We have constructed the Rice Genome Information Service System (RGISS), which is an information service system of the Oryza sativa L. ssp. japonica (rice) genome, using the released version of rice Build 3.0 pseudomolecules based on the Ensembl architecture. The nonredundant library, composed of 3,360 clones of BACs, PACs, and fosmids, was used to construct supercontigs. RGISS contains 50,717 annotated genes from GenBank, 56,161 predicted genes from FgeneSH, and information on 9,587 markers, which includes STS, SSR, and EST-based RFLP. The 20,180 ESTs sequenced by the Korea National Institute of Agricultural Biotechnology (NIAB) were aligned and mapped into 168,792 exons. By gene ontology analysis, the classified protein numbers in the rice genome were 6158, 4531, and 12,364 proteins, which were mapped to molecular function, cellular component, and biological process, respectively.
Biological Processes ; Biotechnology ; Clone Cells ; Databases, Nucleic Acid ; Exons ; Expressed Sequence Tags ; Gene Ontology ; Genome* ; Information Services* ; Korea ; Polymorphism, Restriction Fragment Length ; Oryza

Many visualization tools have been designed to aid information processing during whole genome projects. We have developed a trace viewer program, ChroView, which can read a chromatogram file and display the chromatogram traces of the four bases. The program can be used to examine sequencing quality and base-calling errors. It can also help researchers to edit and save base-calling results while browsing the traces. Additionally, this program has a basecalling feature which can produce supplementary data for validation of the results from other base-calling programs.
Automatic Data Processing ; Genome

PURPOSE: Kikuchi-Fujimoto disease (KFD) is a benign disease, which is characterized by a cervical lymphadenopathy with fever, and it often mimics malignant lymphoma (ML). 2-[18F]fluoro-2-deoxy-D-glucose positron emission tomography/computed tomography (18F-FDG PET/CT) is a powerful imaging modality for the diagnosis, staging and monitoring of ML, with the limitations including the nonspecific FDG uptake in infectious or inflammatory processes. This study compared clinical manifestations and PET/CT findings between KFD and ML patients. METHODS: We retrospectively reviewed the medical records of 23 patients with KFD and 33 patients with ML, diagnosed histopathologically, between January 2000 and May 2013 at the Department of Pediatrics, Yeungnam University Medical Center. Among them, we analyzed the clinical manifestations, laboratory findings and characteristics, and the amount of 18F-FDG uptake between 8 KFD and 9 ML patients who had 18F-FDG PET/CT. RESULTS: The 18F-FDG PET/CT maximum standardized uptake values (SUVmax) ranged from 8.3 to 22.5 (mean, 12.0) in KFDs, and from 5.8 to 34.3 (mean, 15.9) in MLs. There were no significant differences in SUVmax between KFDs and MLs. 18F-FDG PET/CT with ML patients showed hot uptakes in the extranodal organs, such as bone marrow, small bowel, thymus, kidney, orbit and pleura. However, none of the KFD cases showed extranodal uptake (P<0.001). 18F-FDG PET/CT findings of KFD with nodal involvement only were indistinguishable from those of ML. CONCLUSION: Patients who had extranodal involvement on PET/CT were more likely to have malignancy than KFD.
Academic Medical Centers ; Bone Marrow ; Child* ; Diagnosis ; Electrons ; Fever ; Fluorodeoxyglucose F18 ; Histiocytic Necrotizing Lymphadenitis* ; Humans ; Kidney ; Lymphatic Diseases ; Lymphoma* ; Medical Records ; Orbit ; Pediatrics ; Pleura ; Positron-Emission Tomography ; Positron-Emission Tomography and Computed Tomography* ; Retrospective Studies ; Thymus Gland

The identification of marker chromosomes is important for genetic counseling. However, the origin or composition can rarely be defined with conventional cytogenetic technique alone. In this study, we investigated the incidences and types of marker chromosomes in Korean patients and attempted to establish a cost-effective diagnostic approach for marker chromosomes. We reviewed the karyotypes of 2,984 patients that were requested for the cytogenetic analysis between 1997 and 2003 at the Samsung Medical Center. Ten marker chromosomes were found and identified using fluorescent in situ hybridization (FISH). Among the ten marker chromosomes, six were supernumerary marker chromosomes (SMCs) and the rest were marker chromosomes in Turner syndrome (TS). The incidence of SMCs was 2.01/1,000, slightly higher than that previously reported. Five of six SMCs were satellited marker chromosomes. Three bisatellited marker chromosomes originated from chromosome 15 and two from chromosome 22. The origin of one SMC could not be identified. All marker chromosomes in TS originated from X- or Y chromosome. The application of FISH is indispensable to identify marker chromosomes, and the appropriate selection of probes is necessary for cost-effective analysis. For analyzing satellited marker chromosomes, application of probes for chromosome 15 followed by those for chromosome 22 is recommended and in cases of TS, probes for sex chromosomes should take precedence.
Adolescent ; Adult ; Child ; Child, Preschool ; *Chromosome Aberrations ; *Chromosomes, Human ; Female ; Genetic Counseling ; Genetic Markers ; Human ; In Situ Hybridization, Fluorescence ; Incidence ; Infant ; Infant, Newborn ; Karyotyping ; Korea ; Male ; Turner Syndrome/genetics

