherosclerosis. Circulation 2010; 120:2448-54. [PMID: 19948975 DOI: 10.1161/circulationaha.109.865501] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Many different genetic and clinical factors have been identified as causes or contributors to atherosclerosis. We present a model of preclinical atherosclerosis based on genetic and clinical data that predicts the presence of coronary artery calcification in healthy Americans of European descent 45 to 84 years of age in the Multi-Ethnic Study of Atherosclerosis (MESA). METHODS AND RESULTS We assessed 712 individuals for the presence or absence of coronary artery calcification and assessed their genotypes for 2882 single-nucleotide polymorphisms. With the use of these single-nucleotide polymorphisms and relevant clinical data, a Bayesian network that predicts the presence of coronary calcification was constructed. The model contained 13 single-nucleotide polymorphisms (from genes AGTR1, ALOX15, INSR, PRKAB1, IL1R2, ESR2, KCNK1, FBLN5, PPARA, VEGFA, PON1, TDRD6, PLA2G7, and 1 ancestry informative marker) and 5 clinical variables (sex, age, weight, smoking, and diabetes mellitus) and achieved 85% predictive accuracy, as measured by area under the receiver operating characteristic curve. This is a significant (P<0.001) improvement on models that use just the single-nucleotide polymorphism data or just the clinical variables. CONCLUSIONS We present an investigation of joint genetic and clinical factors associated with atherosclerosis that shows predictive results for both cases, as well as enhanced performance for their combination.
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Affiliation(s)
- Michael McGeachie
- Harvard Partners Center for Genetics and Genomics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Abstract
Association studies involve accessing, parsing, generating, and analyzing large volumes of data, often carried out in many steps over many months. Large-scale surveys of genetic variation, such as the International HapMap Project, and rapidly increasing volumes of single-nucleotide polymorphism (SNP) genotyping data have created exciting opportunities for association studies. However, they have further exacerbated the difficulty of curating and analyzing such data. Haploview is a program developed in Mark Daly's lab at the Broad Institute of MIT and Harvard, which is designed to bundle many everyday analysis tasks into one easy-to-use package. Haploview has several features that are useful throughout different phases of association studies. Several of these features are illustrated in this article by following a hypothetical association study from design to execution. Haploview is used to (1) analyze HapMap data and choose tag-SNPs, (2) evaluate the quality of disease genotype data, (3) test for association, and (4) evaluate a region for follow-up of a positive association.
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