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.

족저압력분포 측정장비를 이용한 골프 스윙시 족저압 분석

이동기,이중숙,이범진,이훈식,김용재,박승범,주종필 한국운동역학회 2005 한국운동역학회지 Vol.15 No.1

D. K. LEE, J. S. LEE, B. J. LEE, H. S. LEE, Y. J. KIM, S. B. PARK, J. P. JOO. PIantar foot pressure analysis during golf swing motion using plantar foot pressure measurement system. Korean Journal of Sport Biomechanics, Vol. 15, No. 1, pp. 75-89, 2005. In this study, weight carrying pattern analysis and comparison method of four foot region were suggested. We used three types of club(driver, iron7, pitching wedge). This analysis method can compare between top class golfer and beginner. And the comparison data can be used to correct the swing pose of trainee. If motion analysis system, which can measure the swing speed and instantaneous acceleration at the point of hitting a ball, is combined with this plantar foot force analysis method, new design development of golf shoes to increase comfort and ball flight distance will be available. 1. Address acting, forces concentrated in rare foot regions and lateral foot of right foot. Back swing top acting, relatively high force occurred in medial forefoot region of left foot and forefoot region of right foot. Impact acting, high force value observed in the lateral rarefoot region of left foot and medial forefoot region of right foot. Finish acting, force concentration observed on the lateral region and rarefoot region of left foot. 2. Forces were increased in address of right foot with clubs length increased. All clubs, back swing top acting, high force value observed in the lateral forefoot region of right foot. All clubs, in impact, high force value observed in the lateral rarefoot region of left foot and medial forefoot region of right foot. Finish acting, force concentration observed on the rarefoot region in driver and lateral foot region in iron on left foot. 3. Right foot forces distribution were increased in address, back swing top and left foot force distribution were increased in impact, finnish

유착성 관절낭염 치료에 있어서 한방 치료와 양방 치료의 임상적 고찰 : 동서협진 모델 개발을 위한 기초 연구를 중심으로

남동우,정인태,김주희,박유선,임사비나,이두익,이재동,이윤호,최도영 경희대학교 동서의학연구소 2006 東西醫學硏究所 論文集 Vol.2006 No.-

Objectives : To observe the effect of acupuncture treatment and western medical treatment on frozen shoulder patients. Methods : 39 voluntary patients were randomly assigned to the Eastern treatment group(E group, n=22) and the Western treatment group(W group, n=17). The E group received acupuncture treatment on LI15, TE14, GB21 and Master Dong's acupuncture points, Shin-gwan and Gyun-joong, twice a week for 4 weeks. The W group received suprascapular nerve block, subacromial injection and trigger point injection, twice a week for 4 weeks. Both groups were instructed to practice self exercise during their daily lives. Evaluations were made before treatment and after treatment using Constant Shoulder Assessment(CSA), Shoulder Pain and Disability Index(SPADI) and the patient's satisfaction concerning the treatment was measured by Visual Analogue Scale(VAS). The obtained data were analyzed and compared. Results : The E group showed significant improvement(p<0.05) according to the CSA and SPADI. The patient's satisfaction scored 5.67 on a scale of 10. The W group showed significant improvement(p<0.05) according to the CSA and SPADI. The patient's satisfaction scored 7.73. But the difference between the two groups were insignificant according to CSA and SPADI. Conclusion : Both acupuncture and nerve block treatment significantly improved frozen shoulder. But the difference of the two treatments was insignificant.

