Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.
Bayes Theorem ; Coat Protein Complex I ; DNA Copy Number Variations ; Ethnic Groups ; Gene Frequency ; Genome ; Humans ; Markov Chains ; Selection, Genetic

Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.
Bayes Theorem ; Coat Protein Complex I ; DNA Copy Number Variations ; Ethnic Groups ; Gene Frequency ; Genome ; Humans ; Markov Chains ; Selection, Genetic

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.
Asian Continental Ancestry Group ; Cataloging ; Coat Protein Complex I ; Genome ; Humans

PURPOSE: To evaluate the performance of the Momguard noninvasive prenatal test by tracing the 'screen positive' results based on preliminary samples from Korean cohorts. MATERIALS AND METHODS: This preliminary study is based on data collected by the LabGenomics Clinical Laboratory (Seongnam, Korea) with informed consent. Only pregnant women who underwent both the Momguard test and karyotyping were included in this study. Momguard test results were compared with those of the karyotyping analysis. RESULTS: Among the 38 cases with 'screen positive' results by Momguard, 30 cases also had karyotyping results available. In three trisomy (T) 18 and three T13 cases, the Momguard results were concordant with the karyotyping results. For the T21 cases, except for one case belonging to the mid-risk zone, Momguard results from 23 out of 24 cases matched the karyotyping results. CONCLUSION: Momguard is a highly reliable screening tool for detecting T13, T18, and T21 cases in independent Korean cohort samples.
Aneuploidy ; Cohort Studies ; Down Syndrome ; Female ; Humans ; Informed Consent ; Karyotyping ; Mass Screening ; Pregnant Women ; Prenatal Diagnosis ; Trisomy

The anatomical description and the relationship between the root apex and the inferior wall of sinus are critical in diagnoses and surgeries of the sinus pathoses, and in dental implantation. So, identification of the proximity between the root apex and the inferior wall of sinus and the clarification of cortical thickness of inferior wall of sinus are indicated the topography of spreading dental infection into the maxillary sinus. Therefore, anatomical knowledge of the topography between the root apex and the inferior wall maxillary sinus are important in the diagnosis and treatment planning of the dental implantation, endodontic procedures, and orthodontic treatment. The purposes of this study were to clarify the morphological and clinical characteristics of the maxillary sinus, especially the inferior wall of sinus in Korean, and to identify the relationship between the inferior wall of maxillary sinus and the roots of maxillary teeth. 24 sides of maxillae of the hemi -sectioned Korean heads were used in this study. All specimens were taken DentaScan reformatted cross -sectional images were taken for the radiographic evaluation of the maxillary teeth and inferior wall of maxillary sinus. All specimens were decalcificated and thenp were sectioned coronally. On the sectioned specimen, 21 metric items were measured using the image analyzing system. The results were as follows: 1. The distance between the each root apex and the inferior wall of maxillary sinus were measured. In the 2nd molar area the distance from the root apex to the inferior wall of sinus was the shortest and the longest in the 1st premolar area. 2. The thickness of the cortical plate of the inferior wall of maxillary sinus was thinnest in the 1st premolar area, whereas, the thickest in the 2nd premolar area. 3. The vertical relationship between the inferior wall and the roots of the maxillary molars was classified into 5 types. Type I (the inferior wall of sinus was located above the level connecting the buccal and lingual root apices) was predominant (54.5% in the 1st molar area, 52.4% in the 2nd molar area). 4. The horizontal relationship between the inferior wall of sinus and root apex were classified into 3 types. Type 2 (the alveolar recess of the inferior wall of sinus was located between the buccal and lingual roots) was predominant (80% in the 1st and 2nd molar area). Taken all together, this study demonstrated various anatomical characteristics and relationships between the maxillary sinus and their surrounding structures. Recognition of these findings may have an impact on the clinical management of patients.
Asian Continental Ancestry Group ; Bicuspid ; Dental Implantation ; Dental Implants ; Diagnosis ; Head ; Humans ; Maxilla ; Maxillary Sinus* ; Molar ; Tooth

