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1.
Int J Mol Sci ; 24(14)2023 Jul 17.
Artículo en Inglés | MEDLINE | ID: mdl-37511320

RESUMEN

Hundreds of genetic variants for body mass index (BMI) have been identified from numerous genome-wide association studies (GWAS) in different ethnicities. In this study, we aimed to develop a polygenic risk score (PRS) for BMI for predicting susceptibility to obesity and related traits in the Korean population. For this purpose, we obtained base data resulting from a GWAS on BMI using 57,110 HEXA study subjects from the Korean Genome and Epidemiology Study (KoGES). Subsequently, we calculated PRSs in 13,504 target subjects from the KARE and CAVAS studies of KoGES using the PRSice-2 software. The best-fit PRS for BMI (PRSBMI) comprising 53,341 SNPs was selected at a p-value threshold of 0.064, at which the model fit had the greatest R2 score. The PRSBMI was tested for its association with obesity-related quantitative traits and diseases in the target dataset. Linear regression analyses demonstrated significant associations of PRSBMI with BMI, blood pressure, and lipid traits. Logistic regression analyses revealed significant associations of PRSBMI with obesity, hypertension, and hypo-HDL cholesterolemia. We observed about 2-fold, 1.1-fold, and 1.2-fold risk for obesity, hypertension, and hypo-HDL cholesterolemia, respectively, in the highest-risk group in comparison to the lowest-risk group of PRSBMI in the test population. We further detected approximately 26.0%, 2.8%, and 3.9% differences in prevalence between the highest and lowest risk groups for obesity, hypertension, and hypo-HDL cholesterolemia, respectively. To predict the incidence of obesity and related diseases, we applied PRSBMI to the 16-year follow-up data of the KARE study. Kaplan-Meier survival analysis showed that the higher the PRSBMI, the higher the incidence of dyslipidemia and hypo-HDL cholesterolemia. Taken together, this study demonstrated that a PRS developed for BMI may be a valuable indicator to assess the risk of obesity and related diseases in the Korean population.


Asunto(s)
Predisposición Genética a la Enfermedad , Hipertensión , Humanos , Índice de Masa Corporal , Estudio de Asociación del Genoma Completo , Obesidad/epidemiología , Obesidad/genética , Factores de Riesgo , Hipertensión/epidemiología , Hipertensión/genética , Hipertensión/complicaciones , República de Corea/epidemiología , Polimorfismo de Nucleótido Simple
2.
BMC Genomics ; 23(1): 261, 2022 Apr 04.
Artículo en Inglés | MEDLINE | ID: mdl-35379174

RESUMEN

BACKGROUND: Colorectal cancer (CRC) is the third most common cancer worldwide and is influenced by environmental and genetic factors. Although numerous genetic loci for CRC have been identified, the overall understanding of the genetic factors is yet to be elucidated. We sought to discover new genes involved in CRC applying genetic association analysis and functional study. RESULTS: We conducted exome array analysis on 194 CRC and 600 control subjects for discovering new candidate CRC genes. Fisher's exact test detected one exome-wide significant functional locus for CRC on SMCO1 (P < 10-6) and two suggestive functional loci on HLA-C and NUTM1 (10-6 ≤ P < 10-4). To evaluate the biological role of three candidate CRC genes, the differential expression of these genes between CRC and non-cancer colorectal cells was analyzed using qRT-PCR and publicly available gene expression data. Of three genes, HLA-C consistently revealed the significant down-regulation in CRC cells. In addition, we detected a reduction in cell viability in the HLA-C overexpression CRC cell line, implying the functional relevance of HLA-C in CRC. To understand the underlying mechanism exerted by HLA-C in CRC development, we conducted RNA sequencing analyses of HLA-C overexpression CRC cells and non-cancer colorectal cells. Pathway analysis detected that significantly down-regulated genes in HLA-C overexpression CRC cells were highly enriched in cancer-related signaling pathways such as JAK/STAT, ErbB, and Hedgehog signaling pathways. CONCLUSIONS: Exome array CRC case-control analysis followed by functional validation demonstrated that HLA-C likely exerts its influence on CRC development via cancer-related signaling pathways.


Asunto(s)
Neoplasias Colorrectales , Antígenos HLA-C , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Genes MHC Clase I , Predisposición Genética a la Enfermedad , Antígenos HLA-C/genética , Proteínas Hedgehog/genética , Humanos , Reproducibilidad de los Resultados , República de Corea
3.
Biochem Genet ; 59(1): 235-255, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-32989646

RESUMEN

Leukemia is the outcome of aggregation of damaged white blood cells. Several genes were reported to be associated with the pathogenesis of leukemia. These genes were computationally analyzed to decipher their codon usage bias (CUB) and to identify the prime factors influencing the codon usage profile as no work was reported yet. The mean values of synonymous codon usage order (SCUO) parameter indicated low CUB of the genes. Significant positive association of SCUO with overall GC and positional GCs might signal the presence of mutational pressure. However, neutrality plot suggested the dominant role of natural selection across the genes. Along with natural selection, the role of mutation pressure was also prominent and that might be responsible for lower CUB (SCUO = 0.19) of genes. Low translational speed might permit accuracy in the process. A strong inverse relationship of translational rate was observed with CUB of genes and folding energy.


