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Kim H.,Hallym University | Cho D.-Y.,LabGenomics Clinical Research Institute | Choi D.H.,Sungkyunkwan University | Choi S.-Y.,LabGenomics Clinical Research Institute | And 10 more authors.
Breast Cancer Research and Treatment | Year: 2012

This investigation is aimed at evaluating the epidemiologic characteristics of BRCA1/2 germline mutations in Korean patients with breast and ovarian cancer (BOC). We analyzed the entire mutational data of BRCA1/2 genes in BOC patients who were tested in Korea since the first Korean report of BRCA1 mutation in 1995 with the exception of the data covered in the Korean Hereditary Breast Cancer (KOHBRA) study, the project launched in 2007 for establishing BRCA1/2 carrier cohorts in Korea. In total, BRCA1/2 gene mutations of 3,922 Korean BOC patients were evaluated, including the unpublished data of 2,139 breast cancer patients examined by four Korean institutions and the data of 1,783 BOC patients covered in ten previous reports. Overall, 420 (150 distinct) pathogenic mutations were identified, 211 (73 distinct) in BRCA1 and 209 (77 distinct) in BRCA2. The majority (134 of 150) of the distinct mutations resulted in premature termination codon of the BRCA1/2 translation. BRCA1 c.4186-1593-4676-1465del was the only large genomic rearrangements mutation. Out of 150 distinct BRCA1/2 mutations, 84 (56 %) mutations were considered specific to Korean BOC. Eighty-five BRCA1/2 mutations were detected in at least two unrelated patients. These recurrent mutations account for 84.5 % (355 of 420) of mutations detected in the Korean population. In the pooled mutational data of BRCA1/2 genes, this study discovered the prevalence of BRCA1/2 mutations in the Korean BOC patients is similar to those found in other ethnic groups. Large genomic rearrangements in BRCA1/2 genes were infrequently detected among the Korean patients with BOC. There were several BRCA1/2 mutation candidates for founder mutations. To further establish a Korean cohort for BRCA1/2 mutations, the nationwide KOHBRA study is in progress. © Springer Science+Business Media, LLC. 2012.

Cho S.-C.,Seoul National University | Kim J.-W.,Seoul National University | Kim H.-W.,University of Ulsan | Kim B.-N.,Seoul National University | And 5 more authors.
Psychiatric Genetics | Year: 2011

Complex phenotypes such as performance on the continuous performance test (CPT) are likely to exhibit epistasis. Genetic polymorphisms of noradrenergic system and brain-derived neurotrophic factor (BDNF), which participates in the differentiation and survival of noradrenergic neurons, have been reported to be associated with the performance on CPT. We evaluated the effect of the adrenergic α-2A receptor (ADRA2A) and BDNF gene-gene interaction on performance on the CPT in a Korean population with attention-deficit/ hyperactivity disorder. In all, 122 participants with attention-deficit/ hyperactivity disorder (8.6±2.3 years, 104 boys and 18 girls) completed the CPT. The DraI polymorphism of ADRA2A (rs583668) and rs11030101 polymorphism of BDNF were genotyped. Significant interaction effect was found of ADRA2A rs553668 and BDNF rs11030101 on response time variability (P=0.011) of the CPT. Our study provides preliminary evidence for the effect of the BDNF and ADRA2A gene-gene interaction on performance on the CPT in attention-deficit/ hyperactivity disorder. © 2011 Wolters Kluwer Health | Lippincott Williams & Wilkins.

