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.

Changes of Sugar Composition and Related Enzyme Activities during Fruit Development of Asian Pear Cultivars ‘Niitaka’ and ‘Whangkeumbae’

Jin-Ho Choi,Jang-Jeon Choi,Chang-Seok Bang,Jung-Sup Lee,Dong-Woog Choi,Hye-Sun Cho,Jun Cheul Ahn 한국원예학회 2009 Horticulture, Environment, and Biotechnology Vol.50 No.6

We report on the seasonal changes of soluble sugar accumulation and several enzyme activities related to sugar metabolism, in two Asian pear cultivars (Pyrus pyrifolia) cultivars ‘Niitaka’ and ‘Whangkeumbae’. Soluble sugar content increased as the fruit developed and its total contents in matured fruits were 104.6 and 95.1 ㎎ㆍg?¹ fresh weight for ‘Niitaka’ and ‘Whangkeumbae’, respectively. However, the fructose-glucose-sucrose-sorbitol ratio was not significantly changed. Sorbitol-6-phosphate dehydrogenase activity was maintained at high level in leaves and low in fruits throughout the fruit development, although the enzyme activity highly fluctuated in young and mature fruits. NAD-dependent sorbitol dehydrogenase activity increased sigmoidally in both leaves and fruits during fruit development, and correlated with accumulation of total sugar in fruits. Sucrose synthase and sucrose phosphate synthase (SPS) activities remained low in leaves, but higher with two peak fluctuations in fruits. The change of soluble sugar contents positively correlated with SPS activity, based on the seasonal fluctuation of SPS activity and soluble sugar accumulation.

Hypersensitivity Reaction Incidence Patterns and Risk Factors of Iodinated Contrast Media

김동휘(Dong-Hwi Kim),문종현(Jong-Hyeon Mun),김준환(Jun-Hwan Kim),윤승완(Seung-Wan Yun),박환상(Hwan-Sang Park),김창곤(Chang-Kon Kim),김영덕(Yeong-Deok Kim) 대한CT영상기술학회 2023 대한CT영상기술학회지 Vol.25 No.1

본 연구의 조사 대상은 본 원 에서 요오드화 조영제를 정맥으로 투여받고 CT 검사를 시행한 72,910명과 과거 조영제 과민반응을 겪었던 환자 2,798명을 대상으로 후향적 조사를 시행하였다. 나이, 성별, 과민반응 증상, 조영제 과민반응 기왕력 환자 전처치방법, 사용한 조영제 등을 분석하였다. 조영제 과민반응 발생은 여성과 60대 미만에서 발생 위험이 높고 과거 조영제 과민반응기왕력이 있더라도 적절한 전처치 약물 투여, 조영제 성분 변경을 시행하면 과민반응 발생 위험이 감소한다. 조영제 성분별과민반응 발생률은 Iopromide가 유의하게 과민반응 발생률이 높았고, Iohexol과 Ioversol이 낮은 발생률을 보였다. 조영제 과민반응 재발을 예방하기 위해서는 전처치 약물 단독 사용보다 선행적으로 원인 조영제를 재사용하지 않고 다른 성분의 조영제로 변경하여 사용하는 것이 우선적으로 시행되어야 하고 더불어 전처치 약물 투여와 함께하는 것이 재발을 예방할 수 있을 것이다. The subjects of this study were 2,798 patients who experienced hypersensitivity reaction of contrast media among 72,910 who had had iodinated contrast media administered intravenously and CT examination at our hospital. Retrospective survey was conducted with these subjects. Their age, gender, hypersensitivity reaction symptoms, prepare methods for the patients who had previous hypersensitivity reaction of contrast media, and contrast media administered were analyzed. When it came to the hypersensitivity reaction incidence of contrast media, women and patients aged less than 60 had the high risk of the reaction. Even if patients had previous contrast media hypersensitivity reaction, their hypersensitivity reaction incidence risk was reduced as they had an appropriate premedication drug administered and contrast media were changed. Regarding the hypersensitivity reaction incidence rate by contrast media, Iopromide’s hypersensitivity reaction incidence rate was significantly high, whereas Iohexol and Ioversol had low incidence rates. In order to prevent contrast media hypersensitivity reaction recurrence, it is preferentially necessary to change a contrast media to a different one without reuse of causative contrast media, rather than to use a premedication drug only. Along with that, it is necessary to administer a premedication drug.

