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Kim J.Y.,Sogang University | Bae J.S.,Samsung | Kim H.J.,National Cancer Center | Shin H.D.,Sogang University | Shin H.D.,SNP Genetics Inc.
BMC Neurology | Year: 2014

Background: Neuromyelitis optica (NMO) is a serious inflammatory demyelinating disease (IDD), characterized by the inflammation and demyelination of optic nerves and spinal cords, which subsequently leads to the loss of function. In a previous genome-wide association study, cluster of differentiation 58 (CD58) region was found to be susceptible for the risk of multiple sclerosis (MS) in Caucasian, and the association between CD58 variants and MS was replicated in Americans. However, no study has been conducted to explore the possible association between CD58 and NMO yet. Thus, this study aimed to investigate the association of CD58 polymorphisms with the risk of NMO in a Korean population.Methods: Using TaqMan assay, 6 single nucleotide polymorphisms (SNPs) were genotyped in 98 NMO patients and 237 normal controls (N = 336). Logistic regression analysis was conducted to find a possible association between CD58 polymorphisms and NMO.Results: The analysis results showed that 6 variations (rs2300747, rs1335532, rs12044852, rs1016140, CD58_ht1, and CD58_ht3) showed significant associations (P = 0.002 ~ 0.008, Pcorr = 0.01 ~ 0.04).Conclusion: The genetic variations in CD58 may be associated with the susceptibility of NMO in a Korean population. Based on previous studies, we suspect that the A allele of rs2300747 may decrease CD58 RNA expression, thus increasing NMO risk. Also, we deduced that the G allele of rs1016140 caused an increase of T cell activity, which in turn eased the access of AQP4 antibody into central nervous system (CNS) and ultimately leading to NMO development. © 2014 Kim et al.; licensee BioMed Central Ltd.

Bae J.S.,Sogang University | Cheong H.S.,SNP Genetics Inc | Kim L.H.,SNP Genetics Inc | NamGung S.,SNP Genetics Inc | And 7 more authors.
BMC Genomics | Year: 2010

Background: Recently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain CNV region has been found to be associated with the onset of diseases. Therefore, CNV is now known as an important genomic variation in biological mechanisms. However, most CNV studies have only involved the human genome. The study of CNV involving other animals, including cattle, is severely lacking.Results: In our study of cattle, we used Illumina BovineSNP50 BeadChip (54,001 markers) to obtain each marker's signal intensity (Log R ratio) and allelic intensity (B allele frequency), which led to our discovery of 855 bovine CNVs from 265 cows. For these animals, the average number of CNVs was 3.2, average size was 149.8 kb, and median size was 171.5 kb. Taking into consideration some overlapping regions among the identified bovine CNVs, 368 unique CNV regions were detected. Among them, there were 76 common CNVRs with > 1% CNV frequency. Together, these CNVRs contained 538 genes. Heritability errors of 156 bovine pedigrees and comparative pairwise analyses were analyzed to detect 448 common deletion polymorphisms. Identified variations in this study were successfully validated using visual examination of the genoplot image, Mendelian inconsistency, another CNV identification program, and quantitative PCR.Conclusions: In this study, we describe a map of bovine CNVs and provide important resources for future bovine genome research. This result will contribute to animal breeding and protection from diseases with the aid of genomic information. © 2010 Bae et al; licensee BioMed Central Ltd.

Forero D.A.,Antonio Nariño University | Lopez-Leon S.,Novartis | Shin H.D.,Sogang University | Park B.L.,SNP Genetics Inc. | Kim D.-J.,Catholic University of Korea
Drug and Alcohol Dependence | Year: 2015

Background: Alcohol-related problems have a large impact on human health, accounting for around 4% of deaths and 4.5% of disability-adjusted life-years around the world. Genetic factors could explain a significant fraction of the risk for alcohol dependence (AD). Recent meta-analyses have found significant pooled odds ratios (ORs) for variants in the ADH1B, ADH1C, DRD2 and HTR2A genes. Methods: In the present study, we carried out a meta-analysis of common variants in 6 candidate genes involved in neurotransmission and neuroplasticity: BDNF, DRD1, DRD3, DRD4, GRIN2B and MAOA. We carried out a systematic search for published association studies that analyzed the genes of interest. Relevant articles were retrieved and demographic and genetic data were extracted. Pooled ORs were calculated using a random-effects model using the Meta-Analyst program. Dominant, recessive and allelic models were tested and analyses were also stratified by ethnicity. Results: Forty two published studies were included in the current meta-analysis: BDNF-rs6265 (nine studies), DRD1-rs4532 (four studies), DRD3-rs6280 (eleven studies), DRD4-VNTR (seven studies), GRIN2B-rs1806201 (three studies) and MAOA-uVNTR (eight studies). We did not find significant pooled ORs for any of the six genes, under different models and stratifying for ethnicity. Conclusions: In terms of the number of candidate genes included, this is one of the most comprehensive meta-analyses for genetics of AD. Pooled ORs did not support consistent associations with any of the six candidate genes tested. Future studies of novel genes of functional relevance and meta-analyses of quantitative endophenotypes could identify further susceptibility molecular factors for AD. © 2015 Elsevier Ireland Ltd.

