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.

한국인에게서 그레이브스병 약물치료의 적정기간

이형숙,이동훈,정희선,이종우,김정은,신승수,정윤석,이관우,김현만 대한내분비학회 2003 Endocrinology and metabolism Vol.18 No.1

연구배경: 그레이브스병의 치료에는 항갑상선제, 수술 및 방사성 요오드법이 선택되어 사용되고 있다. 이중 항갑상선제는 가장 많이 선호되고 있으나 낮은 관해율과 높은 재발율로 장기간 치료기간이 요구된다. 저자들은 그레이브스병 환자에게서, 선택되는 치료법의 선호도와 각 치료법의 관해율을 조사하고자 본 연구를 시행하였다. 또한 본 연구에서는 항갑선제 치료의 적정기간을 평가하고자 하였다. 방법: 아주대학교병원에 내원한 환자 중 1년 이상 추적관찰이 가능한 205명의 그레이브스병 환자를 대상으로 조사하였다. 항갑상제군, 수술군 및 방사성 요오드군은 각각 170명, 29명 그리고 6명이었다. ROC curve를 이용하여 약물치료의 예후예측인자를 분석하였다. 결과: 1) 그레이브스병 환자의 치료 방법의 선택은 항갑상선제군, 수술군 및 방사성 요오드군 각각 170명(83.0%), 29명(14.1%) 그리고 6명(2.9%)으로 항갑상선제 치료가 가장 선호되었다. 2) 그레이브스병의 관해율은 항갑상선제군, 수술군 및 방사성 요오드군에서 각각 60.0%(102/170명), 96.5%(28/29명) 그리고 83.0%(5/6명)으로 수술군이 가장 높았다. 3) ROC curve의 AUC는 치료기간과 진단시 TBII가 각각 0.709 및 0.648이었고 적절한 약물투여 추적 관찰기간은 26개월이었다. 결론: 그레이브스병의 일차 치료법으로는 항갑상선제가 선호되고 있으나 수술 및 방사성 요오드 치료군에 비해 상대적으로 낮은 관해율을 보였다. 따라서 항갑상선제 치료로 26개월 이상 관해가 되지 않을 경우에는 치료 방법의 변경을 고려하는 것이 관해율을 높이는데 도움이 될 것으로 생각된다. Background: Graves' disease in an organ specific autoimmune disease. Three kinds of therapeutic modalities (antithyroid drugs, ablation with radioactive iodine and subtotal thyroidectomy) are frequently performed for the management of this disease. The most popular therapeutic policy for the disease in Korea is antithyroid treatment. We analysed and compared the remission rates of all three modalities for Graves' disease, and evaluated the antithyroid modality to determine the correct duration of treatment. Subjects & Methods : The medical records of 205 patients with Graves' disease were reviewed. For the evaluation of the antithyroid modality medical treatment, antithyroid drugs were administered for more than 1 year. The prognostic factors associated with remission were analysed by means of an ROC curve. Results: 1) Of the 205 patients, proportions that received medical therapy, subtotal thyroidectomy and radioiodine therapy were 83.0, 14.1 and 2.9%, respectively. 2) The remission rates of the medical therapy, surgery and radioiodine therapy were 60.0, 96.5 and 83.0%, respectively. 3) The remission rate of the medical therapy was associated with the duration of medication and TBII activity. The determined proper duration for the antithyroid treatment was 26 months from the ROC curve analysis. Conclusion: The above results suggest that the proper duration of antithyroid treatment for Graves' disease is 26 months, after which time the subtotal thyroidectomy or radioiodine therapy should be considered if the disease has not remitted (J Kor Soc Endocrinol 18:24∼31, 2003).