Saccular coronary artery aneurysm, associated with coronary artery fistula, is a very rare condition. A 48-year-old woman was referred to our hospital for the evaluation of an abnormal shadow on the left cardiac border from a chest X-ray film during regular medical health examination. A huge saccular aneurysm with organized thrombi in the proximal left anterior descending artery (LAD) and coronary artery fistulae from LAD and conus branch of the right coronary artery to pulmonary artery was diagnosed by transthoracic echocardiography, multi-detector computer tomography (MDCT), and coronary angiography. The patient received surgical treatment, including thrombectomy of aneurysm, ligation of the inlet and outlet of aneurysmal sac, coronary artery bypass graft (left internal mammary artery-to-distal LAD), and ligation of fistulae. The postoperative course was uneventful, and postoperative echocardiography and MDCT revealed patent bypass graft; however, a small fistula from proximal LAD across aneurysmal sac to pulmonary artery was observed.
Aneurysm ; Arteries ; Coronary Aneurysm ; Coronary Angiography ; Coronary Artery Bypass ; Coronary Vessels ; Echocardiography ; Female ; Fistula ; Humans ; Ligation ; Pulmonary Artery ; Thorax ; Thrombectomy ; Transplants ; X-Ray Film

Saccular coronary artery aneurysm, associated with coronary artery fistula, is a very rare condition. A 48-year-old woman was referred to our hospital for the evaluation of an abnormal shadow on the left cardiac border from a chest X-ray film during regular medical health examination. A huge saccular aneurysm with organized thrombi in the proximal left anterior descending artery (LAD) and coronary artery fistulae from LAD and conus branch of the right coronary artery to pulmonary artery was diagnosed by transthoracic echocardiography, multi-detector computer tomography (MDCT), and coronary angiography. The patient received surgical treatment, including thrombectomy of aneurysm, ligation of the inlet and outlet of aneurysmal sac, coronary artery bypass graft (left internal mammary artery-to-distal LAD), and ligation of fistulae. The postoperative course was uneventful, and postoperative echocardiography and MDCT revealed patent bypass graft; however, a small fistula from proximal LAD across aneurysmal sac to pulmonary artery was observed.
Aneurysm ; Arteries ; Coronary Aneurysm ; Coronary Angiography ; Coronary Artery Bypass ; Coronary Vessels ; Echocardiography ; Female ; Fistula ; Humans ; Ligation ; Pulmonary Artery ; Thorax ; Thrombectomy ; Transplants ; X-Ray Film

F-18 FDG PET is a metabolic imaging modality that is efficacious in staging and assessment of treatment response for variety of lymphomas. We report usefulness of F-18 FDG PET/CT in evaluating severity of the disease and response to therapy in a patient with subcutaneous panniculitis- like T-cell lymphoma (SPTCL). Here we describe a case of SPTCL in 24-year-old man who had wide spread firm and tender nodular lesions with increased F-18 FDG uptake. After chemotherapy follow up F-18 FDG PET/CT image shows disseminated malignancy and then the patient died with hemophagocytic syndrome. This report suggests that F-18 FDG PET/CT may be useful in determining disease activity at the time of initial diagnosis, after treatment, and evaluating a suspected outcome of SPTCL.
Follow-Up Studies ; Humans ; Lymphohistiocytosis, Hemophagocytic ; Lymphoma ; Lymphoma, T-Cell ; Panniculitis ; Young Adult

