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Diagnostic evaluation of qRT-PCR-based kit and dPCR-based kit for COVID-19
Lee Cherl-Joon,Shin Wonseok,Mun Seyoung,Yu Minjae,Choi Young-Bong,김동희,한규동 한국유전학회 2021 Genes & Genomics Vol.43 No.11
Background Coronavirus disease of 2019 (COVID-19) is well known as a fatal disease, frst discovered at Wuhan in China, ranging from mild to death, such as shortness of breath and fever. Early diagnosis of COVID-19 is a crucial point in preventing global prevalence. Objective We aimed to evaluate the diagnostic competency and efciency with the Allplex™ 2019-nCoV Assay kit and the Dr. PCR 20 K COVID-19 Detection kit, designed based on the qRT-PCR and dPCR technologies, respectively. Methods A total of 30 negative and 20 COVID-19 positive specimens were assigned to the diagnostic test by using different COVID-19 diagnosis kits. Diagnostic accuracy was measured by statistical testing with sensitivity, specifcity, and co-efciency calculations. Results Comparing both diagnostic kits, we confrmed that the diagnostic results of 30 negative and 20 positive cases were the same pre-diagnostic results. The diagnostic statistics test results were perfectly matched with value (1). Cohen’s Kappa coefcient was demonstrated that the given kits in two diferent ways were “almost perfect” with value (1). In evaluating the detection capability, the dilutional linearity experiments substantiate that the Dr. PCR 20 K COVID-19 Detection kit could detect SARS-CoV-2 viral load at a concentration ten times lower than that of the Allplex™ 2019-nCoV Assay kit. Conclusions In this study, we propose that the dPCR diagnosis using LOAA dPCR could be a powerful method for COVID19 point-of-care tests requiring immediate diagnosis in a limited time and space through the advantages of relatively low sample concentration and small equipment size compared to conventional qRT-PCR.
Comparison of digital PCR platforms using the molecular marker
Cherl-Joon Lee,Wonseok Shin,Minsik Song,Seung-Shick Shin,Yujun Park,Kornsorn Srikulnath,Dong Hee Kim,Kyudong Han Korea Genome Organization 2023 Genomics & informatics Vol.21 No.2
Assays of clinical diagnosis and species identification using molecular markers are performed according to a quantitative method in consideration of sensitivity, cost, speed, convenience, and specificity. However, typical polymerase chain reaction (PCR) assay is difficult to quantify and have various limitations. In addition, to perform quantitative analysis with the quantitative real-time PCR (qRT-PCR) equipment, a standard curve or normalization using reference genes is essential. Within the last a decade, previous studies have reported that the digital PCR (dPCR) assay, a third-generation PCR, can be applied in various fields by overcoming the shortcomings of typical PCR and qRT-PCR assays. We selected Stilla Naica System (Stilla Technologies), Droplet Digital PCR Technology (Bio-Rad), and Lab on an Array Digital Real-Time PCR analyzer system (OPTOLANE) for comparative analysis among the various droplet digital PCR platforms currently in use commercially. Our previous study discovered a molecular marker that can distinguish Hanwoo species (Korean native cattle) using Hanwoo-specific genomic structural variation. Here, we report the pros and cons of the operation of each dPCR platform from various perspectives using this species identification marker. In conclusion, we hope that this study will help researchers to select suitable dPCR platforms according to their purpose and resources.
