NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations from next-generation sequencing data

Dong‑Jun Lee,Taesoo Kwon,Chang‑Kug Kim,Young‑Joo Seol,Dong‑Suk Park,Tae‑Ho Lee,Byung‑Ohg Ahn 한국유전학회 2020 Genes & Genomics Vol.42 No.11

Background Sequence variations such as single nucleotide polymorphisms are markers for genetic diseases and breeding. Therefore, identifying sequence variations is one of the main objectives of several genome projects. Although most genomeproject consortiums provide standard operation procedures for sequence variation detection methods, there may be differencesin the results because of human selection or error. Objective To standardize the procedure for sequence variation detection and help researchers who are not formally trainedin bioinformatics, we developed the NGS_SNPAnalyzer, a desktop software and fully automated graphical pipeline. Methods The NGS_SNPAnalyzer is implemented using JavaFX (version 1.8); therefore, it is not limited to any operatingsystem (OS). The tools employed in the NGS_SNPAnalyzer were compiled on Microsoft Windows (version 7, 10) andUbuntu Linux (version 16.04, 17.0.4). Results The NGS_SNPAnalyzer not only includes the functionalities for variant calling and annotation but also providesquality control, mapping, and filtering details to support all procedures from next-generation sequencing (NGS) data to variantvisualization. It can be executed using pre-set pipelines and options and customized via user-specified options. Additionally,the NGS_SNPAnalyzer provides a user-friendly graphical interface and can be installed on any OS that supports JAVA. Conclusions Although there are several pipelines and visualization tools available for NGS data analysis, we developedthe NGS_SNPAnalyzer to provide the user with an easy-to-use interface. The benchmark test results indicate that theNGS_SNPAnayzer achieves better performance than other open source tools.

연령증가에 따른 혈압요소들의 좌심실비대 및 관동맥질환과의 관련성

박재석,박창규,박미영,박재형,김용현,나진오,신성희,서순용,홍순준,박성미,임홍의,김응주,서홍석,오동주,노영무 대한순환기학회 2004 Korean Circulation Journal Vol.34 No.2

혈우병 소견을 가진 뇌출혈 환자 치험(治驗) 1례(例)

정인태,서병관,이현종,하지영,강미경,홍장무,백용현,박동석,최도영,Jung, In-tae,Seo, Byung-kwan,Lee, Hyun-jong,Ha, Ji-young,Kang, Mi-kyeong,Hong, Jang-moo,Baek, Yong-hyeon,Park, Dong-suk,Choi, Do-young 대한침구의학회 2003 대한침구의학회지 Vol.20 No.4

Objective : Hemophilia, a genetically determined disorder, is characterized by abnormality of the coagulation mechanism due to functional deficiency of a specific factor, namely VIII or IX. In this study, the effect of Dong-Si acupuncture therapy on the cerebral hemorrhage patient with hemophilia was evaluated. Methods : We treated him with acupuncture by stimulating Dong-Si acupuncture point(Yuk Wan) and assessed the effect by using manual dynamic evaluation of MRC(Medical Research Council) and Modified Barthel Index. Results : After treatment, the bleeding tendency was grossly reduced and bleeding lesion was absorbed gradually. And manual dynamic evaluation of the upper extremity increased from 4 grade to 5 grade. Conclusions : This result suggest that Dong-Si acupuncture therapy on the cerebral hemorrhage patient with hemophilia was effective. And futher studies are required to concretely prove the effectiveness of Dong-Si acupuncture therapy for treating hemorrhagic diseases.

국내 다기관에서 조사한 지역사회획득 메티실린내성 황색포도알균의 빈도와 임상적 특성

송진수,최평균,송경호,조재현,김성한,방지환,이창섭,박경화,박경운,신수,최희정,김의석,김동민,이미숙,박완범,김남중,오명돈,김의종,김홍빈,최강원 대한감염학회 2006 감염과 화학요법 Vol.38 No.6