Asunto(s)
Codón , Análisis Mutacional de ADN , Genes Relacionados con las Neoplasias , Predisposición Genética a la Enfermedad , Leucemia/genética , Uso de Codones , Biología Computacional , Humanos , Leucemia/metabolismo , Mutación , Nucleótidos/genética , Pliegue de Proteína , ARN Mensajero/metabolismo , Selección Genética
4.
Biotechnol Lett ; 42(10): 1865-1875, 2020 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-32488444

RESUMEN

Obesity is not only a social menace but also an economic burden as it reduces productivity and increases health care cost. We used bioinformatic tools to analyze the CUB of obesity associated genes and compared with housekeeping genes (control) to explore the similarities and differences between two data sets as no work was reported yet. The mean effective number of codons (ENC) in genes associated with obesity and housekeeping gene was 50.45 and 52.03 respectively, indicating low CUB. The relative synonymous codon usage (RSCU) suggested that codons namely CTG and GTG were over-represented in both obesity and housekeeping genes while under-represented codons were TCG, TTA, CTA, CCG, CAA, CGT, ATA, ACG, GTA and GCG in obesity genes and TCG, TTA, CCG, ATA, ACG, GTA, and GCG in housekeeping genes. t test analysis suggested that 11 codons namely TTA (Leu), TTG (Leu), CCG (Pro), CAC (His), CAA (Gln), CAG (Gln), CGT (Arg), AGA (Arg), ATA (Ile), ATT (Ile) and GCG (Ala) were significantly differed (p < 0.05 or p < 0.01) between obesity and housekeeping genes. Highly significant correlation was observed between GC12 and GC3 in obesity and housekeeping genes i.e. r = 0.580** and r = 0.498** (p < 0.01) respectively indicating the effect of directional mutation pressure present in all codon positions.


Asunto(s)
Uso de Codones/genética , Obesidad/genética , Selección Genética/genética , Biología Computacional , Humanos , Mutación/genética
5.
BMC Med Genet ; 20(1): 99, 2019 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-31170924

RESUMEN

BACKGROUND: Metabolic syndrome (MetS), defined as a cluster of metabolic risk factors including dyslipidemia, insulin-resistance, and elevated blood pressure, has been known as partly heritable. MetS effects the lives of many people worldwide, yet females have been reported to be more vulnerable to this cluster of risks. METHODS: To elucidate genetic variants underlying MetS specifically in females, we performed a genome-wide association study (GWAS) for MetS as well as its component traits in a total of 9932 Korean female subjects (including 2276 MetS cases and 1692 controls). To facilitate the prediction of MetS in females, we calculated a genetic risk score (GRS) combining 14 SNPs detected in our GWA analyses specific for MetS. RESULTS: GWA analyses identified 14 moderate signals (Pmeta < 5X10- 5) specific to females for MetS. In addition, two genome-wide significant female-specific associations (Pmeta < 5X10- 8) were detected for rs455489 in DSCAM for fasting plasma glucose (FPG) and for rs7115583 in SIK3 for high-density lipoprotein cholesterol (HDLC). Logistic regression analyses (adjusted for area and age) between the GRS and MetS in females indicated that the GRS was associated with increased prevalence of MetS in females (P = 5.28 × 10- 14), but not in males (P = 3.27 × 10- 1). Furthermore, in the MetS prediction models using GRS, the area under the curve (AUC) of the receiver operating characteristics (ROC) curve was higher in females (AUC = 0.85) than in males (AUC = 0.57). CONCLUSION: This study highlights new female-specific genetic variants associated with MetS and its component traits and suggests that the GRS of MetS variants is a likely useful predictor of MetS in females.


Asunto(s)
Predisposición Genética a la Enfermedad/genética , Estudio de Asociación del Genoma Completo/métodos , Síndrome Metabólico/genética , Polimorfismo de Nucleótido Simple , Adulto , Anciano , Alelos , Pueblo Asiatico/genética , Femenino , Predisposición Genética a la Enfermedad/etnología , Genotipo , Humanos , Masculino , Síndrome Metabólico/diagnóstico , Síndrome Metabólico/etnología , Persona de Mediana Edad , Fenotipo , República de Corea , Factores de Riesgo , Factores Sexuales
6.
Hum Mol Genet ; 25(10): 2070-2081, 2016 05 15.
Artículo en Inglés | MEDLINE | ID: mdl-26911676

RESUMEN

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci.


