This article is a mini-review that provides a general overview for next-generation sequencing (NGS) and introduces one of the most popular NGS applications, whole genome sequencing (WGS), developed from the expansion of human genomics. NGS technology has brought massively high throughput sequencing data to bear on research questions, enabling a new era of genomic research. Development of bioinformatic software for NGS has provided more opportunities for researchers to use various applications in genomic fields. De novo genome assembly and large scale DNA resequencing to understand genomic variations are popular genomic research tools for processing a tremendous amount of data at low cost. Studies on transcriptomes are now available, from previous-hybridization based microarray methods. Epigenetic studies are also available with NGS applications such as whole genome methylation sequencing and chromatin immunoprecipitation followed by sequencing. Human genetics has faced a new paradigm of research and medical genomics by sequencing technologies since the Human Genome Project. The trend of NGS technologies in human genomics has brought a new era of WGS by enabling the building of human genomes databases and providing appropriate human reference genomes, which is a necessary component of personalized medicine and precision medicine.
Chromatin Immunoprecipitation ; Computational Biology ; DNA ; Epigenomics ; Genetics, Medical ; Genome* ; Genome, Human ; Genomics ; High-Throughput Nucleotide Sequencing ; Human Genome Project ; Humans ; Methylation ; Precision Medicine ; Sequence Analysis, RNA ; Transcriptome

We studied host immune parameters which might be related to the activity and the pathogenetic mechanism of chronic active hepatitis. The subjects consisted of 45 cases with hepatitis B virus surface antigen (HBsAg)-positive chronic active hepatitis (CAH), 44 HBsAg-negative CAH, 22 with inactive chronic hepatitis, and 45 cases of normal persons, hepatitis B virus (HBV) carriers, or the patients with acute myocardial infarction. The in vitro assay for the in vivo activated lymphocytes was performed by measuring spontaneous thymidine uptake (SLT) of lymphocytes isolated from peripheral blood. SLT was significantly (p less than 0.001) elevated in cases with HBsAg-positive (1227 +/- 806 cpm) and-negative CAH (1017 +/- 559 cpm) compared to the patients with inactive chronic hepatitis (347 +/- 79 cpm) and to the control group (320 +/- 106 cpm). SLT values observed in 7 cases with active disease (group I and II), in which remission and relapsing phase could be assessable, were elevated from 648 +/- 121 cpm in remission phase to 1548 +/- 606 cpm one to two weeks before the appearance of biochemical evidence (SGPT) of relapse. This pattern of SLT elevation, however, was not observed in patients with inactive hepatitis. Neither the abnormal distribution of T-celi subsets nor the presence of conventional HBV markers were related to the elevated SLT value. Our findings may therefore indicate that SLT might be useful in assessment of the disease activity in patients with CAH.
Adult ; Alanine Transaminase/blood ; Female ; Hepatitis, Chronic/*immunology ; Humans ; Lymphocyte Activation ; Lymphocyte Culture Test, Mixed ; Male ; Middle Aged ; T-Lymphocyte Subsets/immunology

PURPOSE: To evaluate outcome and morbidity in patients with vulvar cancer treated with radiotherapy, concurrent chemoradiotherapy or postoperative radiotherapy. MATERIALS AND METHODS: The records of 24 patients treated with radiotherapy for vulvar cancer between July 1993 and September 2009 were retrospectively reviewed. All patients received once daily 1.8-4 Gy fractions external beam radiotherapy to median 51.2 Gy (range, 19.8 to 81.6 Gy) on pelvis and inguinal nodes. Seven patients were treated with primary concurrent chemoradiotherapy, one patient was treated with primary radiotherapy alone, four patients received palliative radiotherapy, and twelve patients were treated with postoperative radiotherapy. RESULTS: Twenty patients were eligible for response evaluation. Response rate was 55% (11/20). The 5-year disease free survival was 42.2% and 5-year overall survival was 46.2%, respectively. Fifty percent (12/24) experienced with acute skin complications of grade III or more during radiotherapy. Late complications were found in 8 patients. 50% (6/12) of patients treated with lymph node dissection experienced severe late complications. One patient died of sepsis from lymphedema. However, only 16.6% (2/12) of patients treated with primary radiotherapy developed late complications. CONCLUSION: Outcome of patients with vulvar cancer treated with radiotherapy showed relatively good local control and low recurrence. Severe late toxicities remained higher in patients treated with both node dissection and radiotherapy.
Carcinoma, Squamous Cell ; Chemoradiotherapy ; Disease-Free Survival ; Humans ; Lymph Node Excision ; Lymphedema ; Pelvis ; Recurrence ; Retrospective Studies ; Sepsis ; Skin ; Treatment Outcome ; Vulvar Neoplasms

