No abstract available.
Endothelial Cells

BACKGROUND: Hepatitis B virus (HBV) detected in Korean patients almost belongs to genotype C, which is subdivided into subgenotype C1 (or Cs) and C2 (or Ce). It was recently reported that the risk of hepatocellular carcinoma is different between subgenotype C1 and C2. Thus, we studied the distribution of subgenotypes of HBV in Korean chronic hepatitis B (CHB) patients. METHODS: Specimens of 421 patients, who were diagnosed as CHB and underwent antiviral treatment, were used. After sequence analysis for HBV S gene, subgenotype was identified through phylogenetic analysis. Utilizing the same sequence data, the distribution of serotypes was also investigated. RESULTS: Among 421 patient specimens, genotype C was found in 419 (99.5%) and genotype B in 2 (0.5%). Among the genotype C strains, 417 strains were C2 subgenotype and 2 strains were mixed subgenotypes. However, C2 was evidently found even in the mixed sequences. Serotypes of 419 HBV with genotype C were classified as follows: adr, 385 (91.9%), adw, 22 (5.3%), ayr, 2 (0.4%) and mixed serotype, 10 (2.3%). Serotype of both HBV with genotype B was adw. CONCLUSIONS: It was found that HBV detected in Korean CHB patients under treatment almost all belong to the C2 (Ce) genotype.
Antiviral Agents/therapeutic use ; Blood Specimen Collection ; Genotype ; Hepatitis B virus/*classification/genetics ; Hepatitis B, Chronic/diagnosis/drug therapy/*virology ; Humans ; Korea ; Phylogeny ; Sequence Analysis, DNA ; Serotyping

BACKGROUND: Hepatitis B virus (HBV) DNA quantification is necessary for starting and monitoring of antiviral therapy in patients with chronic hepatitis B. This study was intended to assess the clinical performance of Abbott RealTime HBV Quantification kit (Abbott Laboratories, USA). METHODS: The performance was evaluated in terms of precision, linearity, detection sensitivity, cross-reactivity, and carry-over. A correlation with the Real-Q HBV Quantification kit (BioSewoom Inc., Korea) was also examined using serum samples from 64 patients diagnosed with chronic hepatitis B and underwent lamivudine therapy in Asan Medical Center. We verified the trueness of the system by comparing the outputs with the assigned values of the BBI panel (BBI Diagnostics, USA). RESULTS: Within-run and between-run coefficients of variation (CV) were 3.56-4.71% and 3.03-4.98%, respectively. Linearity was manifested ranging from 53 to 10(9) copies/mL and the detection sensitivity was verified to be 51 copies/mL. None of hepatitis C virus showed cross-reactivity. No cross-contamination occurred when negative and positive samples were alternatively placed in a row. It showed a good correlation with the Real-Q HBV (r2=0.9609) and the test results for the BBI panel were also well agreed to the assigned values (r2=0.9933). CONCLUSIONS: The performance of Abbott RealTime HBV Quantification kit was excellent; thus, it should be widely used in starting and monitoring of antiviral therapy in Korean patients with chronic hepatitis B.
Computer Systems ; DNA, Viral/*blood ; Hepatitis B virus/genetics/*isolation & purification ; Hepatitis B, Chronic/*virology ; Humans ; Polymerase Chain Reaction/*methods ; Reagent Kits, Diagnostic ; Viral Load/*methods

BACKGROUND: Since the human genome project was completed in 2003, there have been numerous reports on cancer and related markers. This study was aimed to develop a system to extract automatically information regarding the relationship between cancer and tumor markers from biomedical literatures. METHODS: Named entities of tumor markers were recognized by both a dictionary-based method and machine learning technology of the support vector machine. Named entities of cancers were recognized by the MeSH dictionary. RESULTS: Relational and filtering keywords were selected after annotating 160 abstracts from PubMed. Relational information was extracted only when one of the relational keywords was in an appropriate position along the parse tree of a sentence with both tumor marker and disease entities. The performance of the system developed in this study was evaluated with another set of 77 abstracts. With the relational and filtering keyword used in the system, precision was 94.38% and recall was 66.14%, while without the expert knowledge precision was 49.16% and recall was 69.29%. CONCLUSIONS: We developed a system that can extract relational information between a tumor and its markers by incorporating expert knowledge into the system. The system exploiting expert knowledge would serve as a reference when developing another information extraction system in various medical fields.
Abstracting and Indexing as Topic ; Algorithms ; Database Management Systems ; Humans ; *Medical Informatics Computing ; Neoplasms/metabolism ; Programming Languages ; *PubMed ; Software ; *Tumor Markers, Biological