Asunto(s)
Mapeo Cromosómico , Diabetes Mellitus Tipo 2/genética , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Negro o Afroamericano/genética , Alelos , Pueblo Asiatico/genética , Inhibidor p16 de la Quinasa Dependiente de Ciclina , Inhibidor p18 de las Quinasas Dependientes de la Ciclina/genética , Diabetes Mellitus Tipo 2/patología , Femenino , Humanos , Canal de Potasio KCNQ1/genética , Desequilibrio de Ligamiento , Masculino , Polimorfismo de Nucleótido Simple , Proteínas de Unión al ARN/genética , Elementos Reguladores de la Transcripción/genética , Población Blanca/genética , ARNt Metiltransferasas/genética
7.
Hum Mol Genet ; 24(6): 1791-800, 2015 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-25429064

RESUMEN

Human height is associated with risk of multiple diseases and is profoundly determined by an individual's genetic makeup and shows a high degree of ethnic heterogeneity. Large-scale genome-wide association (GWA) analyses of adult height in Europeans have identified nearly 180 genetic loci. A recent study showed high replicability of results from Europeans-based GWA studies in Asians; however, population-specific loci may exist due to distinct linkage disequilibrium patterns. We carried out a GWA meta-analysis in 93 926 individuals from East Asia. We identified 98 loci, including 17 novel and 81 previously reported loci, associated with height at P < 5 × 10(-8), together explaining 8.89% of phenotypic variance. Among the newly identified variants, 10 are commonly distributed (minor allele frequency, MAF > 5%) in Europeans, with comparable frequencies with in Asians, and 7 single-nucleotide polymorphisms are with low frequency (MAF < 5%) in Europeans. In addition, our data suggest that novel biological pathway such as the protein tyrosine phosphatase family is involved in regulation of height. The findings from this study considerably expand our knowledge of the genetic architecture of human height in Asians.


Asunto(s)
Pueblo Asiatico/genética , Estatura/genética , Polimorfismo de Nucleótido Simple , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Asia Oriental , Femenino , Frecuencia de los Genes , Sitios Genéticos , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Redes y Vías Metabólicas/genética , Persona de Mediana Edad , Proteínas Tirosina Fosfatasas/genética , Población Blanca/genética , Adulto Joven
8.
Hum Mol Genet ; 23(24): 6659-67, 2014 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-25035420

RESUMEN

The electrocardiogram has several advantages in detecting cardiac arrhythmia-it is readily available, noninvasive and cost-efficient. Recent genome-wide association studies have identified single-nucleotide polymorphisms that are associated with electrocardiogram measures. We performed a genome-wide association study using Korea Association Resource data for the discovery phase (Phase 1, n = 6805) and two consecutive replication studies in Japanese populations (Phase 2, n = 2285; Phase 3, n = 5010) for QRS duration and PR interval. Three novel loci were identified: rs2483280 (PRDM16 locus) and rs335206 (PRDM6 locus) were associated with QRS duration, and rs17026156 (SLC8A1 locus) correlated with PR interval. PRDM16 was recently identified as a causative gene of left ventricular non-compaction and dilated cardiomyopathy in 1p36 deletion syndrome, which is characterized by heart failure, arrhythmia and sudden cardiac death. Thus, our finding that a PRDM16 SNP is linked to QRS duration strongly implicates PRDM16 in cardiac function. In addition, C allele of rs17026156 increases PR interval (beta ± SE, 2.39 ± 0.40 ms) and exists far more frequently in East Asians (0.46) than in Europeans and Africans (0.05 and 0.08, respectively).


Asunto(s)
Arritmias Cardíacas/genética , Proteínas de Unión al ADN/genética , Proteínas Musculares/genética , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Intercambiador de Sodio-Calcio/genética , Factores de Transcripción/genética , Adulto , Anciano , Alelos , Arritmias Cardíacas/etnología , Arritmias Cardíacas/fisiopatología , Pueblo Asiatico , Electrocardiografía , Femenino , Frecuencia de los Genes , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Persona de Mediana Edad
9.
Hum Mol Genet ; 23(20): 5492-504, 2014 Oct 15.
Artículo en Inglés | MEDLINE | ID: mdl-24861553

