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Abstract Background: Fat Mass and Obesity-related (FTO) has been one of the genes consistently related to common obesity. Single nucleotide polymorphisms (SNPs) in FTO have been linked with the IRX3 gene. Aim: This study was designed by testing the hypothesis that: i) common SNPs in FTO and IRX3 are associated with obesity and related disorders; ii) there is significant linkage disequilibrium between both genes. Methods: A cross-sectional study was carried out on the Colombian Caribbean Coast. Anthropometric and biochemical variables were measured, and obesity and metabolic disorders were diagnosed. Four SNPs were genotyped: 3 at FTO locus (rs17817449, rs8050136, rs9939609) and one at IRX3 locus (rs3751723). LD between these SNPs was estimated. A logistic regression model was applied to estimate associations. Results: A total of 792 subjects were included. FTO and IRX3 were not in LD (D'≤ 0.03; R2≤ 0.03). TT genotype (rs9939609) was found to be associated with waist circumference (p= 0.04; adj-p= 0.01), and IRX3 SNP with Body Weight Excess (BWE) (OR= 1.06, adj-p= 0.03). One FTO-IRX3 haplotype was associated with BWE (G-A-A-T, rs17817449-rs8050136-rs9939609-rs3751723; OR= 0.67, p= 0.04). The statistical significance of these relations continued after admixture adjustment for a three-hybrid population (p= 0.03). Conclusions: FTO was related to waist circumference, and IRX3 was associated with BWE in Latin American adults. This relation remained statistically significant after an adjustment for sex, age, and genetic ancestry was performed. Despite that these genes were not in LD, findings of a haplotype involving FTO-IRX3 suggest a gene-gene interaction associated with an increased risk of BWE.
Resumen Introducción: FTO (Fat Mass and Obesity-related) se ha relacionado de manera consistente con la obesidad. Recientemente, Polimorfismos de Nucleótido Único (SNP) en este gen se han relacionado con el gen IRX3. Objetivo: Probar la hipótesis de que: i) SNPs en FTO e IRX3 están asociados con la obesidad y trastornos relacionados; ii) existe desequilibrio de ligamiento (LD) significativo entre ambos genes. Métodos: se realizó un estudio transversal en la costa caribe colombiana. Se valoraron variables antropométricas y bioquímicas, la obesidad y trastornos metabólicos. Se genotipificaron 4 SNPs: 3 en FTO (rs17817449, rs8050136, rs9939609) y uno en IRX3 (rs3751723). Se estimó el LD entre estos SNPs. Se aplicó un modelo de regresión logística para estimar asociaciones. Resultados: Se incluyeron 792 sujetos. FTO e IRX3 no se encontraron en LD (D' ≤0.03; R2 ≤0.03). El genotipo TT (rs9939609) se encontró asociado con la circunferencia de la cintura (p= 0.04; adj-p= 0.01), y el SNP IRX3 con el Exceso de Peso (EP) (OR= 1.06, adj-p= 0.03). Se encontró un haplotipo FTO-IRX3 asociado con EP (G-A-A-T, rs17817449-rs8050136-rs9939609-rs3751723; OR= 0.67, p= 0.04). Esta asociación persistió después del ajuste para una población mixta (p= 0.03). Conclusiones: FTO se encontró asociado con la circunferencia de la cintura e IRX3 con EP en adultos latinoamericanos. Estas asociaciones persistieron tras el ajuste por sexo, edad y ascendencia genética. Aunque estos genes no estaban en LD, los hallazgos de un haplotipo entre FTO-IRX3 sugieren una interacción gen-gen asociada con un mayor riesgo de EP.
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RESUMEN La farmacogenética estudia la asociación entre el fenotipo farmacológico de un individuo con su constitución genética, y el diseño de estudios de casos y controles es una metodología de uso frecuente. Este diseño consiste en que se analiza la frecuencia de las variantes genéticas en los casos, es decir, de los pacientes que presentan el fenotipo (desenlaces o resultados) comparado con los controles. Para obtener una calidad metodológica adecuada en este tipo de estudios es importante trabajar con fenotipos precisos, adecuada selección de los casos y controles y tamaño de la muestra; seleccionar una metodología adecuada para la identificación de variantes genéticas; y en el momento del análisis de resultados utilizar el Equilibrio de Hardy-Weinberg (EHW) e interpretar los resultados considerando la posibilidad de un fenómeno de fenoconversión.