BACKGROUND: We developed and evaluated the utility of a multiplex real-time PCR assay that uses melting curve analysis and allows simultaneous identification of vancomycin-resistant genotypes and clinically relevant enterococci. METHODS: The specificity of the assay was tested using 4 reference strains of vancomycin-resistant enterococci (VRE) and 2 reference strains of vancomycin-susceptible enterococci. Ninety-three clinical isolates of enterococci with different glycopeptide-resistant phenotypes were genotyped and identified using a multiplex real-time PCR assay and melting curve analysis. RESULTS: Representative melting curves were obtained for Enterococcus faecium, Enterococcus faecalis, vanA-containing E. faecium, vanB-containing E. faecalis, Enterococcus gallinarum, and Enterococcus casseliflavus. Phenotypic and genotypic analysis of the isolates revealed same results for 82 enterococcal isolates, while in 4 isolates, the glycopeptide-resistant phenotypes were inconsistent with the glycopeptide-resistant genotypes and in the 4 other isolates, species could not be accurately identified. Three isolates with mixed strains, which were detected by the PCR assay, could not be correctly identified using phenotypic methods. CONCLUSIONS: VRE genotyping and identification of clinically relevant enterococci were rapidly and correctly performed using multiplex real-time PCR assay and melting curve analysis.
Bacterial Proteins/genetics ; Carbon-Oxygen Ligases/genetics ; DNA, Bacterial/genetics ; Enterococcus/genetics/*isolation &purification ; Enterococcus faecalis/genetics/isolation &purification ; Enterococcus faecium/genetics/isolation &purification ; Genotype ; Nucleic Acid Denaturation ; Peptide Synthases/genetics ; Phenotype ; *Polymerase Chain Reaction ; Vancomycin Resistance/*genetics

BACKGROUND: Hepatitis B virus (HBV) DNA quantification is important for the management of HBV infection and identification of the development of resistance. The susceptibility to contamination and more variable reproducibility of results with the conventional HBV DNA quantification method have raised the need of a more simple and accurate method for HBV DNA quantification. Real-time quantitative PCR assays recently introduced in the laboratory can meet these needs. In this study, we evaluated the performance of the Real-Q HBV Quantification kit developed in Korea. METHODS: We evaluated the recovery of DNA extraction, the interference of internal control, an analytical sensitivity, specificity, and reproducibility, a clinical specificity, and a reportable range of the Real-Q HBV Quantification kit. The quantification result was also compared to that obtained by the Digene Hybrid-Capture II. RESULTS: The mean percent recovery was 108.6% and there was no interference with the internal control on DNA extraction. None of HIV, hepatitis C virus, or cytomegalovirus showed a cross-reactivity with HBV. This assay detected HBV DNA in a linear range from 10(2) to 10(10) copies/mL, with the detection limit of 56 copies/mL. The assay exhibited a low within-run CV (coefficient of variation) (8.7-11.9%), between-run CV (10.5-14.7%), and between-day CV (13.2-21.4%). No HBV DNA was detected in any of 100 samples without HBV, resulting in a clinical specificity of 100%. The levels of HBV DNA showed a good correlation with those determined with Digene Hybrid-Capture II (R2=0.9827). CONCLUSIONS: The Real-Q HBV Quantification kit showed a good analytical sensitivity, specificity, and high reliability with a broad reportable range. This assay should be clinically useful in managing patients with HBV infection.
Cytomegalovirus ; DNA* ; Hepacivirus ; Hepatitis B virus ; HIV ; Humans ; Korea ; Limit of Detection ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction* ; Reproducibility of Results ; Sensitivity and Specificity

BACKGROUND: Panel reactive antibody (PRA) is to screen and identify HLA antibody. Majority of antibody specificities in high-PRA are directed against cross reactive group (CREG). Thus, this study was to know the advantage of identifying CREG specificity and whether antibody specificities are changed according to CREG classification. METHODS: HLA class I antibodies were identified from 159 sera from 108 patients in Asan Medical Center, who had shown more than 5% PRA by anti-human globulin (AHG)-complement-dependent cytotoxicity (CDC). Tail analysis-based computer program was developed to identify specificities, applying both Rodey (R-ABC) and Takemoto (T-ABC) classification. The results were also compared with those obtained when without CREG application (ABC). RESULTS: Among 151 cases in which HLA specificities was identified, the frequency of CREG specificity was 22.5% in R-ABC and 27.2% in T-ABC. Eleven cases showed CREG specificities only in one classification. However, the individual antigen specificities in one hand were all included in the CREG identified in the other hand. CREG specificities in samples with PRA >50% (60%) were more frequently identified than those in samples with PRA < or =50% (9%) (in R-ABC, P<0.0001). Without applying CREG to interpretation, specificity was not identified in 9 cases. CONCLUSIONS: Application of CREG enhanced the rate of antibody identification. Antibody specificities of those cases where CREG specificities were different between Rodey and Takemoto classifications were almost the same when compared at the individual antigen level. Therefore, it was thought that it makes no difference to use any one of these two classifications in interpreting PRA.
Alleles ; Antibodies/blood ; *Antibody Specificity ; Cross Reactions ; HLA Antigens/genetics/*immunology ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Testing ; Humans ; Kidney Transplantation ; Reproducibility of Results ; Retrospective Studies