RESUMEN

Recent genetic association studies have identified 55 genetic loci associated with obesity or body mass index (BMI). The vast majority, 51 loci, however, were identified in European-ancestry populations. We conducted a meta-analysis of associations between BMI and ∼2.5 million genotyped or imputed single nucleotide polymorphisms among 86 757 individuals of Asian ancestry, followed by in silico and de novo replication among 7488-47 352 additional Asian-ancestry individuals. We identified four novel BMI-associated loci near the KCNQ1 (rs2237892, P = 9.29 × 10(-13)), ALDH2/MYL2 (rs671, P = 3.40 × 10(-11); rs12229654, P = 4.56 × 10(-9)), ITIH4 (rs2535633, P = 1.77 × 10(-10)) and NT5C2 (rs11191580, P = 3.83 × 10(-8)) genes. The association of BMI with rs2237892, rs671 and rs12229654 was significantly stronger among men than among women. Of the 51 BMI-associated loci initially identified in European-ancestry populations, we confirmed eight loci at the genome-wide significance level (P < 5.0 × 10(-8)) and an additional 14 at P < 1.0 × 10(-3) with the same direction of effect as reported previously. Findings from this analysis expand our knowledge of the genetic basis of obesity.


Asunto(s)
5'-Nucleotidasa/genética , Aldehído Deshidrogenasa/genética , Pueblo Asiatico/genética , Proteínas Sanguíneas/genética , Miosinas Cardíacas/genética , Glicoproteínas/genética , Canal de Potasio KCNQ1/genética , Cadenas Ligeras de Miosina/genética , Obesidad/genética , Proteínas Inhibidoras de Proteinasas Secretoras/genética , Aldehído Deshidrogenasa Mitocondrial , Índice de Masa Corporal , Asia Oriental , Femenino , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Masculino , Polimorfismo de Nucleótido Simple
10.
J Cell Mol Med ; 19(6): 1333-45, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25781353

RESUMEN

Oxidative stress-induced reactive oxygen species (ROS) are responsible for various neuronal diseases. Antioxidant 1 (Atox1) regulates copper homoeostasis and promotes cellular antioxidant defence against toxins generated by ROS. The roles of Atox1 protein in ischaemia, however, remain unclear. In this study, we generated a protein transduction domain fused Tat-Atox1 and examined the roles of Tat-Atox1 in oxidative stress-induced hippocampal HT-22 cell death and an ischaemic injury animal model. Tat-Atox1 effectively transduced into HT-22 cells and it protected cells against the effects of hydrogen peroxide (H2O2)-induced toxicity including increasing of ROS levels and DNA fragmentation. At the same time, Tat-Atox1 regulated cellular survival signalling such as p53, Bad/Bcl-2, Akt and mitogen-activate protein kinases (MAPKs). In the animal ischaemia model, transduced Tat-Atox1 protected against neuronal cell death in the hippocampal CA1 region. In addition, Tat-Atox1 significantly decreased the activation of astrocytes and microglia as well as lipid peroxidation in the CA1 region after ischaemic insult. Taken together, these results indicate that transduced Tat-Atox1 protects against oxidative stress-induced HT-22 cell death and against neuronal damage in animal ischaemia model. Therefore, we suggest that Tat-Atox1 has potential as a therapeutic agent for the treatment of oxidative stress-induced ischaemic damage.


Asunto(s)
Apoptosis/efectos de los fármacos , Isquemia/prevención & control , Neuronas/efectos de los fármacos , Estrés Oxidativo/efectos de los fármacos , Proteínas Recombinantes de Fusión/farmacología , Animales , Western Blotting , Línea Celular , Supervivencia Celular/efectos de los fármacos , Proteínas Transportadoras de Cobre , Modelos Animales de Enfermedad , Relación Dosis-Respuesta a Droga , Productos del Gen tat/genética , Productos del Gen tat/metabolismo , Hipocampo/citología , Humanos , Isquemia/fisiopatología , Metalochaperonas/genética , Metalochaperonas/metabolismo , Metalochaperonas/farmacología , Ratones , Microscopía Confocal , Microscopía Fluorescente , Chaperonas Moleculares , Actividad Motora/efectos de los fármacos , Neuronas/metabolismo , Fármacos Neuroprotectores/farmacología , Prosencéfalo/irrigación sanguínea , Especies Reactivas de Oxígeno/metabolismo , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo
11.
Am J Hum Genet ; 91(1): 180-4, 2012 Jul 13.
Artículo en Inglés | MEDLINE | ID: mdl-22726844

