Genome-wide association (GWA) studies may benefit from the inclusion of imputed SNPs into their dataset. Due to its predictive nature, the imputation process is typically not perfect. Thus, it would be desirable to develop a scheme for filtering out the imputed SNPs by maximizing the concordance with the observed genotypes. We report such a scheme, which is based on the combination of several parameters that are calculated by PLINK, a popular GWA analysis software program. We imputed the genotypes of 8,842 Korean individuals, based on approximately 2 million SNP genotypes of the CHB+JPT panel in the International HapMap Project Phase II data, complementing the 352k SNPs in the original Affymetrix 5.0 dataset. A total of 333,418 SNPs were found in both datasets, with a median concordance rate of 98.7%. The concordance rates were calculated at different ranges of parameters, such as the number of proxy SNPs (NPRX), the fraction of successfully imputed individuals (IMPUTED), and the information content (INFO). The poor concordance that was observed at the lower values of the parameters allowed us to develop an optimal combination of the cutoffs (IMPUTED> or =0.9 and INFO> or =0.9). A total of 1,026,596 SNPs passed the cutoff, of which 94,364 were found in both datasets and had 99.4% median concordance. This study illustrates a conservative scheme for filtering imputed SNPs that would be useful in GWA studies
Complement System Proteins ; Genome-Wide Association Study ; Genotype ; HapMap Project ; Humans ; Polymorphism, Single Nucleotide ; Proxy

Closely related species share large genomic segments called syntenic regions, where the genomic elements such as genes are arranged co-linearly among the species. While synteny is an important criteria in establishing orthologous regions between species, non-syntenic regions may display species-specific features. As the first step in cataloging human- or primate-specific genomic elements, we surveyed human genomic regions that are not syntenic with any other non-primate mammalian genomes sequenced so far. Based on the data compiled in Ensembl databases, we were able to identify 10 such regions located in eight different human chromosomes. Interestingly, most of these highly human- or primate-specific loci are concentrated in subtelomeric or pericentromeric regions. It has been reported that subtelomeric regions in human chromosomes are highly plastic and filled with recently shuffled genomic elements. Pericentromeric regions also show a great deal of segmental duplications. Such genomic rearrangements may have caused these large human- or primate-specific genome segments.
Cataloging ; Chromosomes, Human ; Genome ; Genome, Human ; Humans ; Plastics ; Resin Cements ; Segmental Duplications, Genomic ; Synteny

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.
Body Mass Index* ; Dataset ; Genome-Wide Association Study ; Haplotypes* ; Korea ; Linkage Disequilibrium ; Polymorphism, Single Nucleotide

OBJECTIVES: N-Nitrosodimethylamine (NDMA) is classified as a probable human carcinogen by the United States Environmental Protection Agency (US EPA) and is formed during the chlorination of municipal drinking water. In this study, selected nitrosamines were measured in chlorinated drinking water collected from Chuncheon, Kangwon-do, Republic of Korea, and a risk assessment for NDMA was conducted. METHODS: Twelve water samples were collected from 2 treatment plants and 10 household taps. Samples were analyzed for 6 nitrosamines via solid-phase extraction cleanup followed by conversion to dansyl derivatives and high-performance liquid chromatography-fluorescence detection (HPLC-FLD). Considering the dietary patterns of Korean people and the concentration change of NDMA by boiling, a carcinogenic risk assessment from ingestion exposure was conducted following the US EPA guidelines. RESULTS: NDMA concentrations ranged between 26.1 and 112.0 ng/L. NDMA in water was found to be thermally stable, and thus its concentration at the end of boiling was greater than before thermal treatment owing to the decrease in water volume. The estimated excess lifetime carcinogenic risk exceeded the regulatory baseline risk of 10(-5). CONCLUSIONS: This result suggests that more extensive studies need to be conducted on nitrosamine concentration distributions over the country and the source of relatively high nitrosamine concentrations.
Dimethylnitrosamine ; Drinking ; Drinking Water ; Eating ; Family Characteristics ; Halogenation ; Humans ; Nitrosamines ; Oligopeptides ; Phosphatidylcholines ; Republic of Korea ; Risk Assessment ; United States Environmental Protection Agency ; Water