Cho S.-C.,Seoul National University | Son J.-W.,Chungbuk National University | Kim B.-N.,Seoul National University | Kim J.-W.,Seoul National University | And 5 more authors.
Psychiatry Investigation | Year: 2012

Objective The purpose of this study was to investigate the association between the T102C polymorphism in the serotonin 2A receptor gene and attention-deficit/hyperactivity disorder (ADHD) in Korean patients. Methods A total of 189 Korean children with ADHD as well as both parents of the ADHD children and 150 normal children participated in this study. DNA was extracted from blood samples from all of the subjects, and genotyping was conducted. Based on the allele and genotype information obtained, case-control analyses were performed to compare the ADHD and normal children, and Transmission disequilibrium tests (TDTs) were used for family-based association testing (number of trios=113). Finally, according to the significant finding which was showed in the case-control analyses, the results of behavioral characterastics and neuropsychological test were compared between ADHD children with and without the C allele. Results In the case-control analyses, statistically significant differences were detected in the frequencies of genotypes containing the C allele (χ 2=4.73, p=0.030). In the family-based association study, TDTs failed to detect linkage disequilibrium of the T102C polymorphism associated with ADHD children. In the ADHD children, both the mean reaction time and the standard deviation of the reaction time in the auditory continuous performance test were longer in the group with the C allele compared to the group without the C allele. Conclusion The results of this study suggest that there is a significant genetic association between the T102C polymorphism in the serotonin 2A receptor gene and ADHD in Korean children. © Korean Neuropsychiatric Association.

Kim J.,Seoul National University | Kim J.,LabGenomics Clinical Research Institute | Kim K.,Seoul National University | Kim J.H.,Seoul National University
Computational and Mathematical Methods in Medicine | Year: 2016

Background. Interpretation of microarray data remains challenging because biological meaning should be extracted from enormous numeric matrices and be presented explicitly. Moreover, huge public repositories of microarray dataset are ready to be exploited for comparative analysis. This study aimed to provide a platform where essential implication of a microarray experiment could be visually expressed and various microarray datasets could be intuitively compared. Results. On the semantic space, gene sets from Molecular Signature Database (MSigDB) were plotted as landmarks and their relative distances were calculated by Lin's semantic similarity measure. By formal concept analysis, a microarray dataset was transformed into a concept lattice with gene clusters as objects and Gene Ontology terms as attributes. Concepts of a lattice were located on the semantic space reflecting semantic distance from landmarks and edges between concepts were drawn; consequently, a specific geographic pattern could be observed from a microarray dataset. We termed a distinctive geography shared by microarray datasets of the same category as "semantic signature." Conclusions. "Semantic space," a map of biological entities, could serve as a universal platform for comparative microarray analysis. When microarray data were displayed on the semantic space as concept lattices, "semantic signature," characteristic geography for a microarray experiment, could be discovered. © 2016 Jihun Kim et al.

Cho S.-C.,Seoul National University | Kim H.-W.,Seoul National University | Kim B.-N.,Seoul National University | Kim J.-W.,Seoul National University | And 8 more authors.
Psychiatry Investigation | Year: 2010

Objective Attention-deficit/hyperactivity disorder (ADHD) is a complex neuro developmental disorder with a strong genetic component. Brain-derived neurotrophic factor (BDNF), which participates in the differentiation and survival of dopaminergic and noradrenergic neurons, could play a role in ADHD development. We aimed to explore the relationships between ADHD and BDNF gene polymorphism. Methods We conducted a case-control analysis of 202 ADHD subjects and 159 controls, performed a transmission disequilibrium test on 151 trios, and compared the results of a continuous performance test (CPT) according to the genotype of the three single nucleotide polymorphisms (rs11030101, rs6265, rs16917204) in the BDNF gene. Results In the case-control analysis, the AA genotype of the BDNF rs11030101 polymorphism was significantly associated with ADHD only in girls (p=0.024, odds ratio=3.00). The T-G-G haplotype was significantly less frequent (p=0.005) and A-G-G was more frequent (p=0.048) in girls with ADHD than in control girls (global p=0.027). A multivariate analysis of variance for commission errors on the CPT showed a significant main effect for the rs11030101 genotype (p=0.026) and an interaction effect of the rs11030101 genotype and gender (p=0.032) in ADHD probands. Conclusion These results provide preliminary evidence for a gender-specific association between BDNF and ADHD in the Korean population © 2010 Korean Neuro psychiatric Association.

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