RESUMEN

Prolongation of the electrocardiographic QT interval, a measure of cardiac repolarization, predisposes one to ventricular arrhythmias and sudden cardiac death. Since NOS1AP, a regulator of neuronal nitric oxide synthase, was discovered in a genome-wide association study (GWAS) as a novel target that modulates cardiac repolarization, several loci have been linked to the QT interval in studies (QTGEN and QTSCD) of European descendents. However, there has been no GWAS of the QT interval in Asian populations. We conducted a GWAS with regard to the QT interval in Korea Association Resource (KARE [n = 6,805]) cohorts. Replication studies in independent populations of Korean (n = 4,686) and Japanese (n = 2,687) groups validated the association between a SNP, rs13017846, which maps to near SLC8A1 (sodium/calcium exchanger 1 precursor, overall p = 8.0 × 10(-14)), and the QT interval. The minor allele frequency (MAF) of rs13017846 varies widely between ethnicities-0.053 in Europeans (HapMap CEU [Utah residents with ancestry from northern and western Europe from the Centre d'Étude du Polymorphisme Humain collection] samples) versus 0.080 in Africans (HapMap YRI [Yoruba in Ibadan, Nigeria] samples)-whereas a MAF of 0.500 has been reported in Asians (HapMap HCB [Han Chinese in Beijing, China] and JPT [Japanese in Tokyo, Japan] samples). This might explain why this locus has not been identified in Europeans in previous studies.


Asunto(s)
Electrocardiografía , Polimorfismo de Nucleótido Simple , Intercambiador de Sodio-Calcio/genética , Adulto , Anciano , Femenino , Estudio de Asociación del Genoma Completo , Humanos , Síndrome de QT Prolongado/genética , Masculino , Persona de Mediana Edad , Estudios de Validación como Asunto
12.
Hum Reprod ; 30(3): 723-31, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-25574032

RESUMEN

STUDY QUESTION: Are there any novel genetic markers of susceptibility to polycystic ovary syndrome (PCOS)? SUMMARY ANSWER: We identified a novel susceptibility locus on chromosome 8q24.2 and several moderately associated loci for PCOS in Korean women. WHAT IS KNOWN ALREADY: PCOS is a highly complex disorder with significant contributions from both genetic and environmental factors. Previous genome-wide association studies (GWAS) in the Han Chinese population identified several risk loci for PCOS. However, GWAS studies on PCOS remain very few. The aim of this study was to identify novel markers of susceptibility to PCOS through GWAS. STUDY DESIGN, SIZE, DURATION: A two-stage GWAS was conducted. The initial discovery set for GWAS consisted of 976 PCOS cases and 946 controls. The second stage (replication study) included 249 PCOS cases and 778 controls. PARTICIPANTS/MATERIALS, SETTING, METHODS: Patients were diagnosed according to the Rotterdam criteria. Genomic DNAs were genotyped using the HumanOmni1-Quad v1 array. In the replication stage, the 21 most promising signals selected from the discovery stage were tested for their association with PCOS. MAIN RESULTS AND THE ROLE OF CHANCE: One novel locus with genome-wide significance and seven moderately associated loci for PCOS were identified. The strongest association was on chromosome 8q24.2 (rs10505648, OR = 0.52, P = 5.46 × 10(-8)), and other association signals were located at 4q35.2, 16p13.3, 4p12, 3q26.33, 9q21.32, 11p13 and 1p22 (P = 5.72 × 10(-6)-6.43 × 10(-5)). The strongest signal was located upstream of KHDRBS3, which is associated with telomerase activity, and could drive PCOS and related phenotypes. LIMITATIONS, REASONS FOR CAUTION: The limitation of our study is the modest sample size used in the replication cohort. The limited sample size may contribute to a lack of statistical power to detect an association or show a trend in severity. WIDER IMPLICATIONS OF THE FINDINGS: Our findings provide new insight into the genetics and biological pathways of PCOS and could contribute to the early diagnosis and prevention of metabolic and reproductive morbidities. STUDY FUNDING/COMPETING INTERESTS: This work was supported in part by the grant from the Korea Centers for Disease Control and Prevention (2009-E00591-00). The work was also supported by the Ewha Global Top5 Grant 2013 of Ewha Womans University. None of the authors has any conflict of interest to declare.


Asunto(s)
Predisposición Genética a la Enfermedad , Síndrome del Ovario Poliquístico/genética , Adulto , Cromosomas Humanos Par 8 , Femenino , Marcadores Genéticos , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , República de Corea
13.
Clin Endocrinol (Oxf) ; 81(5): 702-10, 2014 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24528214