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.
DNA ; Hepatitis B virus ; Hepatitis B, Chronic ; Humans ; Lamivudine ; Seoul

BACKGROUND: Human leukocyte antigen (HLA) typing based on polymerase chain reaction (PCR) is rapidly replacing the conventional serological method. This study was intended to evaluate Bio- SewoomTM HLA-A, -B, -C PCR/SSP kit (BioSewoom SSP) which had recently been developed in Korea. METHODS: A total of 158 samples from domestic (21) and international (137) HLA proficiency testing (PT) were genotyped with BioSewoom SSP, and its results were compared to consensus results. For comparison with INNO-LiPA HLA-A, -B, -C Typing Kit (INNO-LiPA, Innogenetics, Belgium), 20 samples of Koreans were genotyped with both kits for each HLA-A, -B, -C locus. RESULTS: Among the 21 samples of domestic PT, BioSewoom SSP showed ambiguities as follows: 4 samples (19.0%) in HLA-A, 6 (28.6%) in HLA-B, and 1 (4.8%) in HLA-C. The ambiguities could be resolved by considering the allele distribution of Koreans. Among the 137 samples from international PT, BioSewoom SSP also showed ambiguities as follows: 12 samples (8.8%) in HLA-A, 26 (19.0%) in HLA-B and 6 (4.4%) in HLA-C. Considering the allele distribution of Koreans, the serologic equivalents obtained from BioSewoom SSP showed a full agreement with those of INNO-LiPA in all the loci tested. Twelve (0.007%) among 1,760 PCR reactions from the 21 samples of domestic PT and 20 patient samples produced faint nonspecific bands, but it was negligible. PCR failure of internal control just barely occurred (15 PCR reactions, 0.009%), but it had no bearing on allele assignment. CONCLUSIONS: The performance of BioSewoom SSP was comparable to that of INNO-LiPA. All the ambiguities could be resolved by considering the allele distribution of Koreans. It is concluded that BioSewoom SSP has good performance to be used in routine HLA laboratories.
Alleles ; Genotype ; HLA-A Antigens/*genetics ; HLA-B Antigens/*genetics ; HLA-C Antigens/*genetics ; Histocompatibility Testing/*methods ; Humans ; Polymerase Chain Reaction/*methods ; Reagent Kits, Diagnostic

BACKGROUND: Panel reactive antibody (PRA) test is used to determine whether a patient awaiting transplantation is previously sensitized. Tail analysis algorithm is widely used to identify antibody specificities, but it is very difficult to perform manually. METHODS: To develop a web-based program, PHP (5.1.2), Apache (2.0.55), and MySQL (5.0.22) were used. Tail analysis algorithm was applied to identify specificities, which analyzed statistically 2 x 2 tables representing reactivities to broad antigens, splits and cross reactive groups (CREG). Exploiting two CREG classifications of Rodey (R) and Takemoto (T), antibody specificities were identified by 3 methods (ABC, R-ABC, T-ABC) simultaneously. Performance of the system was evaluated using 159 samples that showed > or =6 PRA% by a lymphocytotoxicity assay. RESULTS: A web-based system that can identify HLA antibody specificities was implemented on www.koreanhla.com. Among 159 samples tested, antibody specificities were identified in 151 (95.0 %), but not in 8 samples with PRA >97%. Among the 151 samples, 110 showed broad or split specificities and 41 CREG specificities. CONCLUSIONS: We developed a web-based computer program for the identification of HLA antibody specificities. Accessible to everyone on the internet, this program should be of help in sharing PRA results among laboratories.
Algorithms ; *Antibody Specificity/genetics ; HLA Antigens/genetics/*immunology ; Histocompatibility Testing ; Humans ; Internet ; *Software