ABSTRACT Pharmacogenetics studies the association between the pharmacological phenotype of an individual with his/her genetic constitution. Case-control studies is a commonly used methodology when performing pharmacogenetics research. This design analyses the frequency of genetic variants in cases; that is, of those patients who have a particular phenotype (outcomes or results) compared with controls. For obtaining adequate methodological quality in pharmacogenetic case-control studies, it is important to work with precise phenotypes, have adequate case and control selection and appropriate sample size; select an adequate methodology for the identification of genetic variants, analyze the results using Hardy-Weinberg Equilibrium (HWE); and interpret the results considering the possibility of a phenoconversion phenomenon.
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OBJECTIVE: Ubiquitin-specific peptidase 46 gene (USP46) polymorphisms is part of ubiquitin-proteasome system, which is responsible for dynamic cellular processes such as the regulation of cell cycle. USP46 has been reported to be associated with major depressive disorder. The objective of the present study was to investigate the association of USP46 polymorphisms with affective temperamental traits in healthy subjects. METHODS: A total of 557 Korean healthy volunteers were recruited, and 545 subjects (328 male, 217 female) were included in the final analysis. The DNA of the subjects was isolated from saliva samples. Two single-nucleotide polymorphisms (SNPs) rs346005, rs2244291 in USP46 were genotyped. Affective temperaments were assessed using the Korean version of Temperament Evaluation of the Memphis, Pisa, Paris, and San Diego Autoquestionnaire (TEMPS-A). RESULTS: A significant association was found between rs346005 genotypes and TEMPS-A only in male subjects. In particular, subjects with the CC genotype of rs346005 showed a more depressive temperament than subjects with AA or CA genotypes in males. For rs2244291, there were no associations between the rs2244291 genotypes and TEMPS-A scores. CONCLUSION: Some affective temperaments may serve as a genetic predisposing factors for affective disorders, such as depressive disorder, via vulnerability genes related to the ubiquitin-proteasome system.
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Humans , Male , Causality , Cell Cycle , Depressive Disorder , Depressive Disorder, Major , DNA , Genetic Association Studies , Genotype , Healthy Volunteers , Mood Disorders , Saliva , Temperament , VolunteersABSTRACT
Introducción. El cáncer colorrectal es una carga para la salud pública en Colombia y el mundo. Estudios de asociación genética han identificado regiones cromosómicas asociadas a esta enfermedad, mostrando riesgo variable entre poblaciones, debido a la historia demográfica y la ancestría genética. Objetivo. Estudiar el riesgo que aportan 20 marcadores al cáncer colorrectal en Colombia, empleando 955 casos y 972 controles del consorcio CHIBCHA, analizando conjuntamente el efecto de la ancestría genética global y local. Metodología. Las muestras se genotipificaron usando microarreglos Axyom Affymetrix LAT y CUSTOME, para obtener los genotipos genómicos globales, incluyendo 20 SNPs de riesgo. Los análisis estadísticos se realizaron en PLINK (asociaciones), ADMIXTURE (ancestría global), Elai (ancestría local) y R (modelos logísticos). Resultados. Once regiones cromosómicas resultaron asociadas presentando ORs entre 1.14 y 1.41 (p<0.05): 18q21.1, 19q13.11, 10p14, 14q.2.2, 20p12.3, 8q23.3, 6p21.2, 15q13.3 y 8q24.21. Una mayor ancestría europea se asoció con el riesgo a nivel global (OR=3.016, IC 95%:1.162-7.894, p=0.00325), y a nivel cromosómico local se detectaron las regiones 6q23.2 (ORajustado=1.378, IC95%: 1.202-1.580, Pajustado=4.2e-6) y 4p13 (ORajustado=1.301, IC95%:1.137-1.489; Pajustado=0.00013). Conclusiones. La ancestría podría considerarse un factor en la explicación de la susceptibilidad en Colombia, indicando que la mezcla genética de origen amerindio y europeo, influye en la estructura poblacional y explicaría las diferencias en la incidencia del CCR entre poblaciones latinas y europeas.