SNL-EFDC를 이용한 군산항 유사퇴적고 계산의 비교 연구

이동주 ( Dong-joo Lee ),송상현 ( Sang-hyun Song ) 한국환경기술학회 2015 한국환경기술학회지 Vol.16 No.4

본 논문은 Ziegler, Lick, and Jones에 의해 개발된 SEDZLJ라 부르는 유사역학 알고리즘이 계산되는 SNL-EFDC 모델을 이용하여 군산항의 퇴적고 계산에 관하여 연구하였다. SEDZLJ모듈은 SEDflume 이나 Annular flumes로부터 얻은 현장 침식률 및 침식 한계전단응력 자료를 직접 결합할 필요가 있다. 군산항에서는 SEDflume 자료를 구할 수 없기 때문에 Ryu와 Yim에 의한 Annular flumes 실험으로부터 얻은 현장 침식률 및 침식 한계전단응력 자료를 이용하였다. SNL-EFDC 모델이 군산항의 유사퇴적고를 계산하기 위해 적용되었고 관측된 부유사 농도와 퇴적고를 사용하여 검증되었다. 유사 퇴적고 계산에 대한 모델의 적용성은 NSEC가 0.72로 침식과 퇴적의 물리적 변화가 적절하게 재현됨이 입증되었다. 부가적으로 검증된 모델은 저면 활성층두께에 대한 매개변수 α값의 영향을 조사하기 위해 사용되었고, Lee와 Park에 의해 수행된 SEDTM을 이용한 유사이동 계산의 결과와 비교하기 위해 사용되었다. 그 결과, 매개변수 α값의 변화는 유사퇴적고 계산에 미미한 영향이 미치는 것으로 나타났다. SEDZLJ에 의한 결과를 SEDTM의 것과 비교할 때 SEDZLJ모듈이 군산항에서 SEDTM 보다 NSEC가 0.03향상 되어 토사이송 과정을 재현함이 확인되었다. This paper was studied on the sediment deposition height computation at Gunsan port using recently advanced SNL-EFDC model which the sediment dynamics algorithm was called as SEDZLJ developed by Ziegler, Lick and Jones. SEDZLJ module needs to directly incorporate site-specific erosion rate and critical shear stress data from SEDflume or Annularflumes. Here this model attempted to use site-specific erosion rate and critical shear stress data from Annular flumes experiment by Ryu and Yim instead of unavailable SEDflume data at Gunsan port. SNL-EFDC was applicated to calculate deposition height at Gunsan port and verified using observed values for suspended sediment concentration and sediment deposition height. The model applicability for sediment deposition height computation was evaluated as NSEC 0.72 and verified that it reproduced the physical variations of erosion and deposition. In addition, the verified model was used to investigate the effect of parameter “α” on the active bed layer thickness and used to compare with the result of sediment transport computation using SEDTM done by Lee and Park. As a result, it was found that the change of parameter “α” value has a negligible effect on sediment deposition height computation. As results of SEDZLJ are compared with those of SEDTM, it was identified that SEDZLJ module reproduces the sediment transport process more appropriately than SEDTM at Gunsan port with advanced NSEC 0.03.

진도(전라남도, 진도군)의 거미상

김주필(Joo Pil Kim),지승환(Seung Hwan Ji),이형민(Hyung Min Lee),이형진(Hyung Jin Lee),이현동(Hyun Dong Lee) 한국거미연구소 2017 한국거미 Vol.33 No.1

2016년 7월 6일부터 8일까지 전라남도 진도군 일대를 한국거미연구회 회원인 김주필, 지승환, 이형민, 이형진, 이현동 등이 채집 조사한 결과 19과 47속 62종의 거미가 조사 연구되어 이에 보고하는 바이다. The author investigated the spiders of Jin island in July 06~08.2016. In the present paper 62 species of 47 genera belongs to 19 families were identified. These specimens are deposited at the Joo-Pil Spider Museum, Namyangju-Si, Gyeonggi-Do.

서초동(서울시 서초구)의 거미상

김주필(Joo Pil Kim),정혜리(Hye ri Jeong),김대희(Dae Hee Kim),박동우(Dong Woo Park),서재웅(Jae Woong Seo),이현우(Hyun woo Lee) 한국거미연구소 2017 한국거미 Vol.33 No.1

2016년 3월 31일부터 7월 31일까지 서울특별시 서초구 서초동에 위치한 서울고등학교 교정 일대를 서울고등학교 환경생물부 부원들이 채집 조사한 결과 20과 43속 53종의 거미가 조사 연구되어 이에 보고하는 바이다. From March 31st to July 31st in 2016, members of an environmental biology club at Seoul High School located in Seocho-gu, Seoul, Dae-Hee Kim, Dong-Woo Park, Jae-Woong Seo and Hyun-woo Lee, collected 20 families 43 genera 53 species of spiders and report the result of the study here.

BEZ235 (PIK3/mTOR inhibitor) Overcomes Pazopanib Resistance in Patient-Derived Refractory Soft Tissue Sarcoma Cells

Kim, Hee Kyung,Kim, Sun Young,Lee, Su Jin,Kang, Mihyeon,Kim, Seung Tae,Jang, Jiryeon,Rath, Oliver,Schueler, Julia,Lee, Dong Woo,Park, Woong Yang,Kim, Sung Joo,Park, Se Hoon,Lee, Jeeyun Neoplasia Press 2016 Translational oncology Vol.9 No.3

<P><I>BACKGROUND:</I> Although pazopanib treatment has become the standard chemotherapy in salvage setting for metastatic sarcoma patients, most patients progress after pazopanib treatment in 4 to 6 months. After failure to pazopanib, patients have limited options for treatment. Therefore, subsequent therapy in patients who failed to pazopanib is urgently needed and the use of patient derived cells or patient derived tumors for accompanying testing with various pharmacological inhibitors could offer additional treatment options for these patients. <I>METHODS:</I> Patient derived tumor cells were collected from ascites at the time of progression to pazopanib and a 13-drug panel was tested for drug sensitivity. We confirmed the results using <I>in vitro</I> cell viability assay and immunoblot assay. We also performed the genomic profiling of PDX model. <I>RESULTS:</I> The growth of patient derived tumor cells was significantly reduced by exposure to 1.0 μM AZD2014 compared with control (control versus AZD2014, mean growth = 100.0% vs 16.04%, difference = 83.96%, 95% CI = 70.01% to 97.92%, <I>P</I> = .0435). Similarly, 1.0 μM BEZ235 profoundly inhibited tumor cell growth <I>in vitro</I> when compared to control (control versus BEZ235, mean growth = 100.0% vs 7.308%, difference = 92.69%, 95% CI = 78.87% to 106.5%, <I>P</I> < .0001). Despite the presence of CDK4 amplification in the patient-derived tumor cells, LEE011 did not considerably inhibit cell proliferation when compared with control (control vs LEE011, mean growth = 100.0% vs 80.23%, difference = 19.77%, 95% CI = 1.828% to 37.72%, <I>P</I> = .0377). The immunoblot analysis showed that BEZ235 treatment decreased pAKT, pmTOR and pERK whereas AZD2014 decreased only pmTOR. <I>CONCLUSION:</I> Taken together, upregulation of mTOR/AKT pathway in sarcoma patient derived cells was considerably inhibited by the treatment of AZD2014 and BEZ235 with downregulation of AKT pathway (greater extent for BEZ235). These molecules may be considered as treatment option in STS patient who have failed to pazopanib in the context of clinical trials.</P>