목적 : 최근 전세계적으로 지역사회획득 메티실린내성 황색포도알균(community-associated methicillin-resistant Staphylococcus aureus, CA-MRSA)의 보고가 증가하고 있다. 하지만, 우리나라에서는 CA-MRSA 감염증에 대한 증례보고만 있을 뿐 아직까지 체계적인 연구결과가 없는 실정이다. 저자들은 국내에서 CA-MRSA의 빈도, 감염증의 임상적 양상, 분리된 균주의 항균제내성 양상을 조사하였다. 재료 및 방법 : 2005년 1월부터 2005년 6월까지 7개 병원에서 MRSA가 분리된 환자의 명단을 파악한 후 의무기록지와 건강보험심사평가원의 자료를 검토하였다. 외래나 응급실에서 혹은 입원 후 72시간 이내에 균주가 분리되고 MRSA 획득과 관련된 위험인자가 없는 경우 CA-MRSA로 정의하였으며, 분리된 균주의 임상적 의미에 따라 원인병원체(pathogen), 집락화(colonizer), 미결정(undetermined)으로 분류하였다. Penicillin과 oxacillin을 제외하고 3개 이상의 다른 계열 항균제에 내성이면 다제내성으로 정의하였다. 결과 : 연구기간동안 총 3,251주의 황색포도알균이 분리되었으며, 이 중 MRSA는 1,900주(58.4%)였다. MRSA 가운데 CA-MRSA는 114주(6.0%) 였으며, 이들이 분리된 부위는 귀(62주), 비뇨기계(14주), 피부 및 연부조직(11주), 호흡기계(10주), 혈액(3주) 등이었다. CA-MRSA 균주 가운데 집락균은 22주, 원인병원체는 22주였으며, 나머지 균주에 대해서는 그 임상적 의미를 결정할 수 없었다. 항균제 감수성 검사를 시행한 73균주 중 47주(64.4%)는 다제내성이었다. CA-MRSA 감염증 22예 중 피부 및 연부조직 감염(9예)과 중이염/외이도염(9예)이 가장 흔하였다. 침습적 감염증(invasive infection)은 4명(원발성 균혈증 3예, 감염성 관절염 1예)에서 확인되었지만, CA-MRSA 감염증으로 사망한 환자는 없었다. 결론 : 병원내 감염증에서는 MRSA가 심각한 문제이지만, 아직까지 지역사회 감염증에서 CA-MRSA는 흔하지 않았다. Background : Methicillin-resistant Staphylococcus aureus (MRSA) infection has emerged in patients who do not have the established risk factors. In Korea, little is known about the epidemiology and clinical features of community-associated MRSA (CA-MRSA). Material and Methods : Clinical microbiology laboratory databases of 7 hospitals were reviewed to identify the patients from whom MRSA was isolated during the period of January to July 2005. Only one isolate per patient was enrolled. In order to identify the risk factors of MRSA acquisition, the medical records and the Health Insurance Review Agency databases were reviewed. CA-MRSA was defined as MRSA isolated from patient without established risk factors. We analyzed patient demographics, underlying medical conditions, characteristics of infection, and antimicrobial susceptibility profiles. Results : Of total 3,251 S. aureus isolates, 1900 (58.4%) were MRSAs. Of the MRSA isolates, 114 (6.0%) were CA-MRSA. Of 114 CA-MRSA isolates, 22 (19.3%) were colonizers, 22 (19.3%) were pathogens, and the clinical significance of remaining 70 (61.4%) could not be determined. Median age of the 22 patients with CA-MRSA disease was 47 years. Nine patients had skin and soft tissue infections, 9 ear infections, 3 bacteremia, 1 septic arthritis. Seven patients had underlying medical disease. None died of the CA-MRSA infections. Of the 73 isolates of CA-MRSA, 47 (64.4%) were resistant to more than 3 classes of antibiotics besides β-lactams. Conclusion : Although MRSA is highly prevalent among hospital-associated S. aureus infection, CA-MRSA infections are not common.

표준 용매 벤젠의 Rayleigh 비의 온도 의존성

박일현,이종근,윤관한,조동환,민병길,방대석 金烏工科大學校 2000 論文集 Vol.21 No.-

The Rayleigh ratio of benzene is a very important physical constant with which the integrated scattered intensity of laser light scattering can be converted into the absolute value. In this study temperature dependence of Rayleigh ratio of this solvent has been investigated with two different methods in the temperature range of 25-75℃. It was found that in the direct measurement the non-linear behavior of its Rayleigh ratio were observed as increasing temperature even if the scattering volume correction was applied to the scattered intensity of benzene. However the result of indirect measurement based upon the invariance of molecular weight of standard polystyrene polymer for any polymer solution temperature showed us that its temperature dependence up to 75℃ could be expressed with the Benoit's linear equation rather than the non-linear one. It seems that the scattered intensity in direct method has more complicate contributions at the elevated temperature. Further research works are necessary in order to solve such discrepancy clearly.

로케트 工學에 관한 硏究 : 第1報 : 亞音速 亂流流動에서 飛行翼模型의 剝離現象 Ⅰst Report : Separation of Airfoils in Subsonic Turbulent Flow

朴煥奎,金鍾一,金鎭興,李茂錫,朴吉文,鄭洛奎,李行男,李東起 조선대학교 동력자원연구소 1984 動力資源硏究所誌 Vol.6 No.2

Separation, pressure and velocity distributions were studied fully developed two dimensinonal, incompressible flow over a flat airfoil in subsonic wind tunnel. Velocity and turbulence were measured with a two channel constant temperature hot wire anemometer and pressure with a pitot tube and pressure tranducer system. The experimental results were obtained as follow: (1) Turbulent intensity of shear layer just outside the separation point is considered to affect the size of separation bubble. (2) Static pressure coefficient is separated into three regions according to its value change. (3) Separation point is varied with the change of attack angle. (4) Velocity distributions and boundary layers normal to airfoil surface are changed as variation of attack angle of airfoil.