RESUMEN

OBJECTIVE: Genome-wide association studies have identified many obesity/body mass index (BMI)-associated loci in Europeans and East Asians. Since then, a large number of studies have investigated the role of BMI-associated loci in the development of type 2 diabetes (T2D). However, the results have been inconsistent. The objective of this study was to investigate the associations of eleven obesity/BMI loci with T2D risk and explore how BMI influences this risk. METHODS: We retrieved published literature from PubMed and Embase. The pooled odds ratios (OR) with 95% confidence intervals (CI) were calculated using fixed- or random-effect models. RESULTS: In the meta-analysis of 42 studies for 11 obesity/BMI-associated loci, we observed a statistically significant association of the FTO rs9939609 polymorphism (66 425 T2D cases/239 689 normoglycaemic subjects; P = 1·00 × 10(-41) ) and six other variants with T2D risk (17 915 T2D cases/27 531 normoglycaemic individuals: n = 40 629-130 001; all P < 0·001 for SH2B1 rs7498665, FAIM2 rs7138803, TMEM18 rs7561317, GNPDA2 rs10938397, BDNF rs925946 and NEGR1 rs2568958). After adjustment for BMI, the association remained statistically significant for four of the seven variants (all P < 0·05 for FTO rs9939609, SH2B1 rs7498665, FAIM2 rs7138803, GNPDA2 rs10938397). Subgroup analysis by ethnicity demonstrated similar results. CONCLUSIONS: This meta-analysis indicates that several BMI-associated variants are significantly associated with T2D risk. Some variants increase the T2D risk independent of obesity, while others mediate this risk through obesity.


Asunto(s)
Índice de Masa Corporal , Diabetes Mellitus Tipo 2/genética , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple , Dioxigenasa FTO Dependiente de Alfa-Cetoglutarato , Estudios de Casos y Controles , Diabetes Mellitus Tipo 2/epidemiología , Sitios Genéticos/genética , Estudio de Asociación del Genoma Completo , Humanos , Proteínas/genética
14.
J Med Genet ; 50(4): 212-9, 2013 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-23349225

RESUMEN

BACKGROUND: Osteoporotic fracture (OF) as a clinical endpoint is a major complication of osteoporosis. To screen for OF susceptibility genes, we performed a genome-wide association study and carried out de novo replication analysis of an East Asian population. METHODS: Association was tested using a logistic regression analysis. A meta-analysis was performed on the combined results using effect size and standard errors estimated for each study. RESULTS: In a combined meta-analysis of a discovery cohort (288 cases and 1139 controls), three hospital based sets in replication stage I (462 cases and 1745 controls), and an independent ethnic group in replication stage II (369 cases and 560 for controls), we identified a new locus associated with OF (rs784288 in the MECOM gene) that showed genome-wide significance (p=3.59×10(-8); OR 1.39). RNA interference revealed that a MECOM knockdown suppresses osteoclastogenesis. CONCLUSIONS: Our findings provide new insights into the genetic architecture underlying OF in East Asians.


Asunto(s)
Proteínas de Unión al ADN/genética , Osteoporosis/genética , Fracturas Osteoporóticas/genética , Proto-Oncogenes/genética , Sitios de Carácter Cuantitativo/genética , Factores de Transcripción/genética , Anciano , Estudios de Casos y Controles , Regulación de la Expresión Génica , Técnicas de Silenciamiento del Gen , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Proteína del Locus del Complejo MDS1 y EV11 , Persona de Mediana Edad , Osteogénesis/genética , Osteoporosis/patología , Fracturas Osteoporóticas/patología , Polimorfismo de Nucleótido Simple
15.
Genet Epidemiol ; 36(4): 340-51, 2012 May.
Artículo en Inglés | MEDLINE | ID: mdl-22539395

RESUMEN

Recent meta-analyses of European ancestry subjects show strong evidence for association between smoking quantity and multiple genetic variants on chromosome 15q25. This meta-analysis extends the examination of association between distinct genes in the CHRNA5-CHRNA3-CHRNB4 region and smoking quantity to Asian and African American populations to confirm and refine specific reported associations. Association results for a dichotomized cigarettes smoked per day phenotype in 27 datasets (European ancestry (N = 14,786), Asian (N = 6,889), and African American (N = 10,912) for a total of 32,587 smokers) were meta-analyzed by population and results were compared across all three populations. We demonstrate association between smoking quantity and markers in the chromosome 15q25 region across all three populations, and narrow the region of association. Of the variants tested, only rs16969968 is associated with smoking (P < 0.01) in each of these three populations (odds ratio [OR] = 1.33, 95% CI = 1.25-1.42, P = 1.1 × 10(-17) in meta-analysis across all population samples). Additional variants displayed a consistent signal in both European ancestry and Asian datasets, but not in African Americans. The observed consistent association of rs16969968 with heavy smoking across multiple populations, combined with its known biological significance, suggests rs16969968 is most likely a functional variant that alters risk for heavy smoking. We interpret additional association results that differ across populations as providing evidence for additional functional variants, but we are unable to further localize the source of this association. Using the cross-population study paradigm provides valuable insights to narrow regions of interest and inform future biological experiments.


