Genome-Wide Analysis Reveals Four Novel Loci for Attention-Deficit Hyperactivity Disorder in Korean Youths

OBJECTIVES: The molecular mechanisms underlying attention-deficit hyperactivity disorder (ADHD) remain unclear. Therefore, this study aimed to identify the genetic susceptibility loci for ADHD in Korean children with ADHD. We performed a case-control and a family-based genome-wide association study (GWAS), as well as genome-wide quantitative trait locus (QTL) analyses, for two symptom traits. METHODS: A total of 135 subjects (71 cases and 64 controls), for the case-control analysis, and 54 subjects (27 probands and 27 unaffected siblings), for the family-based analysis, were included. RESULTS: The genome-wide QTL analysis identified four single nucleotide polymorphisms (SNPs) (rs7684645 near APELA, rs12538843 near YAE1D1 and POU6F2, rs11074258 near MCTP2, and rs34396552 near CIDEA) that were significantly associated with the number of inattention symptoms in ADHD. These SNPs showed possible association with ADHD in the family-based GWAS, and with hyperactivity-impulsivity in genome-wide QTL analyses. Moreover, association signals in the family-based QTL analysis for the number of inattention symptoms were clustered near genes IL10, IL19, SCL5A9, and SKINTL. CONCLUSION: We have identified four QTLs with genome-wide significance and several promising candidates that could potentially be associated with ADHD (CXCR4, UPF1, SETD5, NALCN-AS1, ERC1, SOX2-OT, FGFR2, ANO4, and TBL1XR1). Further replication studies with larger sample sizes are needed.

The Interaction Between Allelic Variants of CD86 and CD40LG: A Common Risk Factor of Allergic Asthma and Rheumatoid Arthritis

PURPOSE: Allergic asthma (AA) and rheumatoid arthritis (RA) are immune tolerance-related diseases, and immune tolerance is known to be influenced by costimulatory molecules. In this study, we sought to identify common genetic susceptibility in AA and RA. METHODS: Two hundred cases of AA, 184 cases of RA, and 182 healthy controls were recruited at the Seoul National University Hospital, Seoul, Korea. Eight single nucleotide polymorphisms (SNPs) in five genes coding costimulatory molecules, namely, -318C>T, +49A>G, and 6230G>A in CTLA4, IVS3+17T>C in CD28, -3479T>G and I179V in CD86, -1C>T in CD40, and -3458A>G in CD40LG were scored, and genetic interactions were evaluated by multifactor dimensionality reduction (MDR) analysis. RESULTS: MDR analysis revealed a significant gene-gene interaction between -3479T>G CD86 and -3458A>G CD40LG for AA. Subjects with the T/T genotype of -3479T>G CD86 and the A/A genotype of -3458A>G CD40LG were found to be significantly more likely to develop AA than those with the T/T genotype of -3479T>G CD86 and A/- genotype of -3458A>G CD40LG (adjusted OR, 6.09; 95% CI, 2.89-12.98; logistic regression analysis controlled by age). Similarly those subjects showed a significant risk of developing RA (adjusted OR, 39.35; 95% CI, 15.01-107.00, logistic regression analysis controlled by age). CONCLUSIONS: Our findings suggest that a genetic interaction between CD86 and CD40LG favors the development of both AA and RA.

Association of CYP2C19*2 and *3 Genetic Variants with Essential Hypertension in Koreans

PURPOSE: The cytochrome P450 2C19 (CYP2C19) metabolizes arachidonic acid to produce epoxyicosanoid acids, which are involved in vascular tone and regulation of blood pressure. Recent findings suggest that CYP2C19 gene might be considered as a novel candidate gene for treatment of cardiovascular disease. The aim of the present study was to evaluate the association between two variants, CYP2C19*2 (681G>A) and CYP2C19*3 (636G>A) and the development of essential hypertension (EH) in Koreans. MATERIALS AND METHODS: We carried out an association study in a total of 1190 individuals (527 hypertensive subjects and 663 unrelated healthy controls). The CYP2C19 polymorphisms were genotyped using the SNaPShot(TM) assay. RESULTS: The distribution of alleles and genotypes of CYP2C19*3 showed significant difference between hypertensive patients and normal controls (p=0.011 and p=0.013, respectively). Logistic regression analysis indicated that the CYP2C19*3 (636A) allele carriers were significantly associated with EH [odds ratio, 0.691; 95% confidence interval (CI), 0.512-0.932, p=0.016], in comparison to wild type homozygotes (CYP2C19*1/*1). Neither genotype nor allele distribution of CYP2C19*2 polymorphism showed significant differences between hypertensive and control groups (p>0.05). CONCLUSION: Our present findings strengthen the evidence of an association between CYP2C19 gene polymorphism and EH prevalence. In particular, the CYP2C19*3 defective allele may contribute to reduced risk for the development of EH.