간경변증 환자에서 Escherichia coli 균혈증 합병 시 간기능 장애에 따른 C-reactive protein 생성 능력에의 영향

박완범,강철인,김동민,이기덕,장희창,김홍빈,오명돈,이효석,최강원 대한감염학회 2003 감염과 화학요법 Vol.35 No.5

목적 : C-reactive protein(CRP)은 간에서 생성되는 급성 반응물질이다. 하지만 간부전증 환자에서 CRP의 반응이 간기능에 따라 어느 정도 영향을 받는지는 별로 알려진 바가 없다. 본 연구에서는 간기능에 따른 CRP 생성 능력을 평가하고자 하였다. 방법 : E. coli 균혈증이 있는 간경변증 환자 30명을 대상으로 하였고 간기능은 균혈증이 발생하기 전 2개월 이내에 측정된 혈청 빌리루빈, 혈청 알부민, 프로트롬빈시간, Child-Pugh 점수로 평가하였다. 대조군 A는 간질환이 없으면서 E. coli 균혈증이 발생한 환자 30명으로 하였고 대조군 B는 간경변증이 있으면서 급성 감염의 증거가 없는 환자 30명으로 하였다. 환자군과 대조군 간에 CRP의 최대값을 비교하였다. 결과 : CRP의 최대값은 환자군에서 7.3±5.0㎎/dL, 대조군 A에서 17.9±8.3㎎/dL로 환자군에서 유의하게 낮았다.(P<0.001). 간경변증 환자에서 CRP의 생성은 Child-Pugh 점수에 비례하여 감소하였으나(P=0.004) Child=Pugh class C의 간기능을 가진 환자군에서도 대조군 B와 비교하여 의미있는 CRP의 생성을 보였다(5.3±3.2 vs. 0.5±0.4㎎/dL, P<0.001). 결론 : 간기능부전 환자에서 CRP 반응은 간기능 저하 정도에 따라 둔화되지만 심한 간기능 장애를 가진 환자에서도 CRP의 생성은 유지된다. Background : C-reactive protein (CRP) is an acute phase reactant produced in the liver. To assess the influence of liver dysfunction on the production of CRP, we evaluated CRP response to E. coli bacteremia in patients with or without liver cirrhosis (LC). Methods : 30 LC patients who developed spontaneous peritonitis with E. coli bacteremia were enrolled in the study. Baseline values of total bilirubin, serum albumin, and prothrombin time were obtained within 2 months prior to infection. Liver dysfunction was categorized according to the Child-Pugh score. 30 patients with E. coli bacteremia who had no underlying liver dysfunction were included as a control group. Matched-control of 30 LC patients without evidence of acute infection was also included. The peak CRP values were compared among the groups. Results : In the patients with E. coli bacteremia, the mean value of peak CRP was 7.3 (+/- 5.0) ㎎/dL in LC patients, 17.9 (+/- 8.3) mg/dL in patients without liver dysfunction (p<0.001). In the advanced LC patients with Child-Pugh class C, the level of CRP was 5.2 (+/- 3.3) ㎎/dL in patients with E. coli bacteremia, 0.5 (+/- 0.4) ㎎/dL in patients without acute infection (P<0.001). Child-Pugh score had correlation with decrease of CRP (linear regression test, P=0.004). Conclusion : CRP response during E. coli bacteremia was attenuated but maintained even in patients with advanced liver dysfunction.