장기간 수영훈련이 중년여성의 혈장 지질 및 아포단백질에 미치는 영향

김영준,장성동,어경철 동아대학교 스포츠과학연구소 2000 스포츠科學硏究論文集 Vol.18 No.-

The purpose of this study is to analyze the effects of long-term swimming excercise on thefat and aplipoprotein of middle-aged women. For the purpose, 14 middle-aged women who have no disease and do not any regular excercise are selected. They are divided into two groups. One is an exercise group(swimming group, Age : 39.0±2.12) consisting of seven members who are to make swimming exercise for eight weeks, and the other is a control group(control group, Age : 38.3±3.12). The effects of the exercise on fat and aplioprotein in blood are then examined. In terms of exercising method, the period, time and frequency of the swimming are determined as eight weeks, fifty minutes a day and five days a week respectively, The result of the study is as follows. 1.FFA, TG, TC and TC/HDL in blood plasma significantly decrease than before swimming, but LDL-C and HBL-C show no changes. 2.Aplipoprotein a and b in blood plasma show no changes over the eight weeks' exercise. Consequently, swimming exercise for eight weeks does not have an influence on LDL-C and HDL-C but on FFA, TG, TC and TC/HDL. The intensity, period and frequency of exercise should be maintained for change in cholesterol.

대장암종에서 암관련 유전자들의 Promoter Methylation과 암종 발생 및 진행과의 관게에 대한 연구

정동준,이정은,민영기,조성우,백무준,양승하,김의한,김창진 순천향대학교 교수학습개발센터 2004 Journal of Soonchunhyang Medical Science Vol.10 No.3

The colorectal corcinoma is one of the most common malignant tumor in Korea and its carcinogenic mechanism has not been elucidated exactly yet. So far, the most common carcinogenic mechanism has been known to be multiple genetic changes. But, the CpG island hypermethylation has been revealed to be one of the most important carcinogenic mechanism second to the genetic changes. The epigenetic changes characteristically imprint and transfer to the next generation without changes of nucleotide sequences. When the CpG island of promoter or 5'- exon 1 of a specific gene is methylated by DNA methyltrasferases (DNMTs), the gene expression is inhibited. Carcinogenic mechansisms by promoter methylation has been well known, but the progression of the cancer has not been elucidated yet. The molecular researches on the carcinogenic mechanisms largely depended on the tumor tissue containing various components of cell, due to difficulties in harvesting pure homogeneous tumor cells. Promoter methylatonof the cancer related genes as APc, hMLH2, p16, DAP-K and MGMT in 50 cases of sporadic colorectal carcinoma was studied. The pure normal colorectal epithelial cells, and cancer cells from superficial and deep invasive portion were harvested respectively by laser captured microdissection(LCM), and DNA was extracted from them. The promoter methylation was studied by methylation specific poymerase reaction (MSP) after bisulfite modification of the DNA and the expression of the genes by immunohistochemistry. The results suggests that promoter methylation of the cancer related genes are closely related with the colorectal carcinogenesis and it occurrs from early phase of carcinogenesis, progressing constantly to the late stage. And the promoter methylation of normal epithelial cells increased by age. The p15, known to be the genes related to hematologic malignancy, was closely related to the colorectal carcinoma as well.