The anatomical description and the relationship between the root apex and the inferior wall of sinus are critical in diagnoses and surgeries of the sinus pathoses, and in dental implantation. So, identification of the proximity between the root apex and the inferior wall of sinus and the clarification of cortical thickness of inferior wall of sinus are indicated the topography of spreading dental infection into the maxillary sinus. Therefore, anatomical knowledge of the topography between the root apex and the inferior wall maxillary sinus are important in the diagnosis and treatment planning of the dental implantation, endodontic procedures, and orthodontic treatment. The purposes of this study were 1) to clarify the morphological and clinical characteristics of the maxillary sinus, especially the inferior wall of sinus in Korean, 2) to identify the relationship between the inferior wall of maxillary sinus and the roots of maxillary teeth, and 3) to evaluate the degree of accuracy of DentaScan reformatted images of the maxillary sinus. 33 sides of maxillae of the hemi -sectioned Korean heads were used in this study. All specimens were taken periapical radiographs, computed tomography and DentaScan reformatted cross -sectional images were taken for the radiographic evaluation of the maxillary teeth and inferior wall of maxillary sinus. From the CT images, 3 -dimentional reconstructive images of maxillary sinuses were made using the V -works TM 3.0 program. All specimens were decalcificated and then were sectioned coronally. On the sectioned specimen, 21 metric items were measured using the image analyzing system. The results were as follows: 1. In 6 categories of maxillary sinus according to their lateral aspects and shapes of the inferior walls, flat (54.5%) and round (21.2%) inferior wall of maxillary sinus were prominent. In 58.4%, the anterior limit of maxillary sinus was located in the 1st premolar area and the posterior limit was in the 3rd molar and maxillary tuberosity area (93.9%). The lowest level of the maxillary sinus was in the 1st molar and 2nd molar area. 2. From the 3 -dimentional reconstructive images of maxillary sinus, the maximum anteroposterior length of sinus was 39.3 +/-4.2 mm, the maximum height was 37.1 +/-5.6 mm, and the maximum width was 32.6 +/-6.5 mm. And the average volume of sinus was 15.1 +/-6.2 ml. All measurements were larger in male than female. Taken all together, this study demonstrated various anatomical characteristics and relationships between the maxillary sinus and their surrounding structures. Recognition of these findings may have an impact on the clinical management of patients.
Asian Continental Ancestry Group ; Bicuspid ; Dental Implantation ; Dental Implants ; Diagnosis ; Female ; Head ; Humans ; Male ; Maxilla ; Maxillary Sinus* ; Molar ; Tooth

PURPOSE: To evaluate the effect of suprapubic magnetic stimulation (SMS) with the use of an arm-type magnetic stimulator for the treatment of patients with neurogenic detrusor overactivity. MATERIALS AND METHODS: Eleven patients with neurogenic detrusor overactivity were enrolled in this study. All patients underwent more than 16 SMS sessions, two times per week, with the use of an arm-type magnetic stimulator. Objective success was defined as a significant reduction (> or =50%) in the total number of leakage episodes per 24 hours, whereas subjective success was defined as the request to continue treatment. RESULTS: Five (71.4%) of 7 patients who had urinary incontinence before treatment reported objective success, and 3 patients showed no incontinence. A total of 6 (75.0%) of 8 patients showed increased average voiding volume. One patient showed an adverse effect of back pain after SMS and dropped out. Seven patients (70.0%) of 10 patients wanted to continue this treatment. They showed significant improvements in frequency/volume chart data, quality of life scores, and urodynamic data. CONCLUSIONS: SMS can be a safe, non-invasive and effective option for the treatment of neurogenic detrusor overactivity.
Back Pain ; Humans ; Quality of Life ; Urinary Bladder ; Urinary Incontinence ; Urodynamics