PURPOSE: To evaluate the clinical, radiographic results of a modified Chiari osteotomy for dysplastic hips associated with early osteoarthritis. MATERIALS AND METHODS: 17 dysplastic hip patients were examined, and treated with modified Chiari osteotomy, which is dome-shaped pelvic osteotomy. Their mean age at surgery was 33.5 years old (range: 14-53 years), and the mean follow-up period was 28.2 months (range: 12-73 months). In the clinical evaluation, limping, range of motion and Harris Hip Score (HHS) were used and in the radiographic evaluation, center edge angle, acetabular angle, head coverage, weight bearing joint space and minimal joint space were evaluated. RESULTS: Six out of 13 patients who had an antalgic gait improved, and the level of abduction, internal rotation and external rotation showed significant improvement at the final follow-up. The radiographic results showed that the acetabular angle improved significantly from 47.5degrees preoperatively to 40.0degrees at the last follow-up. The center edge angle showed significant improvement from 9.9degrees preoperatively to 38.5degrees at the last follow-up and the head coverage also showed significant improvement from 57.9% preoperatively to 82.4% at the last follow-up. CONCLUSION: A modified Chiari osteotomy is an effective method for a dysplastic hip with a mild and moderate grade of osteoarthritis, and shows improved clinical and radiographic results.
Acetabulum ; Follow-Up Studies ; Gait ; Head ; Hip* ; Humans ; Joints ; Osteoarthritis ; Osteotomy* ; Range of Motion, Articular ; Weight-Bearing

BACKGROUND: We evaluated characteristics of infectious complications in pediatric patients who received monoclonal antibody (mAb) therapy after allogeneic hematopoietic cell transplantation (HCT).METHODS: Between February 2004 and May 2009, 17 pediatric patients (<19 years at diagnosis) who received mAbs were identified as a study group (mAb group). One hundred twenty-two pediatric allogeneic HCT patients (<19 years at diagnosis) who did not receive mAb during the same period were identified as a control group (non-mAb group). A retrospective chart review of medical records was performed for the incidence of infectious complications and mortality.RESULTS: In the mAb group, 12 of the 17 patients (70.6%) had 29 infectious complications (1.71 episodes per person), whereas 89 of the 122 patients (73.8%) had 162 infectious complications (1.32 episodes per person) in the non-mAb group (P=0.838). Although, there were no significant differences in characteristics or incidence of infectious complications between the two groups, the infection-associated mortality rate was significantly higher in the mAb group compared to non-mAb group (29.4% vs. 8.2% P=0.021; RR 3.44, 95% CI, 1.407 to 8.433).CONCLUSION: The mAb therapy was associated with significantly high mortality in pediatric allogeneic HCT recipients.
Cell Transplantation ; Child ; Humans ; Incidence ; Medical Records ; Retrospective Studies ; Transplants

PURPOSE: To estimate the current cancer burden in Korea, newly diagnosed cancer cases and cancer incidence rates were calculated for the years 2003~2005. MATERIALS AND METHODS: The cancer incidence cases and rates were calculated from the Korea National Cancer Incidence Database. Crude and age-standardized incidence rates were calculated by gender for specified cancer sites in 5-year age groups. RESULTS: From 2003 to 2005, 398,824 cases of cancer were newly diagnosed in Korea (218,856 in men and 179,968 in women). For all sites combined, the crude incidence rate (CR) was 300.0 and 248.2 for men and women and the age-standardized incidence rate (ASR) was 297.0 and 191.2 per 100,000, respectively. Among men, five leading cancers were stomach (CR 66.0, ASR 64.2), lung (CR 48.5, ASR 50.3), liver (CR 44.9, ASR 42.1), colon and rectum (CR 37.9, ASR 37.2), and prostate cancer (CR 12.7, ASR 13.8). Among women, five leading cancers were breast (CR 37.3, ASR 29.0), thyroid (CR 36.2, ASR 28.8), stomach (CR 34.1, ASR 25.4), colon and rectum (CR 28.0, ASR 21.1), and lung cancer (CR 17.9, ASR 12.8). In the 0~14-year-old group, leukemia was the most common in both sexes; in the 15~34 group, the most common cancer was stomach cancer for men and thyroid cancer for women; in the 35~64 group, stomach cancer for men and breast cancer for women; among those 65 and over, lung cancer for men and stomach cancer, for women, respectively. CONCLUSION: The cancer incidence rates have increased in recent years, and more cancers are expected to develop as Korea is quickly becoming an aged society. The cancer incidence statistics in this report can be used as an important source to effectively plan and evaluate the cancer control program in Korea.
Aged ; Breast ; Breast Neoplasms ; Colon ; Female ; Humans ; Incidence ; Korea ; Leukemia ; Liver ; Lung ; Lung Neoplasms ; Male ; Prostatic Neoplasms ; Rectum ; Stomach ; Stomach Neoplasms ; Thyroid Gland ; Thyroid Neoplasms