한국인 성인 남성의 불건강한 식습관과 위암발병에 대한 낙관적 편견 및 자기효능감 간의 관계 연구

이동숙(Lee Dong Suk) 한국재활간호학회 2003 재활간호학회지 Vol.6 No.2

The purpose of this study was to identify the relationships of optimistic bias about gastric cancer, self-efficacy of healthy dietary behavior and unhealthy dietary habit in Korean adult men.<br/> The subjects were 394 men aged from 20 to 64 who lived in Seoul, Kyonggi Do, Kwang-Ju, Jeonnam Do. Data was collected by questionnaire surveys using convenient sampling. The instruments used for this study were extracted and modified from Lee's(2003). The collected data was analyzed using descriptive statistics, Pearson correlation coefficient, and stepwise multiple regression with SPSS/PC 10.0 version.<br/> Unhealthy dietary habit in adult men indicated a significantly negative correlation to optimistic bias about gastric cancer(r=-.159, p=.002) and self-efficacy of healthy dietary behavior(r=-.470. P=.000). The most significant predictors influencing unhealthy dietary habit in adult men were age and self-efficacy of healthy dietary behavior. The variance explained was about 24%.<br/> These results suggested that men of young age and lack of self-efficacy of healthy dietary behavior are likely to have unhealthy dietary behavior. Therefore. considering age and facilitating self-efficacy are needed in nursing education and intervention for dietary habit change.<br/> <br/> <br/>

자기 효능의 개념 분석

서순림,이은남,박송자,양영희,이동숙,최은옥,구미옥,김인자,이인숙,김성재,박영임,이은옥 서울대학교 간호대학 간호과학연구소 1997 간호학 논문집 Vol.11 No.1

Today human needs for health promotion and maintenance are increasing. The nursing progression has a great responsibility for helping clients to practice good health behavior. self efficacy was found to be potent predictor in initiating and maintaining the health-related behavior. Therefore, the concept is important in nursig intervention for change of health behavior. The purpose of this paper was to analyze and clarify the meaning of the concept, self efficacy. This study used Walder & Avant's process of concept analysis. Critical attributes of self efficacy were : 1) positive perception of his won capability; 2) intrapersonal strength; 3) possibility of being learned; 4) individuality; 5) specificity; 6) generalizability. Antecedents of self efficacy consist of those facts that 1) new situation occurs; 2) individuals have needs to change the new situation; 3) there are some required actions in new situation. Consequences occurring as a result of self efficacy consist of those facts that 1) individual initiates the of failure; 5) cope with the situation; 6) controls the situation; 7) the level of self efficacy is enhanced; 8) the level of self-esteem is enhanced.

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.

Plenary Session 2 : PS-2-1 ; Outcomes of hepatitis B virus recurrence after liver transplantation: a multicenter analysis in Korea

( Hee Yeon Kim ),( Jong Young Choi ),( Dong Goo Kim ),( Myoung Soo Kim ),( Soon Il Kim ),( Shin Hwang ),( Sung Gyu Lee ),( Kwang Woong Lee ),( Kyung Suk Suh ),( Young Seok Han ),( Dong Lak Choi ),( Se 대한간학회 2012 춘·추계 학술대회 (KASL) Vol.2012 No.-