Introduction: Colorectal cancer is a public health burden in the world and Colombia. Recent genome wide association studies have identified chromosomal regions associated with the disease, depicting variable risk between populations, owing to the demographic history and genetic ancestry. Objective: We aimed to study the colorectal cancer risk in Colombia provided for 20 genetic markers, by using 955 cases and 972 controls from the CHIBCHA consortium, in the context of global and local genetic ancestry. Methodology: The samples were genotyped using Axyom Affymetrix LAT and CUSTOME array in order to obtain the global genome genotypes including 20 risk SNPs. Statistical analysis was performed in PLINK (associations), ADMIXTURE (global ancestry), Elai (local ancestry) and R language (logistic models). Results: Eleven chromosomal regions were associated with ORs ranging between 1.14-1.41 (p<0.05): 18q21.1, 19q13.11, 10p14, 14q.2.2, 20p12.3, 8q23.3, 6p21.2, 15q13.3 y 8q24.21. On average, a higher global European ancestry was associated with colorectal cancer risk (OR=3.016, IC 95%:1.162-7.894, p=0.00325). At the local chromosomal level two regions presented a significant increment of European ancestry 6q23.2 (OR adjusted=1.378, CI95%: 1.202-1.580, p adjusted =4.2e-6) and 4p13 (OR adjusted =1.301, CI95%:1.137-1.489; p adjusted =0.00013). Conclusions: Genetic ancestry can be considered as a relevant factor for the colorectal cancer susceptibility in Colombia. Both Native American and European ancestry are accounting for the most part of population structure in the sample we studied, which could explain the differences for the colorectal cancer incidence between Latin American and European populations.
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Humans , Genetic Association Studies , Colorectal Neoplasms , Colombia , Genetic Predisposition to DiseaseABSTRACT
ABSTRACT Background: Antiretroviral therapy (ART) saved millions from HIV-1 infection and AIDS, but some patients do not experience adequate CD4+ T cells gain despite achieving viral suppression. The genetic component of this condition is not yet completely elucidated. Objective: To identify predictive genetic markers of immune response to ART. Methods: Case-control study. Out of 176 HIV-infected patients recruited in the city of Recife, Northeast Brazil, 67 patients with no immunologic response were the cases and the remaining 109 patients who responded were the controls. A set of 94 selected single nucleotide polymorphisms (SNPs) involved in antiretroviral drugs pharmacodynamic pathways and immune system homeostasis were genotyped, while the remaining 48 were ancestry informative markers (AIMs) for controlling for eventual hidden population structure. Results: Male patients were overrepresented in non-responder group (p = 0.01). Non-responders also started with lower absolute CD4+ T cell counts (p < 0.001). We found five SNPs significantly associated with the outcome, being three more frequent in non-responders than responders: rs2243250 (IL4) A allele (p = 0.04), rs1128503 (ABCB1) A allele (p = 0.03) and rs707265 (CYP2B6) A allele (p = 0.02), whereas the other two were less frequent in non-responders: rs2069762 (IL2) C allele (p = 0.004) and rs4646437 (CYP3A4) A allele (p = 0.04). Conclusion: Some significant univariate associations remained independently associated at multivariate survival analysis modeling, such as pre-treatment CD4+ T cells counts, IL2 and ABCB1 genotypes, and use of protease inhibitors, yielding a predictive model for the probability for immune response. More studies are needed to unravel the genetic basis of ART immunological non-response.
Subject(s)
Humans , Male , Female , Adolescent , Adult , Middle Aged , Young Adult , HIV Infections/immunology , HIV Infections/drug therapy , Polymorphism, Single Nucleotide/immunology , Anti-Retroviral Agents/pharmacology , Immune System/drug effects , Brazil , Genetic Markers , Multivariate Analysis , Retrospective Studies , Statistics, Nonparametric , CD4 Lymphocyte Count , Viral Load , Antiretroviral Therapy, Highly Active , Immunogenetic Phenomena/drug effects , Immunogenetic Phenomena/genetics , Genetic Association Studies , Gene FrequencyABSTRACT
OBJECTIVES: Genome-wide association studies (GWASs) and meta-analyses indicate that single-nucleotide polymorphisms (SNPs) in the a-1C subunit of the L-type voltage-dependent calcium channel (CACNA1C) gene increase the risk for schizophrenia and bipolar disorders (BDs). We investigated the association between the genetic variants on CACNA1C and schizophrenia and/or BDs in the Korean population. METHODS: A total of 582 patients with schizophrenia, 336 patients with BDs consisting of 179 bipolar I disorder (BD-I) and 157 bipolar II disorder (BD-II), and 502 healthy controls were recruited. Based on previous results from other populations, three SNPs (rs10848635, rs1006737, and rs4765905) were selected and genotype-wise association was evaluated using logistic regression analysis under additive, dominant and recessive genetic models. RESULTS: rs10848635 showed a significant association with schizophrenia (p=0.010), the combined schizophrenia and BD group (p=0.018), and the combined schizophrenia and BD-I group (p=0.011). The best fit model was dominant model for all of these phenotypes. The association remained significant after correction for multiple testing in schizophrenia and the combined schizophrenia and BD-I group. CONCLUSION: We identified a possible role of CACNA1C in the common susceptibility of schizophrenia and BD-I. However no association trend was observed for BD-II. Further efforts are needed to identify a specific phenotype associated with this gene crossing the current diagnostic categories.
