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Lee, Ahwon,Kang, Jun,Lee, Hyoungnam,Lee, Youn Soo,Choi, Youn Jin,Lee, Keun Ho,Nistala, Goutam J,Scafe, Charles R.,Choi, Jongpill,Yoo, Jaeeun,Han M.D, Eunhee,Kim, Yonggoo,Kim, Myungshin Elsevier 2019 Pathology, research and practice Vol.215 No.11
<P><B>Abstract</B></P> <P><B>Introduction</B></P> <P>The detection of <I>BRCA1/2</I> mutations is important because PARP1 inhibitors are approved for germline and/or somatic <I>BRCA</I>-mutated advanced ovarian cancer. Next-generation sequencing (NGS) is increasingly used in clinical practice for <I>BRCA1</I>/2 mutations. The purpose of this study was to consider several conditions of NGS <I>BRCA1/2</I> assay applicable to clinical laboratory tests, in particular for using formalin fixed paraffin embedded (FFPE) ovarian tissues.</P> <P><B>Materials and methods</B></P> <P>We selected 64 ovarian cancer patients and performed Oncomine™ BRCA assay using FFPE tissue. Effect of FFPE sample quality was analyzed by NGS quality parameters including deamination metric. Somatic variants were selected by removing germline variants of peripheral blood and interpreted as pathogenic, variants of unknown significance, and false positive.</P> <P><B>Results</B></P> <P>We found a positive relationship between the number of variants over the deamination metric and FFPE age (<I>P</I> < 0.001) with a cutoff values of approximately 0.7 and 60 months, respectively. When comparing NGS results with Sanger sequencing, NGS misreported 3 of 15 variants using default parameters which were corrected after changing parameters. We detected somatic variants in eight patients and classified them into pathogenic (n = 3), VUS (n = 3) and false positive (n = 2).</P> <P><B>Conclusions</B></P> <P>This study is important for improving <I>BRCA1/2</I> mutation detection capabilities of NGS analytical pipelines and strategy to overcome their limitations using FFPE tissue in ovarian cancer patients.</P>
한윤수(Han yunsu),이종휘(Lee Jonghwi),강형남(Kang Hyoungnam),백승인(Baeg Seungin),천병식(Chun Byungsik) 한국지반환경공학회 2011 한국지반환경공학회논문집 Vol.12 No.10
최근 국내에서는 지반개량 재료로 무기질계 급결재와 초미립자 시멘트를 주원료로 하는 NDS(Natural and Durable Stabilizer)공법 등의 개발이 활발하게 연구되어 왔다. 하지만 기존의 연구에서는 NDS의 재령일별 강도발현 과정에 있어서의 화학적인 변화과정 및 강도발현의 원리를 설명해 주지는 못하고 있는 실정이었다. 따라서 무기질계 주입재의 대중화를 위해서는 경화과정의 메커니즘 규명이 확실하게 선행되어야 한다고 판단하였고, 일축압축시험, SEM분석, XRD분석을 재령일 별로 실시하여 각각의 결과값을 분석하였다. 또한 그 특징을 더욱 분명히 구별하기 위하여 물유리계 주입재의 대표적인 예인 SGR 또한 동일한 시험을 실시하여 비교대상으로 하였다. 시험결과 NDS의 강도발현 메커니즘을 일축압축강도-SEM-XRD의 유기적 상관성을 통해 도출할 수 있었고 그 성능의 우수함을 확인하였다. Recently, NDS(Natural and Durable Stabilizer)method and other similar methods are composed of inorganic accelerating agent and the ultra-super fine cement have been studied as the ground improvement material in Korea. However, in the existing research, the chemical changing process of NDS in the strength development mechanism with the elapsed curing time and the principles of strength development did not give an explanation. For the popularization of the inorganic grout material, it determined that the mechanism verifying of the curing process had to be clearly preceded. Therefore, unconfined compression test, SEM and XRD analysis were performed by the elapsed curing time and were analyzed. In addition, the same trial for SGR method, that is the representative example of the water glass grout material, was selected as comparative target in order to distinguish properties of NDS more clearly. The result of experiment, the strength development mechanism of NDS could be investigated through the close correlation of the unconfined compression strength - SEM - XRD analysis, and excellence of a performance was confirmed.