High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array
Lee, Haeun,Lee, Cherl-Joon,Kim, Dong Hee,Cho, Chun-Sung,Shin, Wonseok,Han, Kyudong Korea Genome Organization 2021 Genomics & informatics Vol.19 No.3
Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the Lab On An Array (LOAA) dPCR analyzer (Optolane) was launched last year. The LOAA dPCR is a semiconductor chip-based separation PCR type equipment. The LOAA dPCR includes Micro Electro Mechanical System that can be injected by partitioning the target gene into 56 to 20,000 wells. The amount of target gene per wells is digitized to 0 or 1 as the number of well gradually increases to 20,000 wells because its principle follows Poisson distribution, which allows the LOAA dPCR to perform precise absolute quantification. LOAA determined region of interest first prior to dPCR operation. To exclude invalid wells for the quantification, the LOAA dPCR has applied various filtering methods using brightness, slope, baseline, and noise filters. As the coronavirus disease 2019 has now spread around the world, needs for diagnostic equipment of point of care testing (POCT) are increasing. The LOAA dPCR is expected to be suitable for POCT diagnosis due to its compact size and high accuracy. Here, we describe the quantitative principle of the LOAA dPCR and suggest that it can be applied to various fields.
김철교(Cherl-Kyo Kim),하승범(Seung-Beom Ha),이준석(Joon-Suk Lee),최철훈(Chul-Hoon Choi) 대한설비공학회 2001 대한설비공학회 학술발표대회논문집 Vol.2001 No.-
기존의 대형 건물위주의 BAS(Building Automation System)를 중소형 건물에 적용할 수 있도록 새로운 개념의 건물자동화 시스템을 개발하였다. 기존의 BAS는 경제성 및 운영관리상의 어려움으로 널리 보급되지는 못했다. 본 연구개발에서는 BAS의 시스템 구성을 모듈화를 통하여 간소화 하고 필요한 기능만을 고려하였으며, 설비, 조명, 전력, 출입관리 시스템 상호간의 직접적인 연동이 가능하도록 하였다. 또한 운영관리의 효율화 및 기술지원이 가능하도록 인터넷을 이용하여 원격으로 시스템 설정, 진단 및 모니터링 기능을 구현할 수 있는 원격관리 시스템을 개발하였다.
Kim, Joon Mee,Sohn, Jin Hee,Cho, Mee-Yon,Kim, Woo Ho,Chang, Hee Kyung,Jung, Eun Sun,Kook, Myeong-Cherl,Jin, So-Young,Chae, Yang Seok,Park, Young Soo,Kang, Mi Seon,Kim, Hyunki,Lee, Jae Hyuk,Park, Do Yo Springer Japan 2016 GASTRIC CANCER Vol.19 No.4
<P><B>Background</B></P><P>Discrepancies in the clinicopathologic parameters pre- and post-endoscopic submucosal dissection (ESD) sometimes necessitate additional surgical resection. The aim of this study was to assess such discrepancies in clinicopathologic parameters before and after ESD in the context of reducing the risk of failure of curative ESD.</P><P><B>Methods</B></P><P>Data on 712 early gastric cancer patients were prospectively collected from 12 university hospitals nationwide. The inclusion criteria were differentiated carcinoma <3 cm in size, no ulceration, submucosal invasion <500 μm, and no metastasis. Clinicopathologic factors were compared retrospectively.</P><P><B>Results</B></P><P>The discrepancy rate was 20.1 % (148/737) and the most common cause of discrepancy was tumor size (64 cases, 8.7 %). Ulceration, undifferentiated histology, and SM2 invasion were found in 34 (4.6 %), 18 (2.4 %), and 51 cases (6.9 %), respectively. Lymphovascular invasion (LVI) was observed in 34 cases (4.6 %). Cases with lesions exceeding 3 cm in size showed more frequent submucosal invasion, an elevated gross morphology, and upper and middle locations (<I>p</I> < 0.05). In the cases with ulceration, depth of invasion (DOI) was deeper than in the cases without ulceration (<I>p</I> = 0.005). Differentiation was correlated with DOI and LVI (<I>p</I> = 0.021 and 0.007). DOI was correlated with tumor size, ulceration, differentiation, LVI, gross type, and location. There were statistically significant differences between mucosal cancer cases and submucosal cancer cases in tumor size, differentiation, ulceration, LVI, and location.</P><P><B>Conclusions</B></P><P>The overall discrepancy rate was 20.1 %. To reduce this rate, it is necessary to evaluate the DOI very cautiously, because it is correlated with other parameters. In particular, careful checking for SM-invasive cancer is required due to the high incidence of LVI irrespective of the depth of submucosal invasion.</P>