대중교통 서비스 품질 평가의 국내외 연구 동향 및 시사점 (A Review on the evaluation of transit quality of service)

이상준(Sang-Jun Lee),김형수(Hyung-Su Kim),정동재(Dong-Jae Jung),장수은(Justin S. Chang) 한국철도학회 2011 한국철도학회 학술발표대회논문집 Vol.2011 No.5

Internal and external conditions are currently changing-e.g, climate change increased awareness of energy crisis, and accelerated paradigm about green growth. Accordingly, revitalization of public transportation which enables green transportation system is receiving more attention than the past. Meanwhile, as the incom level increased, people required better quality of service, and consequently, various proposals about improving the services are being promoted. Generally, the quality of the spaces within transit in developed countries is represent the quality of life, thus concerns about the transit service of quality are emerging. This study, through the domestic and abroad studies about transit service quality, redefines transit service quality including rail and reviews the related categories. In that order this study deducts each type of evaluation categories and factors, with comparing and reviewing with various cases in Korea and overseas. Based on the whole process, the paper elicits implications and proposes to the research about the evaluation of transit quality of service

한국인의 건강관련 행동변인에 관한 연구

김상국,장주호,김경지,강동원,전병관 경희대학교 사회체육연구소 1996 體育科學論叢 Vol.- No.9

This study is for research on the cause of behavioral change in relation to health of Koreaans in order to enhance the quality of life. For this We have surveyed against 3,000 adults of 8 cities and provinces nationwide. Looking the result of this study synthetically, most of the subjects of study were thinking that they are 'jealthy'(62.9% for male, 50.0%) and of drinker(83.2%) formale, which harm our health are high. The ratio of having stress often were high for voth male and female(27.1% for male 31.4% for female), and the main cause of the stress were shown as wok related to their company(56.7%) for male and as family problem (44.1%) for female, They responded to resolve it mainly in 'patient'(36.5% for male, 51.0% for female). This shows that they need something positive way of resolving the stress. Korean people likes modicines too much and it was surveyed to have worsened their health due to ovenuse of medicines. They hardly have medical check up and even there were people who don't know is medical check up, so it was shown to nood activ promotion of it. As the result of study on te cause of behavioral change related to health of Koreans for the enhancement of people[s' lives, We would like to suggest some guidelines for healithy life. A. It needs to promote and educate for reducing smoking and drinking which harm our health B. The plan or programs for resolving stress of the people must be studied concretely on the level of gorvernment. C. For the checking condition of health well, ti must be done and consulted with specialists. D. The eating habits of our people must be changed in consulting with specialists in order to protcet and cure from the most serious digestive troubles.

자궁경부 상피종양에서 human papillomavirus 감염과 survivin 발현

윤재호,정동준,이정은,박동명,배동한,선우재근,백무준,김창진 순천향의학연구소 2004 Journal of Soonchunhyang Medical Science Vol.10 No.1

Human papillomavirus (HPV) has been considered a causative agent of uterine cervical carcinoma. HPV is a DNA oncogenic virus, which is well known as a causative virus in uterine cervical carcinoma. The virus is classified into two groups genotypically, low risk and high risk, according to the carcinogenic potentiality, and the determination of the viral genotype is important in clinical practice. Recently, numerous genotypes can be determined by high throughput method using DNA chip. Survivin is a recently characterized inhibitor of anti-apoptosis (IAP) protein, which is abundantly expressed in most solid and hematological malignancies, but undetectable in normal adult tissues. In this study, HPV genotypes are determined by DNA chip and the expression of survivin was examined by immunohistochemistry in 80 cases of uterine cervical intraepithelial neoplasia (CIN) and invasive carcinoma to see the roles of HPV and survivin in the carciogenesis of uterine cervical epithelial neoplasia. The results were as follows: 1. HPV positive rate was 72.5%, while negative rate was 27.5% in 80 cases of CIN and invasive carcinoma. The CIN and invasive carcinoma showed higher HPV positive rate (p <0.05). 2. HPV positive rate according to the histologic grade were 60%, 65%, 77% and 90% in CINI, CINII, CINII and invasive carcinoma, respectively. HPV positive rate showed increasing tendency according to the histologic grade, though there was no statistical significance. 3. The most frequent genotype was type 16 and the next were 58, 52, 18 and 33 in order of frequency. 4. Survivin was expressed in 96.3% of CIN and invasive carcinoma. The expression rate of survivin showed no significant difference between the histologic grade of CIN and invasive carcinoma, but showed tendency of increased expression rate in invasive carcinoma. 5. Survivin was expressed in HPV positive and in HPV negative each as in 95.5% and 96.6% respectively. There was no significant difference of survivin expression between HPV positive and negative cases. The above results suggest that HPV has no effect on the regulation of survivin expresson level in the uterine cervical intraepithelial neoplasia and invasive carcinomas.