BACKGROUND: Titanium dioxide (TiO2) thin film photocatalyst generates strong oxidizing power when illuminated with Ultra Violet (UV) light with wavelengths of less than 385 nm. In this study, we evaluated the bactericidal activity of it against Escherichia coli, Aspergillus fumigatus and Mycobacterium tuberculosis. METHODS: The TiO2 film were prepared from titanium isopropoxide solution and it was coated on either inner(test) or outer(control) side on Petri dish. annealing at 500 degrees C. The test and control suspension of E. coli, A. fumigatus and M. tuberculosis were grown in the chamber coated inner and outer side. respectively with UV light. For the blank, cell suspensions were grown in TiO2 coated Petri dishes without UV light. The bactericidal activities were estimated by survival ratio calculated from the number of viable cells which form the nutrient agar. RESULTS: In the test, the survival ratio for E. coli and M tuberculosis decreased to a negligible level (i.e., essentially complete sterilization) within 1hr and 2 hr, respectively. and that for 11. fumigatus decreased markedly to about 15% within 6 hr. In the control, the survival ratio for E. coli, A. fumigatus and M. tuberculosis decreased to 40% within 150 min. 6 he and 2 hr, respectively. In the blank, the survival ratio for E. coli and M tuberculosis decreased only about 67% within 150 min and 40% within 2hr. In A. fumigatus, TiO2 only caused little Sterilization within 4 hr. CONCLUSIONS: TiO2 photocatalysts under UV light clearly showed bactericidal activity against E. coli, A. fumigarus and M. tuberculosis. This feature render TiO2 photocatalysts to be applicable to eliminate microorganism from indoor air environment combined with ventilation.
Agar ; Aspergillus fumigatus* ; Aspergillus* ; Escherichia coli* ; Escherichia* ; Mycobacterium tuberculosis ; Sterilization ; Suspensions ; Titanium* ; Tuberculosis* ; Ultraviolet Rays ; Ventilation ; Viola

Elizabethkingia meningoseptica (Chryseobacterium meningoseptica) is a ubiquitous Gram-negative bacillus in the natural and hospital environments. This microorganism causes neonatal meningitis but rarely causes infections in adults, with most adult cases occurring in severely immunocompromised patients. Since E. meningoseptica is inherently resistant to the usual empiric therapy aimed at Gram-negative bacilli and MIC breakpoints for resistance and susceptibility of E. meningoseptica have not been established by the Clinical and Laboratory Standards Institute, it is very difficult to select effective antibiotics for the treatment of E. meningoseptica infection. We report here three cases of E. meningoseptica isolates (two from blood and one from CSF) from adult patients admitted to Seoul St. Mary's hospital over a 3-year period. To the best of our knowledge, this is the first report of adult meningitis due to E. meningoseptica in Korea.
Adult ; Anti-Bacterial Agents ; Bacillus ; Humans ; Immunocompromised Host ; Korea ; Meningitis