Asunto(s)
Cromosomas Humanos Par 15 , Variación Genética , Fumar/efectos adversos , Adolescente , Adulto , Negro o Afroamericano , Anciano , Anciano de 80 o más Años , Pueblo Asiatico , Población Negra , Femenino , Frecuencia de los Genes , Genética de Población , Humanos , Enfermedades Pulmonares/etiología , Enfermedades Pulmonares/genética , Neoplasias Pulmonares/etiología , Neoplasias Pulmonares/genética , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Fenotipo , Riesgo , Población Blanca
16.
Biochem Biophys Res Commun ; 430(1): 294-300, 2013 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-23159613

RESUMEN

Diabetes mellitus (DM) is characterized by hyperglycemia. Glyoxalase 1 (GLO) has considerable potential as a possible therapeutic agent for DM. However, the precise action of GLO remains unclear in DM. In this study, we examined the protective effects of GLO protein in a streptozotocin (STZ)-induced diabetes animal model using cell-permeable Tat-GLO protein. Purified Tat-GLO protein was efficiently transduced into RINm5F cells in a time- and dose-dependent manner and protected cells against sodium nitroprusside (SNP)-induced cell death and DNA fragmentation. Furthermore, Tat-GLO protein significantly inhibited blood glucose levels and altered the serum biochemical parameters in STZ-induced diabetic mice. These results demonstrate that transduced Tat-GLO protein protects pancreatic cells by the inhibition of STZ-mediated toxicity. Therefore, Tat-GLO protein could be useful as a therapeutic agent against DM.


Asunto(s)
Diabetes Mellitus Experimental/terapia , Lactoilglutatión Liasa/administración & dosificación , Fragmentos de Péptidos/administración & dosificación , Proteínas Recombinantes de Fusión/administración & dosificación , Proteínas Recombinantes/administración & dosificación , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/administración & dosificación , Animales , Línea Celular , Permeabilidad de la Membrana Celular , Diabetes Mellitus Experimental/prevención & control , Humanos , Lactoilglutatión Liasa/genética , Lactoilglutatión Liasa/metabolismo , Masculino , Ratones , Ratones Endogámicos ICR , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/metabolismo , Transporte de Proteínas , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Recombinantes/metabolismo , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/genética , Productos del Gen tat del Virus de la Inmunodeficiencia Humana/metabolismo
17.
J Hum Genet ; 58(1): 16-20, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23171997

RESUMEN

Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) promise to address the challenge posed by the limited availability of primary cells needed as a source of genomic DNA for genetic studies. However, the genetic stability of LCLs following prolonged culture has never been rigorously investigated. To evaluate genotypic errors caused by EBV integration into human chromosomes, we isolated genomic DNA from human peripheral blood mononuclear cells and LCLs collected from 20 individuals and genotyped the DNA samples using the Affymetrix 500K SNP array set. Genotype concordance measurements between two sources of DNA from the same individual indicated that genotypic discordance is negligible in early-passage LCLs (<20 passages) but substantial in late-passage LCLs (>50 passages). Analysis of concordance on a chromosome-by-chromosome basis identified genomic regions with a high frequency of genotypic errors resulting from the loss of heterozygosity observed in late-passage LCLs. Our findings suggest that, although LCLs harvested during early stages of propagation are a reliable source of genomic DNA for genetic studies, investigations that involve genotyping of the entire genome should not use DNA from late-passage LCLs.


Asunto(s)
Transformación Celular Viral/genética , Variación Genética , Leucocitos Mononucleares/virología , Adulto , Anciano , Línea Celular Transformada , Células Cultivadas , Genotipo , Herpesvirus Humano 4/fisiología , Humanos , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple/genética , Integración Viral
18.
J Hum Genet ; 58(6): 362-5, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23575436

RESUMEN

Most recently, 1-h hyperglycemia has been recognized as an additional risk factor for type 2 diabetes. To date, previous genome-wide association studies for glycemic traits have a limited impact on the fasting state and 2-h plasma glucose level in an oral glucose challenge. To identify genetic susceptibility in different stages of glucose tolerance, we performed a meta-analysis for glycemic traits including 1-h plasma glucose (1-hPG) from 14 232 non-diabetic individuals in the Korean population. Newly implicated variants (MYL2, C12orf51 and OAS1) were found to be significantly associated with 1-hPG. We also demonstrated associations with gestational diabetes mellitus. Our results could provide additional insight into the genetic variation in the clinical range of glycemia.