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Humans , Bipolar Disorder , Calcium Channels , Genetic Association Studies , Genome-Wide Association Study , Logistic Models , Models, Genetic , Phenotype , Polymorphism, Single Nucleotide , SchizophreniaABSTRACT
Objective:To investigate the genetic association of single nucleotide polymorphisms (SNPs) in gamma-aminobutyric acid type A (GABAA) receptor genes cluster on chromosome 15q12 with autism in Chinese Han population.Methods:Totally 502 autism trios of Chinese Han ethnicity (including 502 autism individuals and 1004 healthy biological parents) were selected.All children met the autism diagnosis of Diagnostic and Statistical Manual of Mental Disorders,Fourth edition (DSM-Ⅳ).Genotyping for 15 selected tag SNPs in three GABAA receptor genes (GABRB3,GABRA5,and GABRG3) was performed using Agena Bioscience MassARRAY platform.The family-based association test for 15 tag SNPs was performed to compare the transmitted frequency of al leles of heterozygous genotypes from parents to offspring in autism trios.Results:The C allele of rs7180500 in GABRG3 and the A allele of rs4906902 in GABRB3 exhibited the preferential transmission from parents to affected offspring (Z =3.573,P ＜0.001;Z =3.141,P =0.002),and the association was significant after Bonferroni correction.Conclusion:It suggests that GABRG3 and GABRB3 which located in chromosome 15q12 might be susceptibility genes in Chinese Han population.
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Meta-analysis used for genetic association studies became popular among researchers,with the amount of published papers increased rapidly.In this paper,we will focus on the introduction on the selection of genetic models.Traditionally,methods used for Meta-analysis on genetic association studies was to calculate the statistics based on available genetic models which not only increasing the probability of false-positives but also making the interpretation of results more difficult.Hence,a critical step in the Meta-analysis of genetic association studies was to choose the appropriate inheritance model.The aim of this paper was to introduce the theory of Bayesian analysis regarding the genetic model-free approach,in performing the Meta-analysis for studies related to genetic associations.
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Meta-analysis used for genetic association studies became popular among researchers,with the amount of published papers increased rapidly.In this paper,we will focus on the introduction on the selection of genetic models.Traditionally,methods used for Meta-analysis on genetic association studies was to calculate the statistics based on available genetic models which not only increasing the probability of false-positives but also making the interpretation of results more difficult.Hence,a critical step in the Meta-analysis of genetic association studies was to choose the appropriate inheritance model.The aim of this paper was to introduce the theory of Bayesian analysis regarding the genetic model-free approach,in performing the Meta-analysis for studies related to genetic associations.
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OBJECTIVES: Previous genome-wide association studies have indicated the association between ankyrin 3 (ANK3) and the vulnerability of schizophrenia. We investigated the association between single nucleotide polymorphisms (SNPs) covering the whole ANK3 locus and schizophrenia in the Korean population. METHODS: The study subjects were 582 patients with schizophrenia and 502 healthy controls. Thirty-eight tag SNPs on ANK3 and five additional SNPs showing significant association with schizophrenia in previous studies were genotyped. RESULTS: Three (rs10994181, rs16914791, rs1938526) of 43 SNPs showed a nominally significant association (p < 0.05) with at least one genotype model. But none of these associations remained significant after adjusting for multiple testing errors with Bonferroni's correction. CONCLUSIONS: We could not identify a significant association between ANK3 and schizophrenia in the Korean population. However, three SNPs showing an association signal with nominal significance need to be investigated in future studies with higher statistical power and more specific phenotype crossing the current diagnostic categories.