Genetic Variations in TXNRD1 as Potential Predictors of Drug-Induced Liver Injury

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.

Vitamin D Receptor Gene TaqI, BsmI and FokI Polymorphisms in Korean Patients with Tuberculosis

BACKGROUND: The active metabolite (1, 25-dihydroxycholecalciferol) of vitamin D (25-hydroxycholecalciferol) leads to activation of macrophages and deficiency of vitamin D seems to be involved in the risk of tuberculosis. The effects of vitamin D are exerted by interaction with the vitamin D receptor (VDR) and may be influenced by polymorphism in the VDR gene. In this study, variation in the VDR gene was investigated in Korean population with tuberculosis. METHODS: We typed three VDR polymorphisms of restriction endonuclease sites for TaqI, BsmI and FokI in 155 patients with tuberculosis and 105 healthy volunteers. RESULTS: The frequencies of FokI genotypes determined from TB patients were 29.13% for FF, 56.31% for Ff, and 14.56% for ff. We observed 1.4-fold increased prevalence of the Ff genotype in TB patients compared with normal healthy groups (p=0.0857). However, there was no significant association between the genotype groups, TB patient and normal control, for FokI polymorphism. There was also no significant association between VDR gene and tuberculosis in another polymorphism (BsmI and TaqI). CONCLUSION: Three polymorphisms (TaqI, BsmI and FokI) in the VDR gene do not appear to be responsible for host susceptibility to human tuberculosis in Korean population.

Vitamin D Receptor Gene TaqI, BsmI and FokI Polymorphisms in Korean Patients with Tuberculosis

BACKGROUND: The active metabolite (1, 25-dihydroxycholecalciferol) of vitamin D (25-hydroxycholecalciferol) leads to activation of macrophages and deficiency of vitamin D seems to be involved in the risk of tuberculosis. The effects of vitamin D are exerted by interaction with the vitamin D receptor (VDR) and may be influenced by polymorphism in the VDR gene. In this study, variation in the VDR gene was investigated in Korean population with tuberculosis. METHODS: We typed three VDR polymorphisms of restriction endonuclease sites for TaqI, BsmI and FokI in 155 patients with tuberculosis and 105 healthy volunteers. RESULTS: The frequencies of FokI genotypes determined from TB patients were 29.13% for FF, 56.31% for Ff, and 14.56% for ff. We observed 1.4-fold increased prevalence of the Ff genotype in TB patients compared with normal healthy groups (p=0.0857). However, there was no significant association between the genotype groups, TB patient and normal control, for FokI polymorphism. There was also no significant association between VDR gene and tuberculosis in another polymorphism (BsmI and TaqI). CONCLUSION: Three polymorphisms (TaqI, BsmI and FokI) in the VDR gene do not appear to be responsible for host susceptibility to human tuberculosis in Korean population.

Association between genetic variations of the transforming growth factor beta receptor type III and asthma in a Korean population

Transforming growth factor-beta (TGF-beta) and its receptors have been suggested to play key roles in the pathogenesis of asthma. The aim of this study was to evaluate the effects of genetic variations in the TGF-beta receptor type III (TGFBR3) on asthma and on its related phenotypes in the general population. A cohort of 2,118 subjects aged from 10 to 18 years responded to a questionnaire concerning asthma symptoms and risk factors. Methacholine airway hyperresponsiveness (AHR), skin test responses to common aeroallergens, and serum total IgE levels were evaluated in the cohort. A total of 19 SNPs for TGFBR3 were found using direct re-sequencing in 24 healthy adults. Of these, informative SNPs [+44T>C (S15F) and +2753G>A at 3'UTR] were selected and scored using the high throughput single base extension method. Atopy was identified in subjects with 44T>C allele [P = 0.04, OR (95% CI) = 0.79 (0.62-0.99)] and in subjects with Ht1 (CG) more frequently than in subjects with other haplotypes [P = 0.04, OR (95% CI) = 1.27 (1.01-1.59)]. The A allele in 2753G>A was more common in subjects with non-atopic asthma [OR (95% CI) = 1.76 (1.01-3.05)]. A significant association was found between non-atopic asthma and 44T_2753A [OR (95% CI) = 2.16 (1.22-3.82)]. Genetic variations in TGFBR3 appear to be associated with a genetic predisposition to development of asthma and to phenotypes of asthma. Also, the minor allele 2753G and the haplotype TA in the TGFBR3 gene were associated with a pathogenesis of non-atopic asthma.