서울·경기지역 병원직원의 혈액매개 감염노출에 대한 다기관 조사연구

박미라,김정은,박은숙,최정실,정선영,송영구,홍성관,김준명,허애정,양동규,조영주 대한병원감염관리학회 2003 의료관련감염관리 Vol.8 No.1

임상교정 교육용 멀티미디어 데이터베이스 웹서버 구축에 관한 연구

박재우,이종기,장영일,남동석,김명기,양원식,김태우,백승학 대한치과교정학회 2000 대한치과교정학회지 Vol.30 No.2

본 연구는 인터넷상의 가상공간에 다양한 자료로 구성된 환자 증례를 통해, 교정을 배우고자 하는 임상의나 학생들의 교육에 필요한 멀티미디어 데이터베이스를 구축하기 위한 것이다. 이러한 시스템을 구현하기 위해서는 이미지 자료의 처리, computer network를 통한 빠른 정보처리 기능, 진단 분석법의 개발, 데이터베이스의 구축 기술, 데이터베이스와 인터넷과의 연계, 증례를 통한 교육방법론과 같은 기술적 문제점들이 있다. 진단과 치료계획을 위한 분석은 모델 분석과 두부방사선 사진분석으로 나누어 제공하였다. 모델분석법은 arch length discrepancy와 Bolton tooth ratio를 환자 정보란에 제공하였다. 두부방사선 사진분석은 초진란에 제공하였다. Cephalometric analysis ver 2.0과 Power Ceph pro 3.3.5를 이용하여 Tweed, Steiner, Jarabak분석법 등을 제공하였으나, 본문에서는 주로 Kim's analysis와 몇 가지 계측치를 추가하여 설명하였고, 나머지는 tracing란에서 제시하였다. 또한 치료 종료 후나 보정란에서 치료 전, 후의 두부방사선 사진을 중첩해서 보여줌으로써 치료에 의한 효과를 직접 볼 수 있도록 하였다. The Objective of this research was to construct the multimedia database system that was necessary for the education of the practitioners and the students. To establish this system, there were technical problems as follows : 1) The processing of the images, 2) The rapid processing of the information with the computer network, 3) The development of diagnosis tools, 4) The technique to establish the database system, 5) The link between the database system and the internet, and 6) The method to educate through many cases. The analysis for diagnosis and treatment planning were provided as two parts : model analysis and cephalometric analysis. As a model analysis, arch length discrepancy and Bolton tooth ratio were provided for the part of patient information. Cephalometric analyses were provided in the part of initial diagnosis. The Cephalometric analysis ver 2.0 and the PowerCeph pro 3.3.5 were used to show Tweed, Steiner and Jarabak analysis. In the main part, Kim's analysis and some measurements were added. In the post-treatment or retention part, we show the superimposition of the cephalometrics with which you can find the effectiveness of the various orthodontic treatment. The address of this home page is "http://damis.snu.ac.kr/orthodontics"

수직적 안모유형에 따른 치료 후 교합평면 안정성에 관한 연구

박정은,차경석,이진우,정동화 대한치과교정학회 2006 대한치과교정학회지 Vol.36 No.5

본 연구는 수직적 안모유형에 따른 치료 후 교합평면 변화양상을 조사하여 향후 적절한 치료계획과 기전의 설정에 도움이 되고자 시행하였다. 골격성 1급 부정교합으로 진단되어 비발치로 치료받은 성인 60명(남자 28명, 여자 32명)을 대상으로 하였으며, Ricketts법의 facial axis, facial depth, mandibular plane angle, lower face height, mandibular arc의 5개 항목을 이용하여 한국 성인의 정상교합자 통계치의 기준에 따라 short face type (1군), average face type (2군), long face type (3군)으로 분류하였다. 각 군의 치료 전, 치료 종료, 종료 후 1년의 측모두부 방사선사진 계측치를 비교 분석하였다. 1군은 치료 종료 시와 비교하여 유지기간에 일반적 교합평면각, 기능적 교합평면각, L6/L1, MP-L6 항목이 유의하게 감소하였고 (p<0.01) L1-FOP 항목은 유의하게 증가하였다(p<0.001). 2군은 유지기간에 유의한 변화를 보이지 않았으며 3군은 유지기간에 기능적 교합평면각이 유의하게 증가하였다(p<0.05). 기능적 교합평면각의 치료 후 변화량은 각 군 간에 유의한 차이를 보였으며 특히, 1군과 3군 간에 매우 큰 유의성을 보였다. 따라서 치아의 압하, 정출 및 치료 후 전치부 피개 등에 있어 유지기간 중 교합평면각 변화의 고려가 필요하다고 생각된다. Objective: The purpose of this study was to find changes in the occlusal plane related to different vertical facial patterns and suggest treatment goals and conduct possible treatment mechanisms. Methods: 60 adult patients (28 males, 32 females) who had been diagnosed as Class I skeletal malocclusion and treated without extraction were selected. Patients were divided into three groups; short face type (group 1), average face type (group 2) and long face type (group 3), using the data on normal occlusion of Korean adults. Results: The results were achieved by analyzing cephalometric tracings of each group at pre-treatment, end-treatment and post-treatment (about 1 year recall check). The inclination of the occlusion plane tends to gradually increase as the face becomes longer. In group 1, COP-X, FOP-X, L6/L1, MP-L6 were significantly decreased, and L1-FOP was significantly increased during the retention period (T3-T2). Group 2 showed no significant change. In group 3, FOP-X was significantly increased during the retention period (T3-T2). During the retention period, FOP-X showed significant change among each group, especially between group 1 and group 3. Conclusion: These results suggest that changes of occlusal plane inclination according to facial vertical pattern need to be considered during the retention period for intrusion, extrusion, and incisor overbite.