PURPOSE: To report the first case of the Raoultella planticola endophthalmitis after the phacoemulsification and posterior chamber multi-focused intraocular lens (IOL) implantation. CASE SUMMARY: A healthy 49-year-old male visited our clinic with a sudden visual disturbance and ocular pain 2 days after phacoemulsification and multi-focused IOL implantation in his right eye. On initial ophthalmic examination, severe corneal edema and hypopyon were observed. The retina could not be visualized due to vitreous opacity and anterior chamber inflammation. Therefore, the patient immediately underwent pars plana vitrectomy. Vancomycin hydrogen chloride (HCl) 0.3 mg/0.1 mL was injected into the anterior part and vancomycin HCl 1.0 mg/0.1 mL and ceftazidime 2.0 mg/0.1 mL were injected into the intravitreal part. The culture test of aqueous humor and vitreous body fluid revealed Raoultella planticola, thus, systemic antibiotic (ceftazidime) and antibiotic eye drops (vancomycin and ceftazidime) were administered. After 4 months of follow-up, best-corrected visual acuity improved to 20/20 in the affected eye after surgery. CONCLUSIONS: In the present case, we found that endophthalmitis due to Raoultella planticola can be successfully treated. We suggest that atypical bacteria should be considered in the differential diagnosis of endophthalmitis after cataract surgery.
Anterior Chamber ; Aqueous Humor ; Bacteria ; Cataract* ; Ceftazidime ; Corneal Edema ; Diagnosis, Differential ; Endophthalmitis* ; Follow-Up Studies ; Humans ; Hydrochloric Acid ; Inflammation ; Lenses, Intraocular ; Male ; Middle Aged ; Ophthalmic Solutions ; Phacoemulsification ; Retina ; Vancomycin ; Visual Acuity ; Vitrectomy ; Vitreous Body

BACKGROUND: We evaluated the performance of the AdvanSure MDR-TB GenoBlot Assay kit (AdvanSure MDR-TB, LG Life Science, Korea) to detect mutations related to rifampin (RFP)- and isoniazid (INH)-resistant Mycobacterium tuberculosis complex in respiratory specimens. METHODS: From February 2010 to June 2010, a total of 542 M. tuberculosis clinical isolates were collected from pulmonary tuberculosis patients in six university hospitals across Korea. We analyzed the conventional drug susceptibility testing (DST) and compared the results with those of the AdvanSure MDR-TB. RESULTS: Compared with the conventional DST, the overall agreement rates, sensitivity, and specificity were 98.2% (532/542), 84.6% (33/39), and 99.2% (499/503), respectively, for RFP resistance and 96.1% (521/542), 79.7% (59/74), 98.7% (462/468), respectively, for INH resistance. The three common rpoB mutations were rpoB S531L (53.8%), rpoB D516V (15.4%) and rpoB H526R (7.7%) in RFP-resistant strains. For INH resistance, the katG S315T mutation (58.1%) was the most common, followed by inhA C-15T (23.0%) and katG S315N (4.1%). CONCLUSION: The AdvanSure MDR-TB showed high concordance with the conventional DST and would be helpful for early detection of RFP and INH resistance, although it requires improved sensitivity.
Biological Science Disciplines ; Hospitals, University ; Humans ; Isoniazid ; Korea ; Mycobacterium ; Mycobacterium tuberculosis ; Rifampin ; Sensitivity and Specificity ; Tuberculosis ; Tuberculosis, Pulmonary

BACKGROUND: We analyzed the prevalence of anti-tuberculosis drug resistance in Mycobacterium tuberculosis isolates from respiratory specimens of patients with newly diagnosed and previously treated tuberculosis. METHODS: From February 2010 to July 2010, a total of 542 M. tuberculosis clinical isolates were collected from pulmonary tuberculosis patients in six university hospitals distributed throughout Korea. We analyzed the results of anti-tuberculosis drug resistance tests according to treatment history and geographic location. RESULTS: Among the 542 isolates, 473 (87.3%) were from newly diagnosed cases and 69 (12.7%) were from previously treated cases. The rates of multi-drug resistance (MDR), fluoroquinolone (ofloxacin, levofloxacin, and moxifloxacin) resistance, and extensive drug resistance (XDR) were 3.8%, 1.1-1.5%, and 0%, respectively, in new cases, and 21.7%, 13.0-17.4%, and 4.3%, respectively, in previously treated cases. In the previously treated cases, the proportions of XDR-TB in MDR-TB were 20% (3/15). The resistance rates were variable according to geographic location. CONCLUSION: As the anti-tuberculosis drug resistance rates are much higher in newly diagnosed cases than in previously treated patients, efforts should be made to ensure that tuberculosis treatment is successful. In addition, before the selection of an anti-tuberculosis drug treatment for previously treated patients, the susceptibility test results, including to fluoroquinolone, should be verified.
Dietary Sucrose ; Drug Resistance ; Drug Resistance, Multiple ; Extensively Drug-Resistant Tuberculosis ; Hospitals, University ; Humans ; Korea ; Mycobacterium ; Mycobacterium tuberculosis ; Ofloxacin ; Prevalence ; Tuberculosis ; Tuberculosis, Pulmonary