Subject(s)
Humans , Ankyrins , Genetic Association Studies , Genome-Wide Association Study , Genotype , Phenotype , Polymorphism, Single Nucleotide , SchizophreniaABSTRACT
Cerebral small vessel disease (SVD) is an important cause of stroke and cognitive impairment among the elderly and is a more frequent cause of stroke in Asia than in the US or Europe. Although traditional risk factors such as hypertension or diabetes mellitus are important in the development of cerebral SVD, the exact pathogenesis is still uncertain. Both, twin and family history studies suggest heritability of sporadic cerebral SVD, while the candidate gene study and the genome-wide association study (GWAS) are mainly used in genetic research. Robust associations between the candidate genes and occurrence of various features of sporadic cerebral SVD, such as lacunar infarction, intracerebral hemorrhage, or white matter hyperintensities, have not yet been elucidated. GWAS, a relatively new technique, overcomes several shortcomings of previous genetic techniques, enabling the detection of several important genetic loci associated with cerebral SVD. In addition to the more common, sporadic cerebral SVD, several single-gene disorders causing cerebral SVD have been identified. The number of reported cases is increasing as the clinical features become clear and diagnostic examinations are more readily available. These include cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy, COL4A1-related cerebral SVD, autosomal dominant retinal vasculopathy with cerebral leukodystrophy, and Fabry disease. These rare single-gene disorders are expected to play a crucial role in our understanding of cerebral SVD pathogenesis by providing animal models for the identification of cellular, molecular, and biochemical changes underlying cerebral small vessel damage.
Subject(s)
Aged , Humans , Asia , CADASIL , Cerebral Hemorrhage , Cerebral Small Vessel Diseases , Diabetes Mellitus , Europe , Fabry Disease , Genetic Association Studies , Genetic Loci , Genetic Research , Genetic Techniques , Genetics , Genome-Wide Association Study , Hypertension , Leukoencephalopathies , Models, Animal , Retinaldehyde , Risk Factors , Stroke , Stroke, LacunarABSTRACT
Objective To explore the impacts of catechol-O-Methyltransferase (COMT) gene polymorphisms on the outcomes of methylphenidate treatment for attention deficit hyperactivity disorder (ADHD) in children. Methods One hundred seventy-seven ADHD children of Chinese Han descent received open-labelled dose titration with methylpheni?date to achieve optimal response in 2~4 weeks. The behavior changes were evaluated by using ADHD diagnostic scale (parent version) before and after treatment. COMT gene rs4680 (Val158Met) and rs165599 were genotyped using fluores?cent real-time PCR. The genotype distribution and treatment outcomes including remission, response and non-response were analyzed. Results The treatment response differed significantly among patients with different genotypes of rs4680 (P0.05). Conclu?sion COMT gene rs4680 (Val158Met) polymorphism is associated with methylphenidate response in a Han Chinese popu?lation. Patients with G allele is more likely to benefit from methylphenidate treatment in comparison with A/A genotype.
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Objective To assess the methodological quality of Meta-analyses on papers published in Chinese journals regarding studies on genetic association.Methods Meta-analyses of genetic association study published in Chinese journals up to December 2012 had been searched through on 4 Chinese electronic databases (China biomedicine database,CNKI,Wanfang database and VIP Information).Articles independently selected by both two researchers under definite inclusion and exclusion criteria were included in this study (with consultation on a third researcher if inconsistent opinions existed).A Measurement Tool for the Assessment of Multiple Systematic Reviews (AMSTAR) checklist was used to evaluate the methodological quality together with the methodological quality score being calculated.Results Totally,440 articles were included in this study,with mean score of the methodological quality score (maximum score is 11) as 5.77.Among the 440 articles,none had met the requirement of total 11 items in AMSTAR,with 89.5％ and 38.6％ of them had a priori design or duplicate study selection and data extraction.72.7％ of them performed a comprehensive literature search and 14.8％ included studies regardless of their publication status.10.9％ and 92.5％ of them provided a list of including or excluding studies or stated characteristics of the included ones.32.0％ of them assessed the scientific quality of those included studies,with 50.0％ of them mentioned their qualities when formulating the conclusions.93.2％ of them used appropriate methods to combine data while 82.3％ assessed the likelihood of publication bias.0.5％ of them declared the conflict of interests.Conclusion Our results from Meta-analyses showed an acceptable quality regarding their methodology related to genetic association on papers being published in Chinese journals.Improvement is needed especially on aspects as:selection of studies,data extraction,publication status with list of inclusion and exclusion,quality assessment and declaration on conflict of interests,etc.