Although autism spectrum disorder (ASD) has been thought to have a substantial genetic background, major contributing genes have yet to be identified or successfully replicated. Immunological dysfunction has been suggested to be associated with ASD, and T cell-mediated immunity was considered important for the development of ASD. In this study, we analyzed 163 ASD subjects and 97 normal controls by genomic quantitative PCR to evaluate the association between the copy number variation of the 7q34 locus, harboring the TCRB gene, and ASDs. As a result, there was no significant difference of the frequency distribution of TCRB copy numbers between ASD cases and normal controls. TCRB gene copy numbers ranged from 0 to 5 copies, and the frequency distribution of each copy number was similar between the two groups. The proportion of the individuals with <2 copies of TCRB was 52.8% (86/163) in ASD cases and 57.1% (52/91) in the control group (p=0.44). The proportion of individuals with >2 copies of TCRB was 11.7% (19/163) in ASD cases and 12.1% (11/91) in the control group (p=0.68). After the effects of sex were adjusted by logistic regression, ORs for individuals with <2 copies or >2 copies showed no significant difference compared with the diploid copy number as reference (n=2). Although we could not see the positive association, our results will be valuable information for mining ASD-associated genes and for exploring the role of T cell immunity further in the pathogenesis of ASD.
Autistic Disorder ; Child ; Coat Protein Complex I ; Diploidy ; Electrolytes ; Gene Dosage ; Immunity, Cellular ; Logistic Models ; Mining ; Polymerase Chain Reaction ; Autism Spectrum Disorder

Together with single nucleotide polymorphism (SNP), copy number variations (CNV) are recognized to be the major component of human genetic diversity and used as a genetic marker in many disease association studies. Affymetrix Genome-wide SNP 5.0 is one of the commonly used SNP array platforms for SNP-GWAS as well as CNV analysis. However, there has been no report that validated the accuracy and reproducibility of CNVs identified by Affymetrix SNP array 5.0. In this study, we compared the characteristics of CNVs from the same set of genomic DNAs detected by three different array platforms; Affymetrix SNP array 5.0, Agilent 2X244K CNV array and NimbleGen 2.1M CNV array. In our analysis, Affymetrix SNP array 5.0 seems to detect CNVs in a reliable manner, which can be applied for association studies. However, for the purpose of defining CNVs in detail, Affymetrix Genome-wide SNP 5.0 might be relatively less ideal than NimbleGen 2.1M CNV array and Agilent 2X244K CNV array, which outperform Affymetrix array for defining the small-sized single copy variants. This result will help researchers to select a suitable array platform for CNV analysis.
Coat Protein Complex I ; DNA ; Genetic Markers ; Genetic Variation ; Humans ; Polymorphism, Single Nucleotide

To discover genetic markers for autism spectrum disorder (ASD), we previously applied genome-wide BAC array comparative genomic hybridization (array-CGH) to 28 autistic patients and 62 normal controls in Korean population, and identified that chromosomal losses on 8p23.1 and on 17p11.2 are significantly associated with autism. In this study, we developed an 8.5K ASD-specific BAC array covering 27 previously reported ASD-associated CNV loci including ours and examined whether the associations would be replicated in 8 ASD patient cell lines of four different ethnic groups and 10 Korean normal controls. As a result, a CNV-loss on 8p23.1 was found to be significantly more frequent in patients regardless of ethnicity (p<0.0001). This CNV region contains two coding genes, DEFA1 and DEFA3, which are members of DEFENSIN gene family. Two other CNVs on 17p11.2 and Xp22.31 were also distributed differently between ASDs and controls, but not significant (p=0.069 and 0.092, respectively). All the other loci did not show significant association. When these evidences are considered, the association between ASD and CNV of DEFENSIN gene seems worthy of further exploration to elucidate the pathogenesis of ASD. Validation studies with a larger sample size will be required to verify its biological implication.
Autistic Disorder ; Cell Line ; Child ; Clinical Coding ; Coat Protein Complex I ; Comparative Genomic Hybridization ; Ethnic Groups ; Genetic Markers ; Humans ; Sample Size ; Autism Spectrum Disorder