도로의 빗물받이 간격을 고려한 우수관거 최적설계

장동일,이정호,전환돈,김중훈,Chang, Dong-Eil,Lee, Jung-Ho,Jun, Hwan-Don,Kim, Joong-Hoon 한국방재학회 2008 한국방재학회논문집 Vol.8 No.5

본 연구에서는 도로 측구에 매설된 우수관거와 함께 빗물받이 간격을 최적화하는 우수관거 최적 설계 모형을 제시하였다. 빗물받이 간격이 변화하면 각 측구에 대한 유역면적이 변화하게 되며, 각 측구로 유입되는 유량을 또한 변화시키게 된다. 각 측구로 유입되는 유량이 달라질 경우 하부에 매설된 우수관거의 필요용량이 달라지므로 관경의 변화가 요구되는 결과를 낳는다. 즉 빗물받이 간격이 달라진다면 빗물받이 개수, 각 우수관거의 관경 및 연장, 그리고 관거별 경사 등의 설계조합이 달라진다. 그에 따라서 최소비용을 위한 빗물받이 간격 별 우수관의 설계조합은 최적화를 통하여 해결해야한다. 수리학적 조건을 만족하는 빗물받이 간격 및 우수관의 설계조합을 유전자 알고리즘을 통하여 결정하였다. 도로의 조건들은 실제도로에 맞게 가정하였으며 강우조건은 서울지방의 재현기간 10년 지속시간 1시간 강우를 사용하였다. 현재 하수도 시설기준 및 여러 기준에 의해 포괄적으로 소개된 빗물받이 적정 간격은 $10{\sim}30\;m$이므로 본 모형을 이용한 빗물받이 최적 간격에 대한 해의 탐색은 이 범위 내에서 이루어졌다. 본 연구는 도로의 경사조건에 따른 빗물받이 최적간격과 우수관의 최적조합을 최소 건설비용을 통하여 제시하였으며 본 연구에 의해 획득된 결과에 의하면 노면경사에 따라 최적 빗물받이 간격이 다르며 빗물받이 간격에 따라 공사비용을최대 20% 감소시킬 수 있었다. This study presented a design model optimizing a distance of inlet with drainage pipe laid under the gutter in road. When the distance of inlet changed, a basin for the gutter divided by the distance of inlet and the inflow coming into the gutter would be changed. In this case, the change of inlet distance causes the change of a diameter of drainage pipe and slope because of the change of capacity. Therefore, the optimization is needed to design the combination of them for the distance of inlet. Genetic Algorithm is used to determine the optimal combination of them. The conditions of road and the precipitation were assumed like a real and the range of inlet distance adopted $10{\sim}30\;m$ which has been introduced in domestic. This model presented the optimal distance of inlet and the combination of pipe and slope through the minimum cost. The result of the study is that the optimal distance of inlet is different from each slope of road and it can reduce about 20% of total cost for the distance of inlet.

정신분열병에 대한 리스페리돈의 효과 및 안정성

이민수,김용구,김영훈,연병길,오병훈,윤도준,윤진상,이철,정희연,강병조,김광수,김동언,김명정,김상훈,김희철,나철,노승호,민경준,박기창,박두병,백기청,백인호,손봉기,손진욱,양병환,양창국,우행원,이정호,이종범,이홍식,임기영,전태연,정영조,정영철,정인과,정인원,지익성,채정호,한상익,한선호,한진희,서광윤 大韓神經精神醫學會 1998 신경정신의학 Vol.37 No.1