Kim Y.-J.,Soonchunhyang University | Park S.-W.,Soonchunhyang University | Kim T.-H.,Soonchunhyang University | Park J.-S.,Soonchunhyang University | And 3 more authors.
BMC Medical Genetics | Year: 2013

Background: Asthma is a common respiratory disease that is characterized by bronchial hyperresponsiveness and airway obstruction due to chronic airway inflammation. Atopic asthma is a typical IgE-mediated disease in which the enhanced production of IgE is driven by the activation of Th2 cells, which release a distinct pattern of cytokines, including interleukin 4 (IL4) and IL3, in response to specific antigen presentation. To evaluate the methylation status of the whole genomes of bronchial mucosa tissues from subjects who lacked or had sensitization to Dermatophagoides farina (Df) and Dermatophagoides pteronyssinus (Dp). Methods: The genome-wide DNA methylation levels in the bronchial mucosa tissues of atopic asthmatics (N = 10), non-atopic asthmatics (N = 7), and normal controls (N = 7) were examined using microarrays. Results: In the bronchial mucosa of atopic asthmatics, hypermethylation was detected at 6 loci in 6 genes, while hypomethylation was detected at 49 loci in 48 genes compared to those of non-atopic asthmatics. Genes that were assigned the ontologies of multicellular organismal process, response to organic substance, hormone metabolic process, and growth factor receptor binding were hypomethylated. The methylation levels in the mucosa of asthmatics and normal controls were similar. Conclusions: The bronchial mucosa of asthmatics who are atopic to Df or Dp have characteristic methylation patterns for 52 genes. The genes and pathways identified in the present study may be associated with the presence of atopy in asthmatics and therefore represent attractive targets for future research. © 2013 Kim et al.; licensee BioMed Central Ltd.

Park B.L.,SNP Genetics Inc. | Kim J.W.,Hallym University | Cheong H.S.,SNP Genetics Inc. | Kim L.H.,SNP Genetics Inc. | And 10 more authors.
Human Genetics | Year: 2013

Alcohol dependence (AD) is a multifactorial and polygenic disorder involving complex gene-to-gene and gene-to-environment interactions. Several genome-wide association studies have reported numerous risk factors for AD, but replication results following these studies have been controversial. To identify new candidate genes, the present study used GWAS and replication studies in a Korean cohort with AD. Genome-wide association analysis revealed that two chromosome regions on Chr. 4q22-q23 (ADH gene cluster, including ADH5, ADH4, ADH6, ADH1A, ADH1B, and ADH7) and Chr. 12q24 (ALDH2) showed multiple association signals for the risk of AD. To investigate detailed genetic effects of these ADH genes on AD, a follow-up study of the ADH gene cluster on 4q22-q23 was performed. A total of 90 SNPs, including ADH1B rs1229984 (H47R), were genotyped in an additional 975 Korean subjects. In case-control analysis, ADH1B rs1229984 (H47R) showed the most significant association with the risk of AD (p = 2.63 × 10-21, OR = 2.35). Moreover, subsequent conditional analyses revealed that all positive associations of other ADH genes in the cluster disappeared, which suggested that ADH1B rs1229984 (H47R) might be the sole functional genetic marker across the ADH gene cluster. Our findings could provide additional information on the ADH gene cluster regarding the risk of AD, as well as a new and important insight into the genetic factors associated with AD. © 2013 Springer-Verlag Berlin Heidelberg.