Association of Single Nucleotide Polymorphisms in PIM-1 Gene with the Risk of Korean Lung Cancer / Journal of the Korean Cancer Association, 대한암학회지

PURPOSE: The expression of the PIM-1 gene, which is a proto-oncogene that encodes a serine/threonine kinase, is associated with multiple cellular functions such as proliferation, differentiation, apoptosis and tumorigenesis. In particular, several studies have reported that the PIM-1 gene is associated with the development of lymphoma, leukemia and prostate cancer. Therefore, this study was conducted to evaluate the association between the single nucleotide polymorphisms in the PIM-1 gene and the risk of lung cancer occurrence in the Korean population. MATERIALS AND METHODS: To evaluate the role of the PIM-1 gene in the development of lung cancer, the genotypes of the PIM-1 gene were determined in 408 lung cancer patients and 410 normal subjects. RESULTS: We found that the T-C-T-C haplotypes of the PIM-1 gene (-1196 T>C, IVS4 +55 T>C, IVS4 +1416 T>A and +3684 C>A) were associated with an increased risk of lung cancer [adjusted odds ratio (aOR): 3.98; 95% CI: 1.24~12.75, p-value: 0.020]. In particular, these haplotypes showed an increased risk of lung cancer in males (aOR: 5.67; 95% CI: 1.32~24.30, p-value: 0.019) and smokers (aOR: 7.82; 95% CI: 1.75~34.98, p-value: 0.007). CONCLUSIONS: The present results suggest that the T-C-T-C haplotype of the PIM-1 gene could influence the risk of developing smoking-related lung cancer in the Korean population. Additional functional studies with an larger sample sized analysis are warranted to reconfirm our findings.

Distribution of HLA-A, B, C Allele and Haplotype Frequencies in Koreans / 대한진단검사의학회지

BACKGROUND: The HLA system is known to be the most polymorphic gene cluster in the human genome. HLA allele and haplotype distribution varies widely among different ethnic groups. In this study, we examined the frequency of HLA class I alleles and haplotypes in 309 healthy Koreans. METHODS: We typed HLA-A, -B, and -C genes at the allelic level in 109 unrelated Korean individuals using a sequence-based typing. With the additional data of 200 healthy Koreans from dbMHC (http: //www.ncbi.nlm.nih.gov/mhc/), allele and haplotype frequencies were estimated by the maximum likelihood method. Serological typing results of 49 individuals were compared with the results highly resolved. RESULTS: A total of 22 HLA-A, 41 HLA-B, and 21 HLA-C alleles were found in this study. Alleles showing frequencies of more than 10% in each HLA locus were A*2402 (22.5%), A*0201 (15.7%), A*3303 (14.4%), A*1101 (11.0%), B*5101 (12.1%), Cw*0102 (18.8%), and Cw*1402 (10.2%). The most common A-B-C haplotypes at a frequency of more than 3% were A*3303-B*5801-Cw*0302 (5.2%), A*2402-B*5101-Cw*1402 (4.5%), A*1101-B*1501-Cw*0401 (4.3%), A*3303-B*4403-Cw*1403 (4.0%), A*3001-B*1302-Cw*0602 (3.7%), and A*0207-B*4601-Cw*0102 (3.2%). Misassignment of HLA-C antigen by serotyping was detected in 11 (22.4%) of 49 individuals. CONCLUSIONS: Our results will be useful as a basic data for studies on anthropology, disease association, and bone marrow transplantation. Misidentification of HLA-C by serotyping is so high that it would be desirable to perform a DNA typing especially in unrelated bone marrow transplantation.

Association between Schizophrenia and the Genetic Polymorphism of DRD3, DRD4 and HTR2A / 대한진단검사의학회지

BACKGROUND: Dopamine and serotonin receptors are candidate genes for the genetic study of schizophrenia because of their implication in the pathophysiology and etiology of schizophrenia (serotonine- dopamin hypothesis). A population-based association study was performed between schizophrenics and normal controls to identify the susceptibility genes. METHODS: A total of 145 schizophrenics and 242 normal controls were recruited. Ser9Gly polymorphism of DRD3, 12 bp repeat of DRD4, and 102T/C of HTR2A were selected as candidate polymorphism. The molecular techniques such as polymerase chain reaction (PCR)-restriction fragment length polymorphism and PCR-polyacrylamide gel electrophoresis were used. Chi-square analysis was performed to find any differences between two groups and logistic linear regression was tested to evaluate the interaction between three genes. RESULTS: There were no significant differences in allele frequencies and genotype frequencies of the three genetic polymorphism. Stratified by sex, the difference of DRD4 allele (P=0.065) and HTR2A allele (P=0.083) and genotype (P=0.054) was observed between male patients and controls; also noted was the difference of HTR2A genotype (P=0.080) between female patients and controls. Stratified by age of onset, the difference in the linear trend of DRD3 between early-onset patients and normal control (P=0.003) was observed. Stratified by family history, the difference in the linear trend of DRD4 (P=0.008) was also observed. Logistic linear regression with 90 patients who had early-onset phenotype (< or =20 year-old) or family history showed a significant result in interaction term (P=0.053). CONCLUSIONS: The finding that there were significant results only after stratification may imply a different genetic load on each subgroup of the disease. The interaction of genes between DRD3, DRD4, and HTR2A in a subgroup with supposedly high genetic background may support the serotonindopamine hypothesis. This, however, should be verified hereafter in large-scale studies.