OCT Compound로 포매한 전립선 동결절편에서 RNA 추출방법 비교
전성윤(Sung Yoon Jeon),이형남(Hyoungnam Lee),김태정(Tae-Jung Kim),정은선(Eun Sun Jung),이교영(Kyo Young Lee),최영진(Yeong-Jin Choi) 대한비뇨기종양학회 2010 대한비뇨기종양학회지 Vol.8 No.1
Purpose: There are two methods commonly used for the extraction of total RNA. One is a Trizol method and the other is a column method. However, there have been few reports comparing the quality of total RNA extracted by these two methods in fresh frozen OCT compound-embedded (FFOE) tissues. We evaluate the two RNA extraction methods, to know the best quality of total RNA in FFOE tissues. Materials and Methods: Twenty- one fresh frozen human prostate tissues were used for RNA extraction by the classic method using Trizol reagent and the commercially available method, respectively. RNA purity and quality analysis were performed by spectrophotometry and automated electrophoresis system. Results: An A260:A280 ratio of all RNA from two methods were above of 1.8. The ratio of 28S/18S rRNA in Trizol method (tumor=0.93±0.25, nontumor=1.03±0.28) were higher than the column method (tumor=0.58±0.20, nontumor= 0.60±0.28, p<0.001). On gel images, 18S and 28S rRNA were separated and intact in Trizol method but they were not visible as intact bands but fragmented in column method. Conclusions: To purify the best quality RNA from the FFOE tissues for the molecular pathologic study, Trizol method is superior to the column method.
백내장 마우스의 유전적 연쇄지역 D14Mit86의 physical map과 candidate 유전자 탐색
김은민(Eunmin Kim),이상달(Sang Dal Rhee),이형남(Hyoungnam Lee),양승돈(Sung-Don Yang),Masaaki Okumoto,송창우(Chang-Woo Song),김성주(Sung-joo Kim) 한국실험동물학회 2004 한국실험동물학회 학술발표대회 논문집 Vol.2004 No.-
백내장 모델 동물인 CXSD 마우스는 백내장이 상염색체 열성으로 유전되는 모델 마우스로써, 5 주령부터 백내장의 첫 증상이 나타나기 시작하며 10 주령까지 모든 마우스에서 백내장이 유발되는 완전 침투도를 나타낸다. CXSD 마우스의 원인 유전자인 lens rupture 2 (Ir2)를 positional cloning를 통하여 탐색하고자 D14Mit86 부위의 마우스 genomic DNA를 insen로 가지고 있는 BAC 클론들과 YAC 클론들의 Sequence Tagged Site (STS) content를 결정하여 physical map을 작성하였다. 유전자 표식자인 D14Mit86 지역을 기준으로 physical map을 작성한 결과 40중의 BAC 결론과 4종의 YAC 클론으로 29종의 STS의 순서를 결정하였으며, 이 STS map은 5종의 유전자 표식자, 18종의 clone-end markers, 6종의 gene specific EST markers로 구성되어 있다. 본 논문의 physical map에 mapping 된 유전자는 총 6종으로써, Adam 7, Decysin, Adam28, Sic, Nkx3-1과 LAP70이며, 마우스와 인간 사이에 존재하는 homology에 의해 탐색된 유전자들이다. 이 유전자들 중 Adam 7, Decysin, Adam28은 그 위치에 의거하여 Ir2 환인 유전자로서의 가능성이 있다. A recessive cataractous mouse, CXSD, showed the first clinical symptom of cataract at 5 weeks old and the penetrance was complete. Toward the identification of lens rupture 2 (Ir2)gene causing cataract by positional cloning, we constructed an sequence tagged site (STS)-content map of the region around D14Mit86 that was shown to be linked to Ir2 genetically. We determined the physical order of 29 STSs that were dispersed among 4 YAC clones and 40 BAC clones. The markers included 5 genetic, 18 clone-end, 6 gene specific EST markers. The genes include Adam 7, Decysin, Adam28, Sic, Nkx3-1 and LAP70 and Nkx3-1 was known to map to the human chromosome 8p21. Therefore, this map represents the part of mouse genome synteny to that of the human genome. The current map would provide groundwork for identification of Ir2 gene.