Park T.-J.,Sogang University | Kim H.J.,National Cancer Center | Kim J.-H.,Sogang University | Bae J.S.,SNP Genetics Inc. | And 4 more authors.
Neuropathology and Applied Neurobiology | Year: 2013

Aims: Multiple sclerosis (MS) and neuromyelitis optica (NMO) are inflammatory autoimmune diseases that affect the central nervous system. Several genome-wide and candidate gene studies have identified genetic polymorphisms associated with the risk of MS or NMO. In particular, two recently published studies of meta-analysis in European-origin populations have suggested associations of single-nucleotide polymorphisms (SNPs) in CD6, TNFRSF1A and IRF8 with MS. The aim of our study was to assess the associations between SNPs in these three genes and the risk of inflammatory demyelinating disease (IDD) including MS and NMO. To the best of our knowledge, this is the first time such a study has been performed in an Asian population. Methods: A total of 21 SNPs of CD6, TNFRSF1A and IRF8 were genotyped in 178 IDD cases (79 MS and 99 NMO patients) and 237 normal controls in a Korean population. Results: Logistic analyses revealed that one SNP in CD6 (rs12288280, P=0.04) and three SNPs in TNFRSF1A (rs767455, rs4149577 and rs1800693, P=0.01-0.03) were associated with NMO. However, there was no association of IRF8 polymorphisms with IDD, including MS and NMO. Using further information from the SNP Function Prediction website, two exonic splicing enhancers (ESEs), including the polymorphic site of rs767455, were predicted to be binding sites for splicing factors (SRp55, SF2/ASF2 and SF2/ASF1). Conclusion: Although additional studies are needed, our findings could provide information regarding the genetic aetiology of IDD in the Korean population. © 2012 British Neuropathological Society.

Shin H.D.,SNP Genetics Inc. | Shin H.D.,Sogang University | Park B.L.,SNP Genetics Inc. | Shin H.J.,SNP Genetics Inc. | And 4 more authors.
Journal of Clinical Endocrinology and Metabolism | Year: 2010

Context: Similar genetic factors may play role in the pathogenesis of gestational diabetes mellitus (GDM) and type 2 diabetes mellitus (T2DM). However, genetic studies on GDM are relatively scarce as compared with T2DM. Objective: A recent genome-wide association (GWA) study has proved that three KCNQ1 polymorphisms were significantly associated with the risk of T2DM in various ethnic groups. This study aimed to examine possible genetic effects of these KCNQ1 polymorphisms on the risk of GDM. Design: Three KCNQ1 polymorphisms (rs2074196, rs2237892, and rs2237895) were genotyped using TaqMan assay. The genotype distributions between GDM patients and normal controls were analyzed using logistic regression models. In addition, GDM-related phenotypes were analyzed using multiple regression models. Setting: All GDM patients recruited from Cheil General Hospital in Seoul, Korea, between 2003 and 2008. Participants: Participants included 930 Korean females with GDM and the data of healthy controls from the previous GWA study. Results: KCNQ1 polymorphisms of rs2237892 and rs2237895 were significantly associated with the risk ofGDM(P=0.003 and 0.005, respectively). In the analyses of the GDM-related phenotype, only the risk allele of KCNQ1 rs2237895 was significantly associated with a high-level insulin sensitivity oral glucose tolerance test among patients with GDM(P=0.0003, 0.004, and 0.05 for codominant, dominant, and recessive models, respectively). Conclusion: KCNQ1 polymorphisms shown to be associated with increased risk for T2DM in the recent GWA study might also represent genetic factors contributing to the development of GDM in Koreans. Copyright © 2010 by The Endocrine Society.

Cheong H.S.,SNP Genetics Inc. | Park S.-M.,Bucheon Hospital | Kim M.-O.,Bucheon Hospital | Park J.-S.,Soonchunhyang University | And 7 more authors.
Allergy: European Journal of Allergy and Clinical Immunology | Year: 2011