BACKGROUND/AIMS: Relapse has been reported after stopping nucleos(t)ide (NUC) therapy in the majority of chronic HBeAg negative hepatitis patients. However, the ideal treatment duration of HBeAg negative chronic hepatitis B (CHB) is not well known. We investigated the frequency of relapse in HBeAg negative CHB patients receiving NUC therapy. METHODS: The NUC therapy was discontinued at least 3 times undetectable level of HBV DNA leave 6 months space in 45 patients. Clinical relapse was defined as HBV DNA >2,000 IU/mL and alanine aminotransferase (ALT) or aspartate aminotransferase (AST) >2 times of upper limit of normal range. Virological relapse was defined as HBV DNA >2,000 IU/mL. RESULTS: Clinical relapse developed in 16 (35.6%) and 24 (53.3%) patients after stopping therapy at 6 months and 12 months off therapy, respectively. Virological relapse developed 22 (48.9%) and 33 (73.3%) patients at 6 months and 12 months off therapy. The factors such as age, gender, cirrhosis, baseline AST, ALT, HBV DNA levels, treatment duration, and consolidation duration were analyzed to investigate the predictive factors associated with 1 year sustained response. Of these factors, cirrhosis (86.1% in CHB, 22.2% in LC) was significantly associated with 1 year virological relapse rate. Baseline HBV DNA and total treatment duration tended to be associated with virological relapse. CONCLUSIONS: Virological relapse developed in the majority (73.3%) of HBeAg negative CHB patients and clinical relapse developed in the half (53.3%) of patients at 1 year off therapy. Cirrhosis may be associated with the low rate of virological relapse.
Adult ; Age Factors ; Alanine Transaminase/blood ; Antiviral Agents/*therapeutic use ; Aspartate Aminotransferases/blood ; DNA, Viral/analysis ; Drug Administration Schedule ; Female ; Hepatitis B e Antigens/*analysis ; Hepatitis B virus/genetics ; Hepatitis B, Chronic/complications/*drug therapy/virology ; Humans ; Liver Cirrhosis/diagnosis/etiology ; Male ; Middle Aged ; Nucleotides/*therapeutic use ; Recurrence ; Sex Factors

Brucella (B.) canis is mainly transmitted by direct or indirect contact with aborted fetuses and placenta. It's also known to be able to infect human, which likely results in providing veterinarians and companion animal owners for infectious risk. To develop diagnostic ELISA, we cloned and expressed rp1L gene of B. canis, which encodes the ribosomal protein L7/L12. Using this purified recombinant protein, indirect-ELISA (iELISA) was evaluated using 78 positive and 44 negative sera. The sensitivity and the specificity of iELISA were 94% and 89%, respectively. The results indicated that indirect-ELISA using recombinant ribosomal protein L7/L12 may be useful for diagnosis of canine brucellosis.
Aborted Fetus ; Brucella ; Brucella canis ; Brucellosis ; Clone Cells ; Enzyme-Linked Immunosorbent Assay ; Humans ; Pets ; Placenta ; Ribosomal Proteins ; Sensitivity and Specificity ; Veterinarians

Salmonella enterica serotype Choleraesuis causes swine paratyphoid, with clinical findings of enterocolitis and septicemia. However, the clinicopathological features of S. Choleraesuis infections in pigs have not been reported in Korea. We describe the pathological findings of two weaned pigs with S. Choleraesuis infections, presenting with diarrhea, cough, and sudden death. Pathological examination indicated severe necrotic colitis in pig 1 and septicemic lesions in pig 2. Multidrug-resistant S. Choleraesuis was isolated from the pigs’ lungs and intestinal contents. Further research is required for the surveillance of S. Choleraesuis infections in pigs and the virulence estimation in the S. Choleraesuis isolates.

In Korea, brucellosis has been reported periodically in cattle and rarely in dogs; however, it has not previously been screened in domestic animals such as elk, pigs and goats. To investigate the serological prevalence, serum samples were taken from the aforementioned animals annually during 2007-2013 and screened by the rose-bengal test (RBT) or modified RBT, after which positive sera were evaluated by the standard tube agglutination test (STAT). Finally, RBT and STAT-positive sera were confirmed by competitive-ELISA. Brucella abortus biovar 1 was isolated from three elk that were shown to be positive serologically in 2008. There was no evidence of brucellosis in pigs. Based on serological monitoring and investigation of etiological agents, there is no evidence of outbreak of brucellosis in elk, pigs or goats of Korea since 2008. However, the possibility for brucellosis from cattle to affect these other livestock exists; therefore, extensive and continuous serological monitoring is required to maintain their brucellosis-free status.
Agglutination Tests ; Animals ; Animals, Domestic ; Brucella abortus ; Brucellosis* ; Cattle ; Dogs ; Goats ; Korea ; Livestock* ; Prevalence ; Serologic Tests ; Swine