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PURPOSE: Drug-induced liver injury (DILI) is the most common adverse drug reaction; however, it is not easily predicted. We hypothesize that DILI has a common genetic basis. Based on the findings of previous animal studies on toxic hepatitis, we selected the thioredoxin reductase 1 gene (TXNRD1) as a candidate marker of DILI for this genetic association study. METHODS: Records from 118 patients with DILI were extracted from the database of the Adverse Drug Reaction Research Group in South Korea. Causative drugs included antituberculosis drugs (n=68, 57.6%), antibiotics (n=22, 18.6%), antiepileptic drugs (n=7, 5.9%), non-steroidal anti-inflammatory drugs (n=5, 4.2%), and others (n=16, 13.7%). Seven single nucleotide polymorphisms (SNPs) in TXNRD1 (rs10735393, rs4964287, rs4595619, rs10861201, rs11111997, rs4246270, and rs4246271) were scored in 118 DILI patients and in 120 drug-matched controls without liver injury. RESULTS: No differences were found between the frequencies of any of the 7 SNPs in the cases and controls; however, a significant association was found between a TTA haplotype composed of rs10735393, rs4964287, and rs4595619 and DILI using an allele model (odds ratio, 1.79; 95% confidence interval, 1.18-2.73; P=0.008; Bonferroni corrected P=0.024). CONCLUSIONS: These results suggest that genetic variations in TXNRD1 favor the development of DILI, although a larger confirmative study is needed.
Subject(s)
Animals , Humans , Alleles , Anti-Bacterial Agents , Anticonvulsants , Drug-Related Side Effects and Adverse Reactions , Chemical and Drug Induced Liver Injury , Genetic Association Studies , Genetic Variation , Haplotypes , Liver , Polymorphism, Genetic , Polymorphism, Single Nucleotide , Republic of Korea , Thioredoxin Reductase 1ABSTRACT
Oxidative stress, which results in an excessive product of reactive oxygen species (ROS), is one of the fundamental mechanisms of the development of hypertension. In the vascular system, ROS have physical and pathophysiological roles in vascular remodeling and endothelial dysfunction. In this study, ROS-hypertension-related genes were collected by the biological literature-mining tools, such as SciMiner and gene2pubmed, in order to identify the genes that would cause hypertension through ROS. Further, single nucleotide polymorphisms (SNPs) located within these gene regions were examined statistically for their association with hypertension in 6,419 Korean individuals, and pathway enrichment analysis using the associated genes was performed. The 2,945 SNPs of 237 ROS-hypertension genes were analyzed, and 68 genes were significantly associated with hypertension (p < 0.05). The most significant SNP was rs2889611 within MAPK8 (p = 2.70 x 10(-5); odds ratio, 0.82; confidence interval, 0.75 to 0.90). This study demonstrates that a text mining approach combined with association analysis may be useful to identify the candidate genes that cause hypertension through ROS or oxidative stress.
Subject(s)
Data Mining , Genetic Association Studies , Hypertension , Mining , Odds Ratio , Oxidative Stress , Oxygen , Polymorphism, Single Nucleotide , Reactive Oxygen SpeciesABSTRACT
OBJECTIVE: Ossification of the posterior longitudinal ligament (OPLL) has a strong genetic component. Specific gene polymorphisms may be associated with OPLL in several genes which regulate calcification in chondrocytes, change of extracellular collagen matrix and secretions of many growth factors and cytokines controlling bone morphogenesis. Toll-like receptor 5 (TLR5) may play a role in the pathogenesis of OPLL by intermediate nuclear factor-kappa B (NF-kappaB). The current study focused on coding single nucleotide polymorphisms (SNPs) of TLR5 for a case-control study investigating the relationship between TLR5 and OPLL in a Korean population. METHODS: A total of 166 patients with OPLL and 231 controls were recruited for a case-control association study investigating the relationship between SNPs of TLR5 gene and OPLL. Four SNPs were genotyped by direct sequencing (rs5744168, rs5744169, rs2072493, and rs5744174). SNP data were analyzed using the SNPStats, SNPAnalyzer, Haploview, and Helixtree programs. Multiple logistic regression analysis with adjustment for age and gender was performed to calculate an odds ratio (OR). RESULTS: None of SNPs were associated with OPLL in three alternative models (codominant, dominant, and recessive models; p > 0.05). A strong linkage disequilibrium block, including all 4 SNPs, was constructed using the Gabriel method. No haplotype was significantly associated with OPLL in three alternative models. CONCLUSION: These results suggest that Toll-like receptor 5 gene may not be associated with ossification of the posterior longitudinal ligament risk in Korean population.