연구목적 : 본 시험의 목적은 임상시험 시작전에 연구자들을 대상으로 PANSS Workshop을 통하여 PANSS, ESRS에 대한 국내에서의 표준화 작업을 구축하고 새로운 정신병 치료제인 리스페리돈의 효과와 안정성을 재확인하여 리스페리돈 사용에 대한 적정화를 이루는데 있다. 연구방법 : 1996년 4월부터 1996년 9월까지 국내 39개 대학병원 정신과에 입원중인 혹은 증상이 악화되어 입원하는 정신분열병 환자 377명을 대상으로 다시설 개방 연구를 시행하였다. 1주일간의 약물 배설기간을 가진후, 리스페리돈을 8주간 투여하였고, 기준점, 1주, 2주, 4주, 그리고 8주후에 평가되었다. 용량은 제1일에는 리스페리돈 1mg씩 1일 2회, 제2일에는 2mg씩 1일 2회, 제3∼7일에는 3mg씩 1일 2회 투여하였다. 이후 환자의 임상상태에 따라 임의로 증량할 수 있으며, 최대 일일 16mg을 초과하지 않도록 하였다. 추체외로 증상을 조절하기 위한 투약을 허용하였다. 임상증상 및 부작용의 평가는 PANSS(Positive and Negative Syndrome Scale), CGI(Clinical Global Impression) 그리고 ESRS(Extrapyramidal Symptom Rating Scale)을 사용하였다. 연구결과 : 377명중 343명(91%)이 8주간의 연구를 완결하였다. 치료 종결시점인 8주후 PANSS 총점수가 20% 이상 호전된 경우를 약물 반응군으로 정의할때, 약물반응군은 81.3%였다. 리스페리돈에 반응하는 예측인자로는 발병연령, 이전의 입원 횟수, 유병기간이 관련 있었다. 리스페리돈은 1주후부터 PANSS양성, 음성, 및 일반정신병리 점수상에 유의한 호전을 보여 효과가 빨랐다. CGI의 경우도 기준점에 비해 1주후부터 유의한 감소를 나타내었다. ESRS의 경우, 파킨슨 평가점수는 기준점과 비교해 투여 1주, 2주, 4주후 유의하게 증가되었다가 8주후 기준점과 차이가 없었다. Dystonia 평가점수는 1주후만 유의한 증가를 보였으며, dyskinesia 평가점수는 유의한 차이가 없었다. 혈압, 맥박수의 생명징후 및 일반 혈액학 검사, 생화학적 검사, 심전도 검사에서 유의한 변화는 없었다. 결 론 : 이상의 다시설 개방 임상 연구를 통해 리스페리돈은 정신분열병 환자에서 양성증상뿐만 아니라 음성증상 및 전반적인 증상에도 효과적인 것으로 사료된다. 보다 명확한 평가를 위해서는 다른 항정신병약물과의 이중맹검 연구가 필요할 것으로 생각되며, 또한 장기적 치료에 대한 평가도 함께 이루어져야 하겠다. Objective : The purpose of this study was to investigate the efficacy and safety of risperidone in the treatment of Korean schizophrenic patients. Method : This multicenter open study included 377 schizophrenic patients drawn from 39 university hospitals. After a wash-out period of 1 week, the schizophrenic patients were treated with risperidone for 8 weeks and evaluated at 5 points ; at baseline, and 1, 2, 4 and 8 weeks of treatment. The dose was increased from 2mg/day(1mg twice daily) to 6mg/day(3mg twice daily) during the first week and adjusted to a maximum of 16mg/day over the next 7 weeks according to the patient's clinical response. Medication to control extrapyramidal symptoms was permitted. The psychiatric and neurological status of the patients was assessed by PANSS, CGI, and ESRS scales. Results : 343(91%) of 377 patients completed the 8-week trial period. Clinical improvement, as defined by a 20% or more reduction in total PANSS score at end point, was shown by 81.3% of patients. The predictors of response to risperidone were associated older age, shorter duration of illness, fewer previous hospitalization. Risperidone had rapid onset of action ; a significant decrease of the total PANSS and three PANSS factor(positive, negative, general), and CGI was already noticed at the end of first week. For the ESRS, parkinsonism rating scores were significantly increased until week 4 comparing with baseline. Dystonia rating scores were significantly increased until week 1, and dyskinesia rating scores were not significantly changed during the study. Laboratory parameters including vital sign, EKG, hematological, and biochemical values showed no significant changes during the trial. Conclusions : This study suggests that risperidone is generally safe and effective against both the positive and negative symptoms in our group of patients.