Background: The outcome of hepatitis B virus (HBV) infection after liver transplantation (LT) was improved by hepatitis B immunoglobulin (HBIG) and nucles(t)ide analogue (NUA). However, HBV recurrence after LT is critical because the recurrence is occasionally accompanied by a progressive destruction of graft and poor survival. The aims of this study were to investigate the significance HBV recurrence and identity factors associated with HBV recurrence. Methods: From October 1999 to February 2011, a total of 2684 consecutive LT recipients who underwent HBV-associated LT were retrospectively enrolled from 7 transplantation centers in Korea. Results: Prophylaxis regimens were HBIG monotherapy (67.7%) or a combination of HBIG with NUA (22.3%). The recurrence rate of HBV was 6.1% (164 recipients) during mean follow-up duration of 10.9 years. The median time from transplantation to recurrence was 2.1 years (0.1-7.9 years). Of the 1,071 patients with hepatocellular carcinoma (HCC) prior to LT, 155 patients (14.5%) had HCC recurrence after transplantation, and 48 patients (31.0%) had HBV recurrence. Of the 48 patients with recurrence of both HBV and HCC, 25 patients (52.1%) experienced HBV recurrence after HCC recurrence. In the multivariate analysis, pretransplant HCC, pretransplant HBV DNA above 5.5 log copies/mL was independent clinical factors influencing HBV recurrence after LT. The mortality rate among the recipients with HBV recurrence was 34.1% (56 recipients). Mean overall survival was 6.4 years in the HBV-recurrence group and 9.9 years in the HBV-nonrecurrence group (p<0.001). HBV recurrence was not an independent prognostic factor for overall survival. HCC recurrence was the most important factor for overall survival. Conclusions: The overall outcome of LT in HBV-related liver disease was excellent with the current prophylaxis regimen Choon Hyuck David Kwon,8 Suk-Koo Lee8 Pretransplant HBV DNA and HCC were important factors for HBV recurrence. HBV recurrence after LT did not significantly influence on the overall survival without combining of HCC recurrence.

지역사회획득 폐렴의 치료지침 권고안

송재훈,정기석,강문원,김도진,배현주,서지영,심태선,안중현,안철민,우준희,이남용,이동건,이미숙,이상무,이영선,이혁민,정두련,지역사회획득 폐렴 치료지침 제정위원회 대한감염학회 2009 감염과 화학요법 Vol.41 No.3

A successful therapy of community-acquired pneumonia requires appropriate empirical antimicrobial therapy. Etiology and antimicrobial susceptibility of major pathogens of pneumonia can differ by country. Therefore, an ideal treatment guideline of community-acquired pneumonia should be based on the studies performed in each country. We developed a treatment guideline for community-acquired pneumonia in immunocompetent adults in Korea. This guideline was developed by the joint committee of the Korean Society for Chemotherapy, the Korean Society of Infectious Diseases, and the Korean Academy of Tuberculosis and Respiratory diseases.

전산유체역학을 이용한 싸이클론형 전기집진기 고도 설계 연구

이은주,장동순,나혜령,김혜숙 忠南大學校 環境問題硏究所 1995 環境硏究 Vol.13 No.-

A computer program is developed in order to figure out the physical insight of the combined dust removal equipment, that is, cyclonic electrostatic precipitator. The computer program employs Patankar's control-volume based finite-difference method, in which SIMPLEC algorithm is used for the resolution of pressure-linked momentum equation. Further two equation k-ε model is incorperated for Reynolds stresses and many empirical formulae are employed for dust charging and electric resistivity. A series of extensive parametric investigations are performed in terms of tangential velocity(swirl intensity), applied voltage across two electrodes, and particulate diameters, etc. It is found that the electrostatic force gives much more strong effect, expecially for small particulate, on the dust removal than the centrifugal force. Other calculated results are physically acceptable and consistent.

R-12 냉매용 냉동장치의 성능에 미치는 R-12와 R-134a 냉매의 효과

이홍기,장동호,정용진,강형석 강원대학교 산업기술연구소 2000 産業技術硏究 Vol.20 No.B

High pressure, pressure ratio, refrigerating effect, heat transfer from the condenser and the power of the compressor etc. of a self-made refrigeration equipment for R-12 are investigated when R-12 and R-134a are used as the coolants. The comparison between the performance for R-12 and that for R-134a is made. As a result, R-134a is better than R-12 in the view of high pressure, refrigerating effect and the coefficient of performance and vice versa in the view of pressure ratio, exit gas temperature from the compressor and heat transfer from the condenser.

정상인 및 신기능장애환자에서 Carumonam(AMA-1080)의 약동학

임동석,이경훈,엄재호,한진석,김성권,장인진,신상구 大韓臨床藥理學會 1994 臨床藥理學會誌 Vol.2 No.1