PURPOSE: To investigate the outcomes of quantitative lens nuclear opalescence change after pars plana vitrectomy and intravitreal gas injection in patients with idiopathic epiretinal membrane and macular hole. METHODS: All patients were divided into two group according to the kinds of injected gases, either Group 1 (fluid/air exchange) or Group 2 (20% SF₆ gas injection). Lens nuclear opalescence according to the classification of Lens Opacities Classification System (LOCS) III, mean nuclear density and maximal nuclear density of Pentacam® scheimpflug image changed by image J, besides refractive errors were evaluated before surgery and 1, 2, 4, 6, and 12 months after surgery. RESULTS: Out of 40 eyes of 40 patients included in the analysis, 21 received only fluid/air exchange (Group 1) and 19 received 20% SF₆ gas injection (Group 2). There were significant changes in lens nuclear opalescence between the study and control (unaffected) eyes. In both groups, the study eyes experienced significant progression of cataract compared with the control eyes, in terms of mean nuclear density, maximal nuclear density and LOCS III. In comparison according to the kinds of injected gases, there was a significant difference in mean nuclear density after 4 months, maximal nuclear density after 2 months and 4 months, LOCS after 2 months and 4 months, and refractive error after 1, 2, 4, and 6 months between both groups (p = 0.003). CONCLUSIONS: After vitrectomy and intravitreal gas injection, changes in postoperative lens nuclear opalescence of the study eyes progressed more rapidly compared with the control eyes. This study identified that lens nuclear opalescence of Group 2 progressed rapidly, but after 12 months there was no significant difference of lens opacity between the kinds of injected gases.
Cataract* ; Classification ; Epiretinal Membrane* ; Gases ; Humans ; Iridescence ; Refractive Errors ; Retinal Perforations* ; Vitrectomy*

BACKGROUND: Autoimmune thrombocytopenia (AITP) is characterized by autoantibody-induced platelet destruction. Although several studies have shown that pathogenic autoantibodies are mainly IgG directed platelet glycoproteins (GP), a platelet GP specific test is not available in clinical laboratories. The aim of this study was to evaluate the clinical usefulness of a Modified Antigen Capture Enzyme-linked immunosorbent assay (MACE) test in the diagnosis of AITP. METHODS: We investigated fifty-seven patients who showed a platelet count lower than 100 x 10(9)/L and underwent a bone marrow examination. They were classified into primary AITP (P-AITP) (n=21), secondary AITP (S-AITP) (n=15), and non-immune thrombocytopenia (NITP) (n=21) by bone marrow findings and clinical diagnosis. Platelet GP (IIb/IIIa, Ia/IIa, Ib/IX, IV)-specific antibodies and anti-HLA class I antibody were detected by MACE test. RESULTS: Among 57 samples, platelet GP specific antibodies were detected in 8 (22.2%) of 36 patients with AITP and 1 (4.8%) of 21 patients with NITP. The specificities were as follows: GP IIb/IIIa (n=4), GP Ia/IIa (n=5), GP Ib/IX (n=3) and GPIV (n=2). Of the nine patients with platelet GP specific antibodies, four (44.4%) had more than two platelet GP specific antibodies. The sensitivity, specificity, positive predictive value and negative predictive values of the MACE test for AITP were 22.2%, 95.2%, 88.9%, 41.7%, respectively. A previous transfusion history was associated with a higher detection rate of anti-HLA class I antibodies (P<0.05). CONCLUSIONS: The MACE test is a convenient method to detect platelet GP specific antibody and is very specific to diagnose AITP. In clinical practice, even though it is not sensitive, the MACE test would be useful in differentiating AITP from NITP.
Antibodies* ; Autoantibodies ; Blood Platelets* ; Bone Marrow ; Bone Marrow Examination ; Diagnosis ; Enzyme-Linked Immunosorbent Assay* ; Humans ; Immunoglobulin G ; Platelet Count ; Platelet Membrane Glycoproteins ; Purpura, Thrombocytopenic, Idiopathic ; Sensitivity and Specificity ; Thrombocytopenia