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Genomic and epigenomic heterogeneity in molecularsubtypes of gastric cancer 被引量:7
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作者 Byungho Lim Jong-Hwan kim +1 位作者 Mirang kim seon-young kim 《World Journal of Gastroenterology》 SCIE CAS 2016年第3期1190-1201,共12页
Gastric cancer is a complex disease that is affected by multiple genetic and environmental factors. For the precise diagnosis and effective treatment of gastric cancer, the heterogeneity of the disease must be simplif... Gastric cancer is a complex disease that is affected by multiple genetic and environmental factors. For the precise diagnosis and effective treatment of gastric cancer, the heterogeneity of the disease must be simplified; one way to achieve this is by dividing the disease into subgroups. Toward this effort, recent advances in high-throughput sequencing technology have revealed four molecular subtypes of gastric cancer, which are classified as Epstein-Barr viruspositive, microsatellite instability, genomically stable, and chromosomal instability subtypes. We anticipate that this molecular subtyping will help to extend our knowledge for basic research purposes and will be valuable for clinical use. Here, we review the genomic and epigenomic heterogeneity of the four molecular subtypes of gastric cancer. We also describe a mutational meta-analysis and a reanalysis of DNA methylation that were performed using previously reported gastric cancer datasets. 展开更多
关键词 DNA METHYLATION GASTRIC cancer Molecularsubtype Mutation Next-generation SEQUENCING
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Clinical assessment and identification of immuno-oncology markers concerning the 19-gene based risk classifier in stage Ⅳ colorectal cancer 被引量:2
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作者 Jong Lyul Lee Seon Ae Roh +7 位作者 Chan Wook kim Yi Hong Kwon Ye Jin Ha Seon-Kyu kim seon-young kim Dong-Hyung Cho Yong Sung kim Jin Cheon kim 《World Journal of Gastroenterology》 SCIE CAS 2019年第11期1341-1354,共14页
BACKGROUND Genomic profiling of tumors has contributed to the understanding of colorectal cancer(CRC), facilitating diagnosis, prognosis and selection of treatments,including targeted regimens. A report suggested that... BACKGROUND Genomic profiling of tumors has contributed to the understanding of colorectal cancer(CRC), facilitating diagnosis, prognosis and selection of treatments,including targeted regimens. A report suggested that a 19-gene-based risk classifier(TCA19) was a prognostic tool for patients with stage III CRC. The survival outcomes in patients with stage IV CRC are still poor and appropriate selection of targeted therapies and immunotherapies is challenging.AIM To assess clinical implication of TCA19 in patients with stage IV CRC, and to identify TCA19 with involvement in immune-oncology.METHODS A retrospective review of the medical records of 60 patients with stage IV CRC was conducted, assessing clinicopathological variables and progression-free survival(PFS). TCA19 gene expression was determined by quantitative polymerase chain reaction(qPCR) in matched normal and tumor tissues taken from the study cohort. Expression of potential immune-oncology regulatory proteins and targets was examined by immunohistochemistry(IHC), western blot, immunofluorescence staining in tissues from a validation cohort of 10 patients, and in CRC cell lines co-cultured with monocyte in vitro.RESULTS In the patients with TCA19 score higher than the median, the PFS rates of eight patients who received the targeted regimens were significantly higher than the PFS rates of four patients who received 5-fluorouracil-based regimen(P = 0.041).In multivariate analysis, expression of signaling lymphocytic activation molecule family, member 7(SLAMF7) and triggering receptor expressed on myeloid cells 1(TREM1) was associated with PFS in the 60-patient cohort. After checking another 10 validate set, the expression of the IHC, the level of real-time qPCR,and the level of western blot were lower for SLAMF7 and higher for TREM7 in primary and metastatic tumors than in normal tissues. In CRC cells expressing SLAMF7 that were co-cultured with a monocytic cell line, levels of CD 68 and CD73 were significantly lower at day 5 of co-culture than at day 0.CONCLUSION The TCA19 score might be prognostic for target-regimen-specific PFS in stage IV CRC. Down-regulation of SLAMF7 and up-regulation of TREM1 occur in primary and metastatic tumor tissues. 展开更多
关键词 Colorectal cancer Prognosis Immunotherapy Signaling LYMPHOCYTIC activation molecule family member 7 TRIGGERING receptor EXPRESSED on MYELOID cells 1
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KoNA:Korean Nucleotide Archive as A New Data Repository for Nucleotide Sequence Data
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作者 Gunhwan Ko Jae Ho Lee +19 位作者 Young Mi Sim Wangho Song Byung-Ha Yoon Iksu Byeon Bang Hyuck Lee Sang-Ok kim Jinhyuk Choi Insoo Jang Hyerin kim Jin Ok Yang Kiwon Jang Sora kim Jong-Hwan kim Jongbum Jeon Jaeeun Jung Seungwoo Hwang Ji-Hwan Park Pan-Gyu kim seon-young kim Byungwook Lee 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2024年第1期161-167,共7页
During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enor... During the last decade,the generation and accumulation of petabase-scale high-throughput sequencing data have resulted in great challenges,including access to human data,as well as transfer,storage,and sharing of enormous amounts of data.To promote data-driven biological research,the Korean government announced that all biological data generated from government-funded research projects should be deposited at the Korea BioData Station(K-BDS),which consists of multiple databases for individual data types.Here,we introduce the Korean Nucleotide Archive(KoNA),a repository of nucleotide sequence data.As of July 2022,the Korean Read Archive in KoNA has collected over 477 TB of raw next-generation sequencing data from national genome projects.To ensure data quality and prepare for international alignment,a standard operating procedure was adopted,which is similar to that of the International Nucleotide Sequence Database Collaboration.The standard operating procedure includes quality control processes for submitted data and metadata using an automated pipeline,followed by manual examination.To ensure fast and stable data transfer,a high-speed transmission system called GBox is used in KoNA.Furthermore,the data uploaded to or downloaded from KoNA through GBox can be readily processed using a cloud computing service called Bio-Express.This seamless coupling of KoNA,GBox,and Bio-Express enhances the data experience,including submission,access,and analysis of raw nucleotide sequences.KoNA not only satisfies the unmet needs for a national sequence repository in Korea but also provides datasets to researchers globally and contributes to advances in genomics.The KoNA is available at https://www.kobic.re.kr/kona/. 展开更多
关键词 Korea BioData Station Nucleotide sequence Next-generation sequencing repository GENOMICS Deposition and access of big data
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