CaGe: A Web-Based Cancer Gene Annotation System for Cancer Genomics

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.

The usefulness of Doppler ultrasonography and the perinatal outcome of fetal anemia treated with intraumbilical venous transfusion / 대한산부인과학회지

OBJECTIVE: We undertook this study to determine the clinical characteristics and the prognostic factors of neonatal survival in patients with fetal anemia who were treated by intraumbilical venous transfusion (IUT). METHODS: From July 2000 to March 2009, 16 cases of fetal anemia were diagnosed at Asan Medical Center in Seoul, Korea. These patients underwent intraumbilical venous transfusions and were thus included in our study. Doppler measurement of the middle cerebral artery peak systolic velocity was performed before and after cordocentesis in all fetuses. RESULTS: The gestational age at the time of the diagnosis of anemia ranged from 21.3 to 33.6 weeks. There was a linear correlation between pre- and post-procedure fetal hemoglobin (Hb,MoM, (x)) and the MCA-PSV (MoM, (y)), i.e., y=0.810-0.229x, r2=0.542, CI 0.316-0.141, p<0.005; and y=1.374-0.391x, r2=0.499, CI 0.584-0.197, p<0.005. The survival was better in patients with severe anemia than those with mild to moderate anemia (p<0.05), and survival was better in patients with anemia of a known cause than those with anemia of an unknown cause (p<0.001). CONCLUSION: In fetuses with anemia, the severity of the anemia before IUT and the change of hemoglobin concentration after IUT, can be estimated noninvasively using Doppler ultrasonography, on the basis of an increase in the peak velocity of systolic blood flow in the middle cerebral artery. Both severity and etiology were meaningful factors for the survival of neonates with fetal anemia who were treated by intraumbilical venous transfusion. Although fetuses have severe anemia, they expected improved survival through IUT. These data are valuable information for use when counseling the parents of an affected fetus.

Clinical analysis of chorionic villus sampling / 대한주산의학회잡지

OBJECTIVE: The aims of this study were 1) to evaluate the indications of chorionic villus sampling CVS) and the positive predictive value for fetal chromosomal abnormalities, 2) to evaluate the reliability of CVS at Asan Medical Center, 3) to find out the risk factors of procedure-related fetal loss, 4) to find out the risk factors of culture failure, and 5) to compare transabdominal with transvaginal approaches. METHODS: Medical records of the 429 out of 461 patients in whom the CVS for prenatal cytogenetic diagnosis were performed were reviewed retrospectively for the period of June 1998 to June 2006. RESULTS: (1) The most common indications of CVS were abnormal ultrasonic findings including increased nuchal translucency (153/429, 35.7%), a previous history of cytogenetically abnormal baby (125/429, 29.1%), old maternal age (100/429, 23.3%), family history of genetic disease (22/429, 5.1 %), and parental abnormal karyotype (11/429, 2.6%). (2) The positive predictive value of abnormal karyotyping according to the indication of CVS was highest in the cases showing abnormal USG findings, including increased fetal nuchal translucency (28.3%). (3) The trial success rate of CVS was 99.5%(427/429). Culture failure rate was 1.9%.(4) Of the 427 cases, normal karyotype was revealed in 349 cases (81.7%), abnormal karyotype in 66 cases (15.2%), maternal cell contamination in 6 cases (1.4%), and pseudomosaicism and confined placental mosaicism (CPM) in 6 cases (1.4%). (5) Procedure-related fetal loss rate was 1.6% (7/419). (6) The significant risk factor of fetal loss was presence of preprocedure vaginal bleeding. (7) The significant risk factor of culture failure was a small amount (less than 10 mg) of tissue. (8) The gestational age at procedure was significantly different between transabdominal and transvaginal methods. In the transabdominal approach group, the incidence of fundal location of placenta was significantly more common. CONCLUSION: If CVS is performed by an expert operator and at a good quality of genetic laboratory, CVS is a very safe and reliable procedure for prenatal genetic diagnosis.

Stage IIIC epithelial ovarian cancer classified solely by lymph node metastasis has a more favorable prognosis than other types of stage IIIC epithelial ovarian cancer / 부인종양

OBJECTIVE: To verify whether it can be justified to classify patients to stage IIIC epithelial ovarian cancer based on nodal involvement only. METHODS: This study included all consecutive patients with stage IIIC epithelial ovarian cancer who underwent upfront cytoreductive surgery according to the FIGO guideline followed by platinum based chemotherapy from September 1989 to September 2006 at Asan Medical Center. RESULTS: During the study period, a total of 272 patients met the inclusion criteria. Optimal cytoreduction was achieved in 213 patients, and complete cytoreduction was achieved in 85 patients. Median follow-up time was 37 months (range, 6-181 months). The 5-year disease free survival (DFS) and overall survival (OS) rate of all patients were 23% and 57%, respectively. Forty-one patients were allocated to stage IIIC by positive nodes only. Patients with stage IIIC disease due to positive nodes only had significantly longer DFS and OS compared to other stage IIIC patients (p<0.001 and p<0.001). The DFS and OS of these patients was significantly better than those of other stage IIIC patients who achieved complete or optimal cytoreduction (p<0.001 and p<0.001). The outcome was even better than that of stage IIIA and IIIB patients (p<0.05 and p<0.05). CONCLUSION: Patients with stage IIIC epithelial ovarian cancer due to positive nodes only had a more favorable prognosis compared to other stage IIIC patients. Therefore, reevaluation of the current FIGO staging system for stage IIIC epithelial ovarian cancer is required.

Stage IIIC epithelial ovarian cancer classified solely by lymph node metastasis has a more favorable prognosis than other types of stage IIIC epithelial ovarian cancer / 부인종양

OBJECTIVE: To verify whether it can be justified to classify patients to stage IIIC epithelial ovarian cancer based on nodal involvement only. METHODS: This study included all consecutive patients with stage IIIC epithelial ovarian cancer who underwent upfront cytoreductive surgery according to the FIGO guideline followed by platinum based chemotherapy from September 1989 to September 2006 at Asan Medical Center. RESULTS: During the study period, a total of 272 patients met the inclusion criteria. Optimal cytoreduction was achieved in 213 patients, and complete cytoreduction was achieved in 85 patients. Median follow-up time was 37 months (range, 6-181 months). The 5-year disease free survival (DFS) and overall survival (OS) rate of all patients were 23% and 57%, respectively. Forty-one patients were allocated to stage IIIC by positive nodes only. Patients with stage IIIC disease due to positive nodes only had significantly longer DFS and OS compared to other stage IIIC patients (p<0.001 and p<0.001). The DFS and OS of these patients was significantly better than those of other stage IIIC patients who achieved complete or optimal cytoreduction (p<0.001 and p<0.001). The outcome was even better than that of stage IIIA and IIIB patients (p<0.05 and p<0.05). CONCLUSION: Patients with stage IIIC epithelial ovarian cancer due to positive nodes only had a more favorable prognosis compared to other stage IIIC patients. Therefore, reevaluation of the current FIGO staging system for stage IIIC epithelial ovarian cancer is required.