Asunto(s)
2',5'-Oligoadenilato Sintetasa/genética , Pueblo Asiatico/genética , Miosinas Cardíacas/genética , Diabetes Mellitus Tipo 2/genética , Predisposición Genética a la Enfermedad , Cadenas Ligeras de Miosina/genética , Ubiquitina-Proteína Ligasas/genética , Adulto , Anciano , Glucemia/análisis , Diabetes Gestacional/genética , Ayuno/sangre , Femenino , Sitios Genéticos , Estudio de Asociación del Genoma Completo , Genotipo , Prueba de Tolerancia a la Glucosa , Humanos , Hiperglucemia/sangre , Modelos Lineales , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Embarazo , República de Corea , Factores de Riesgo
19.
PLoS Genet ; 6(9): e1001127, 2010 Sep 16.
Artículo en Inglés | MEDLINE | ID: mdl-20862305

RESUMEN

Although more than 20 genetic susceptibility loci have been reported for type 2 diabetes (T2D), most reported variants have small to moderate effects and account for only a small proportion of the heritability of T2D, suggesting that the majority of inter-person genetic variation in this disease remains to be determined. We conducted a multistage, genome-wide association study (GWAS) within the Asian Consortium of Diabetes to search for T2D susceptibility markers. From 590,887 SNPs genotyped in 1,019 T2D cases and 1,710 controls selected from Chinese women in Shanghai, we selected the top 2,100 SNPs that were not in linkage disequilibrium (r(2)<0.2) with known T2D loci for in silico replication in three T2D GWAS conducted among European Americans, Koreans, and Singapore Chinese. The 5 most promising SNPs were genotyped in an independent set of 1,645 cases and 1,649 controls from Shanghai, and 4 of them were further genotyped in 1,487 cases and 3,316 controls from 2 additional Chinese studies. Consistent associations across all studies were found for rs1359790 (13q31.1), rs10906115 (10p13), and rs1436955 (15q22.2) with P-values (per allele OR, 95%CI) of 6.49 × 10(-9) (1.15, 1.10-1.20), 1.45 × 10(-8) (1.13, 1.08-1.18), and 7.14 × 10(-7) (1.13, 1.08-1.19), respectively, in combined analyses of 9,794 cases and 14,615 controls. Our study provides strong evidence for a novel T2D susceptibility locus at 13q31.1 and the presence of new independent risk variants near regions (10p13 and 15q22.2) reported by previous GWAS.


Asunto(s)
Diabetes Mellitus Tipo 2/genética , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple/genética , Alelos , Pueblo Asiatico/genética , China , Cromosomas Humanos/genética , Femenino , Humanos , Masculino , Persona de Mediana Edad , Oportunidad Relativa , Factores de Riesgo
20.
Genes Genomics ; 45(7): 847-854, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37133724

RESUMEN

BACKGROUND: Non-alcoholic fatty liver (NAFL) refers to a disease in which fat builds up in the liver, similar to what occurs for those who drink a lot of alcohol, even in cases of not drinking alcohol at all or only in a small amount. Along with non-alcoholic steatohepatitis (NASH), NAFL is a type of non-alcoholic fatty liver disease (NAFLD). Currently, the prevalence of NAFLD is increasing worldwide. A wide range of comorbidities that can increase the risk of NAFLD includes obesity, type 2 diabetes, dyslipidemia, and metabolic syndrome. OBJECTIVE: This study aimed to discover genetic variants for NAFL in the Korean population. METHODS: Differing from previous studies, we conducted a genome-wide association study for NAFL in the selected subjects without comorbidities to rule out bias due to the inclusion of confounding effects of comorbidities. We grouped 424 NAFL cases and 5,402 controls from the Korean Genome and Epidemiology Study (KoGES) subjects without comorbidities such as dyslipidemia, type 2 diabetes, and metabolic syndrome. All subjects including cases and controls did not consume alcohol at all, or consumed less than 20 g/day for men and less than 10 g/day for women. RESULTS: The logistic association analysis adjusting for sex, age, BMI, and waist circumference identified one novel genome-wide significant variant (rs7996045, P = 2.3 × 10-8) for NAFL. This variant was located in the intron of CLDN10 and was not detected using previous conventional approaches in which confounding effects resulting from comorbidities were not considered in the study design stage. In addition, we detected several genetic variants showing suggestive association for NAFL (P < 10-5). CONCLUSION: The unique strategy in our association analysis of excluding major confounding factors provides, for the first time, an insight into the genuine genetic basis influencing NAFL.


Asunto(s)
Diabetes Mellitus Tipo 2 , Síndrome Metabólico , Enfermedad del Hígado Graso no Alcohólico , Masculino , Humanos , Femenino , Enfermedad del Hígado Graso no Alcohólico/epidemiología , Enfermedad del Hígado Graso no Alcohólico/genética , Enfermedad del Hígado Graso no Alcohólico/metabolismo , Estudio de Asociación del Genoma Completo , Síndrome Metabólico/epidemiología , Síndrome Metabólico/genética , Diabetes Mellitus Tipo 2/epidemiología , Diabetes Mellitus Tipo 2/genética , República de Corea/epidemiología
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