Shin Wonseok,Lee Cherl-Joon,Lee Yong-Moon,Choi Young-Bong,Mun Seyoung,Han Kyudong 한국유전학회 2022 Genes & Genomics Vol.44 No.5
Background: Since COVID-19 was declared the pandemic by the WHO, it has continued to spread. There is a need for rapid, efficient, and accurate diagnostic kits and techniques to control its spread. Objective: The diagnostic capability of the qRT-PCR-based Real-Q 2019-nCoV Detection Kit and dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit was compared and evaluated. Methods: Diagnostic tests for COVID-19 were performed using two different COVID-19 kits and 301 individual specimens with confirmed COVID-19 positive/negative at the government-accredited medical institution. Assessment of diagnostic capability was measured through diagnostic sensitivity, specificity, Cohen's Kappa coefficient, and dilutional linearity tests. Results: The COVID-19 diagnostic test results using two kits and 301 individual specimens perfectly matched the pre-diagnosis results of the medical institution. In addition, the measurement results of diagnostic sensitivity and specificity were "1", indicating high diagnostic capability. Cohen's Kappa coefficient value is "1", which means that the diagnosis concordance between the two kits is "Almost Perfect". As a result of dilutional linearity tests to evaluate their detection capability, both kits were measured with very high detection reliability. Conclusion: Here, we propose that the dPCR-based Dr. PCR™ Di20K COVID-19 Detection Kit has the advantages of the dPCR method reported in the previous study and is suitable for point-of-care testing (POCT) by overcoming the limitations of space, test time, cross-over contamination, and biosafety due to omitting RNA extraction process.
Ultrathin polycrystalline 6,13-Bis(triisopropylsilylethynyl)-pentacene films
Jung, Min-Cherl,Zhang, Dongrong,Nikiforov, Gueorgui O.,Lee, Michael V.,Joo Shin, Tae,Ahn, Docheon,Lee, Han-Koo,Baik, Jaeyoon,Shin, Hyun-Joon,Qi, Yabing American Institute of Physics 2015 Journal of Vacuum Science & Technology. A Vol.33 No.2
Bae, In-Ho,Na, Man-Gyun,Lee, Yoon-Joon,Park, Goon-Cherl Korean Nuclear Society 2009 Nuclear Engineering and Technology Vol.41 No.9
Knowing more about the Local Power Density (LPD) at the hottest part of a nuclear reactor core can provide more important information than knowledge of the LPD at any other position. The LPD at the hottest part needs to be estimated accurately in order to prevent the fuel rod from melting in a nuclear reactor. Support Vector Machines (SVMs) have successfully been applied in classification and regression problems. Therefore, in this paper, the power peaking factor, which is defined as the highest LPD to the average power density in a reactor core, was estimated by SVMs which use numerous measured signals of the reactor coolant system. The SVM models were developed by using a training data set and validated by an independent test data set. The SVM models' uncertainty was analyzed by using 100 sampled training data sets and verification data sets. The prediction intervals were very small, which means that the predicted values were very accurate. The predicted values were then applied to the first fuel cycle of the Yonggwang Nuclear Power Plant Unit 3. The root mean squared error was approximately 0.15%, which is accurate enough for use in LPD monitoring and for core protection that uses LPD estimation.
Jo, Min Jung,Park, Ji Yeon,Song, Joon Seon,Kook, Myeong-Cherl,Ryu, Keun Won,Cho, Soo-Jeong,Lee, Jun Ho,Nam, Byung-Ho,Hong, Eun Kyung,Choi, Il Ju,Kim, Young-Woo WJG Press 2015 WORLD JOURNAL OF GASTROENTEROLOGY Vol.21 No.2
<P>To evaluate the biopathologic features and clinical significance of nodal micrometastasis (MI) in early gastric cancer (EGC).</P>