CA 125치가 증가된 난소종괴 환자에서 악성 감별을 위한 CA 15-3과 TAG 72의 효용성

이수미,김영탁,정동근,남주현,목정은 울산대학교 의과대학 1992 울산의대학술지 Vol.1 No.1

The purpose of our study was to evaluate whether the combined use of serum tumor markers, CA 15-3 and TAG 72 could improve the efficacy for discriminating malignant from benign ovarian masses in patients with elevated serum CA 125 levels. Serum CA 15-3 and TAG 72 were preoperatively measured by immunoradiometric assay in 78 patients with pelvic masses who had elevated serum CA 125 levels above 35 U/ml. In 32 patients with epithelial ovarian cancers, serum CA 125 levels were elevated above 65 U/ml in 97% and serum CA 15-3(>30U/ml) and TAG 72(>10 u/ml) levels were elevated in 59% and 50%, respectively, suggesting relatively low sensitivity of CA 15-3 and TAG 72. However, in 41 patients with benign ovarian tumors, elevations of these two markers were detected only in 7% and 5%, respectively, and particularly, both markers were not elevated among all the aptients over 50 years of age. Coordinate elevations of CA 125(>35U/ml) and CA 15-3(>30U/ml) or TAG 72(>10 U/ml) could discriminate epithelial ovarian cancers from benign masses with a sensitivity of 72% and specificity of 90%. Among patients over 50 years of age, sensitivity and specificity were increased to 79% and 100%, respectively. It is concluded that the combined use of CA 15-3 and TAG 72 with CA 125 could obtain an improved efficacy for discrimination of epithelial ovarian cancer, especially among patients over 50 years of age.

초등학교 영어수업에서 멀티미디어 자료 적용범위에 따른 영어학습의 효관에 관한 연구

이동한,이건옥,제은주 부산교육대학교 교육대학원 1999 논문집 Vol.1 No.-

The purpose of this study is to investigate appropriate proportion of multimediarized environment for the elementary English classroom. For this study, 100% multimediarized English lesson was provided to 4th grade students at Nae-San elementary school and 50% multimediarized English lesson was given to 4th grade students at Min-An elementary school for 4 months from september to december in 1998. To Nae-San, whole class was progressed only by various multimedia materials without direct interaction between the teacher and students from the beginning to the end of lesson. For Min-An, the English lesson was performed with multimedia materials, activities with teacher: one half of the lesson was done by the use of multimedia materials and the other half was done by interaction between the teacher and students. The study result shows that there was no significant difference between Nae-San and Min-An elementary school students performed better than that of Nae-San elementary school students. The result of this study shows that students who have class with 50% multimedia is better than students who have studied with 100% multimedia environment in the point of speaking. In the conclusion, this paper suggests that the language teaching method with 50% multimedia including variable game activities and apposite materials is more effective than that of 100% multimedia.

서부 경남 지역의 하악골 골절에 관한 임상통계학적 분석

주현호,원동환,이상휘,김일현 대한악안면성형재건외과학회 2000 Maxillofacial Plastic Reconstructive Surgery Vol.22 No.5

This is a clinicostatistical study of 578 patients with mandibular fractures who was treated at Gyeongsang National University Hospital during the period of 1988-1999. Results obtained were as follows. 1.In respect of incidence, The ratio of men to women was 5.0 : 1, The age frequency was the highest in the third decade(37.5%), The youngest patient was 3 years and the eldest patient was 87 years and mean age was 29.9 years, The year incidence was the highest frequency as 83 patients in 1998. The monthly incidence was the highest frequency as 66 patients in July auld the least frequency as 34 patients in December. 2.The most frequent cause was traffic accident as 198 patients(41.7%) and the next was fall down 161 patients(27.9%), violence as 112 patients(19.4%) in order. 3.The incidence of associated soft tissue and tooth injury was 62.6%, and concomitant injuries of other parts of body(26.5%) were most commonly caused by traffic accident(79.7%). 4.The most common location was symphysis as 361 number(40.9) and the sum of fracture sites were 925 and there were 1.6 fracture sites per one patient. The most common type of mandible fractures was closed simple type(82.9%) and the ratio of Left to Right except for symphysis was 1.5 : 1. 5.In respcet of treatment, the frequency of open reduction was 423 patients(73.2%) and the incidence of complication was 7.4% and the most common complication was infection