Subject(s)
Humans , Case-Control Studies , Chondrocytes , Clinical Coding , Collagen , Cytokines , Genetic Association Studies , Haplotypes , Intercellular Signaling Peptides and Proteins , Linkage Disequilibrium , Logistic Models , Longitudinal Ligaments , Morphogenesis , Odds Ratio , Ossification of Posterior Longitudinal Ligament , Polymorphism, Single Nucleotide , Spine , Toll-Like Receptor 5 , Toll-Like ReceptorsABSTRACT
Hepatocellular carcinoma (HCC) is associated with hepatitis B virus (HBV) as an etiologic agent in 80% of cases, and is the major cause of death among HBV carriers. Family history of HCC is a known risk factor for the development of HCC among chronically HBV infected patients; therefore, genetic factors are likely to modify the risk of HCC. However, the genetic factors that determine progression to HCC remain mostly to be recovered. It is estimated that there are millions of single nucleotide polymorphisms (SNPs) within human genome and they are likely to explain much of the genetic diversity of individuals. In this review, the natural history of HBV infection and host genetic factors related to HCC, study design and target gene selection for the detection of SNPs related to the occurrence of HCC were discussed. Also, several SNPs or haplotypes, which were reportedly associated with increased or reduced risk of HCC occurrence in patients with chronic HBV infection, were reviewed. Especially, recent studies in Korea, one of the HBV endemic areas, were discussed. Screening of these polymorphisms might be useful in clinical practice to stratify the lower or higher risk group for HCC and might modify the design of HCC surveillance programs in patients with chronic HBV infection, if further genetic susceptibilities are identified. The ongoing studies of the distributions and functions of the implicated allele polymorphisms will not only provide insight into the pathogenesis of HCC, but may also provide a novel rationale for new methods of diagnosis and therapeutic strategies.
Subject(s)
Humans , Biomarkers , Carcinoma, Hepatocellular/diagnosis , Genetic Predisposition to Disease , Hepatitis B, Chronic/complications , Liver Neoplasms/diagnosis , Polymorphism, Single NucleotideABSTRACT
OBJECTIVE: Recent molecular and genetic investigations have suggested that the current nosology for major psychiatric disorders, based on the "two-entities-principal" is not accurate with respect to clinical observations; patient groups that do not fit to the current operative diagnostic boundaries are readily identified. We aimed to perform an investigation of the signal transducer and activator of transcription 6 (STAT6) gene (located on 12q13), which has an important role in the apoptotic cascade, with patients suffering from periodic psychosis. METHODS: Genetic association study has been employed for the current work. Investigated six tag-SNPs were chosen from Hapmap database. RESULTS: Among six tag-SNPs, one marker (rs10783813), located in the STAT6 gene, showed modest association (p<0.05), although no marker or haplotype block showed association after Bonferroni's correction. CONCLUSION: Future studies will reveal the etiological role of STAT6, and of other genes of the apoptotic cascade, in major psychiatric disorders.
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Humans , Genetic Association Studies , Haplotypes , HapMap Project , Psychotic Disorders , STAT6 Transcription FactorABSTRACT
OBJECTIVES: The aim of the current study is to test for the association of DRD4 exon III VNTR polymorphism with attention-deficit hyperactivity disorder(ADHD) in Korean children population. METHODS: 113 Korean children with ADHD, 102 parents, and 133 control subjects participated with the current study. The distribution of genotypes and alleles of DRD4 exon III VNTR in children with ADHD was compared with that in control subjects. In addition, 69 children with ADHD and their parents were analyzed using the transmission disequilibrium test(TDT). RESULTS: We could not find any significant differences in the distribution of genotypes and alleles at DRD4 exon III VNTR polymorphism between children with ADHD and control subjects. In addition, there was no preferential transmission of long allele of DRD4 exon III VNTR polymorphism. CONCLUSION: These results suggest that DRD4 is not associated with ADHD in Korean children population.