Detection of HBV YMDD Mutation by Sequencing Method / 대한진단검사의학회지

BACKGROUND: YMDD motif variants of the hepatitis B virus (HBV) emerge in some chronic hepatitis B patients after prolonged lamivudine treatment. HBV DNA breakthrough may be accompanied by the emergence of YMDD variants. The detection of YMDD motif variants will be necessary since Adefovir dipivoxil was recently approved to be an effective treatment for lamivudine-resistant patients. METHODS: Samples were chosen from twenty-one patients who experienced the DNA breakthrough after an undetectable HBV DNA period by HBV DNA hybrid-capture assay. We tested the samples of each stage for detection of YMDD motif variants by a sequencing method using Accu-Typer(TM) HBV YMDD typing Kit (DNA Link, Seoul, Korea) and ABI PRISM 3700 DNA Analyzer. RESULTS: All 17 samples that were collected before treatment had the wild-type YMDD motif. Of 20 samples amplified, which were from the undetectable HBV DNA period, three (15%) samples showed YMDD mutation. After DNA breakthrough, YMDD mutants were detected in 13 (63%) of 21 samples (YIDD 8 cases, YVDD 5 cases). CONCLUSION: We could reconfirmed that YMDD motif variants were remarkably related to the lamivudin resistance. YMDD motif variants; however, were not detected in one-third of the lamivudine resistance. The sequencing method of our study would be useful in providing the neighboring nucleotide information other than the YMDD motif in patients experiencing DNA breakthrough.

Genotype Analysis of Hepatitis B Virus Isolated from Korean Hepatitis Patients / 대한진단검사의학회지

BACKGROUND: Hepatitis B virus (HBV) is classified into 7 genotypes (A-G) that have distinct geographic distribution. Several studies have suggested that the HBV genotypic differences influence the severity of liver disease and clinical outcomes such that genotype C is associated with more advanced liver diseases and genotype B is associated with the earlier development of hepatocellular carcinoma. With the different genotypes of HBV reported in Shanghai, Taiwan and Japan, wetried to investigate the distribution of the HBV genotype and the utility of HBV genotyping tests in the Korea population. METHODS: A total of 51 HBV DNA positive serum from Korean hepatitis B patients were used for the genotyping. After PCR and sequencing, HBV genotypes were determined by phylogenetic analysis using the NCBI database (www.ncbi.nlm.nih.gov). RESULTS: By phylogenetic analysis in the Pre-S region, all the genotypes of HBV (100%) proved to be C. CONCLUSIONS: All patients in this study had genotype C. This result is consistent with previous studies reporting 96-100% distribution of genotype C in Korea. HBV genotyping in Korea is not informative in predicting individual variation of clinical outcome, so that it is meaningless to genotype HBV in routine laboratory genotyping.

Genotype Analysis of Hepatitis B Virus Isolated from Korean Hepatitis Patients / 대한진단검사의학회지

BACKGROUND: Hepatitis B virus (HBV) is classified into 7 genotypes (A-G) that have distinct geographic distribution. Several studies have suggested that the HBV genotypic differences influence the severity of liver disease and clinical outcomes such that genotype C is associated with more advanced liver diseases and genotype B is associated with the earlier development of hepatocellular carcinoma. With the different genotypes of HBV reported in Shanghai, Taiwan and Japan, wetried to investigate the distribution of the HBV genotype and the utility of HBV genotyping tests in the Korea population. METHODS: A total of 51 HBV DNA positive serum from Korean hepatitis B patients were used for the genotyping. After PCR and sequencing, HBV genotypes were determined by phylogenetic analysis using the NCBI database (www.ncbi.nlm.nih.gov). RESULTS: By phylogenetic analysis in the Pre-S region, all the genotypes of HBV (100%) proved to be C. CONCLUSIONS: All patients in this study had genotype C. This result is consistent with previous studies reporting 96-100% distribution of genotype C in Korea. HBV genotyping in Korea is not informative in predicting individual variation of clinical outcome, so that it is meaningless to genotype HBV in routine laboratory genotyping.