Background: In addition to the dysregulation of arachidonic acid metabolism in aspirin-intolerant asthma (AIA), aspirin acetylsalicylic acid (ASA) exerts effects on inflammation and immunity; however, many of these effects are unknown. Objective: The aim of the study was to evaluate the methylation status of whole genome in blood and polyp tissues with and without aspirin hypersensitivity. Methods: Genome-wide DNA methylation levels in nasal polyps and peripheral blood cells were examined by microarray analysis using five subjects with AIA and four subjects with aspirin-tolerant asthma (ATA). Results: In the nasal polyps of the patients with AIA, hypermethylation was detected at 332 loci in 296 genes, while hypomethylation was detected at 158 loci in 141 genes. Gene ontologic and pathway enrichment analyses revealed that genes involved in lymphocyte proliferation, cell proliferation, leukocyte activation, cytokine biosynthesis, cytokine secretion, immune responses, inflammation, and immunoglobulin binding were hypomethylated, while genes involved in ectoderm development, hemostasis, wound healing, calcium ion binding, and oxidoreductase activity were hypermethylated. In the arachidonate pathway, PGDS, ALOX5AP, and LTB4R were hypomethylated, whereas PTGES was hypermethylated. Conclusion: The nasal polyps of patients with AIA have characteristic methylation patterns affecting 337 genes. The genes and pathways identified in this study may be associated with the presence of aspirin hypersensitivity in asthmatics and are therefore attractive targets for future research. © 2010 John Wiley & Sons A/S.

Choi S.Y.,Chung - Ang University | Kim H.J.,Korea Institute of Science and Technology | Cheong H.S.,SNP Genetics Inc | Myung S.C.,Chung - Ang University
Korean Journal of Urology | Year: 2015

Purpose: Steroid 5-alpha reductase type 2 (SRD5A2) modifies testosterone to dihydrotestosterone (DHT) in the prostate. Single-nucleotide polymorphisms (SNPs) of the SRD5A2 gene might affect DHT. We sought to understand the relationship of SRD5A2 SNPs to prostate cancer in the Korean population.Materials and Methods: Twenty-six common SNPs in the SRD5A2 gene were assessed in 272 prostate cancer cases and 173 controls. Single-locus analyses were conducted by using conditional logistic regression. Additionally, we performed a haplotype analysis for the SRD5A2 SNPs tested.Results: Among the 20 SNPs and 4 haplotypes, there were no statistically significant results in the prostate cancer patients and the controls. In the logistic analysis of SRD5A2 polymorphisms with prostate-specific antigen (PSA) criteria, two SNPs (rs508562, rs11675297) and haplotype 1 displayed significant results (odds ratio [OR], 1.76; p=0.05; OR, 1.88–2.02; p=0.01–0.04; OR, 0.59; p=0.02, respectively). rs508562, rs11675297, rs2208532, and haplotype 1 (OR, 1.49; p=0.05; OR, 2.02; p=0.05; OR, 2.01; p=0.04; OR, 0.56–0.64, p=0.03–0.04, respectively) had significant associations with Gleason score. rs508562, rs11675297, and haplotype 1 (OR, 1.41–2.34; p=0.004–0.05; OR, 1.74–1.82; p=0.03–0.05; OR, 0.42–0.67; p=0.0005–0.03, respectively) were significantly associated with clinical stage.Conclusions: We conclude that there was no significant association between SRD5A2 SNPs and the risk of prostate cancer in the Korean population. However, we found that some SNPs and 1 haplotype influenced PSA level, Gleason score, and clinical stage. © The Korean Urological Association, 2015.

Park Y.M.,University of Ulsan | Cheong H.S.,SNP Genetics Inc. | Lee J.-K.,University of Ulsan
Gene | Year: 2014

Allelic variations in gene expression influence many biological responses and cause phenotypic variations in humans. In this study, Illumina Human Exome BeadChips containing more than 240,000 single nucleotide polymorphisms (SNPs) were used to identify changes in allelic gene expression in hepatocellular carcinoma cells following lipopolysaccharide (LPS) stimulation. We found 17 monoallelically expressed genes, 58 allelic imbalanced genes, and 7 genes showing allele substitution. In addition, we also detected 33 differentially expressed genes following LPS treatment in vitro using these human exome SNP chips. However, alterations in allelic gene expression following LPS treatment were detected in only three genes (. MLXIPL, TNC, and MX2), which were observed in one cell line sample only, indicating that changes in allelic gene expression following LPS stimulation of liver cells are rare events. Among a total of 75 genes showing allelic expression in hepatocellular carcinoma cells, either monoallelic or imbalanced, 43 genes (57.33%) had expression quantitative trait loci (eQTL) data, indicating that high-density exome SNP chips are useful and reliable for studying allelic gene expression. Furthermore, most genes showing allelic expression were regulated by cis-acting mechanisms and were also significantly associated with several human diseases. Overall, our study provides a better understanding of allele-specific gene expression in hepatocellular carcinoma cells with and without LPS stimulation and potential clues for the cause of human disease due to alterations in allelic gene expression. © 2014 Elsevier B.V.All rights reserved.

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