• Genomics & Informatics
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• v.19 no.4
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• pp.41.1-41.10
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• 2021

In addition to mutations and copy number alterations, gene fusions are commonly identified in cancers. In thyroid cancer, fusions of important cancer-related genes have been commonly reported; however, extant panels do not cover all clinically important gene fusions. In this study, we aimed to develop a custom RNA-based sequencing panel to identify the key fusions in thyroid cancer. Our ThyChase panel was designed to detect 87 types of gene fusion. As quality control of RNA sequencing, five housekeeping genes were included in this panel. When we applied this panel for the analysis of fusions containing reference RNA (HD796), three expected fusions (EML4-ALK, CCDC6-RET, and TPM3-NTRK1) were successfully identified. We confirmed the fusion breakpoint sequences of the three fusions from HD796 by Sanger sequencing. Regarding the limit of detection, this panel could detect the target fusions from a tumor sample containing a 1% fusion-positive tumor cellular fraction. Taken together, our ThyChase panel would be useful to identify gene fusions in the clinical field.

• Journal of Biomedical Engineering Research
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• v.38 no.5
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• pp.271-276
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• 2017

Cancer biomarkers are using in the diagnosis, staging, prognosis and prediction of disease progression. But, there are not sufficiently profiled and validated in early detection and risk classification of prostate cancer. In this study, we have devoted to finding a panel of serum biomarkers that are able to detect the diagnosis of prostate cancer. The serum samples were consisted of 111 prostate cancer and 343 control samples and examined. Eleven biomarkers were constructed in this study, and then nine biomarkers were relevant to candidate biomarkers by using t test. Finally, four biomarkers, PSA, ApoA2, CYFRA21.1 and TTR, were selected as the prostate cancer biomarker panel, logistic regression was used to identify algorithms for diagnostic biomarker combinations(AUC = 0.9697). A panel of combination biomarkers is less invasive and could supplement clinical diagnostic accuracy.

• Genomics & Informatics
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• v.15 no.4
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• Journal of Gastric Cancer
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• v.19 no.1
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• pp.1-48
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• 2019

• Journal of Gastric Cancer
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• v.19 no.3
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• pp.372-373
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• 2019

• BMB Reports
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• v.54 no.7
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• pp.386-391
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• 2021

Owing to rapid advancements in NGS (next generation sequencing), genomic alteration is now considered an essential predictive biomarkers that impact the treatment decision in many cases of cancer. Among the various predictive biomarkers, tumor mutation burden (TMB) was identified by NGS and was considered to be useful in predicting a clinical response in cancer cases treated by immunotherapy. In this study, we directly compared the lab-developed-test (LDT) results by target sequencing panel, K-MASTER panel v3.0 and whole-exome sequencing (WES) to evaluate the concordance of TMB. As an initial step, the reference materials (n = 3) with known TMB status were used as an exploratory test. To validate and evaluate TMB, we used one hundred samples that were acquired from surgically resected tissues of non-small cell lung cancer (NSCLC) patients. The TMB of each sample was tested by using both LDT and WES methods, which extracted the DNA from samples at the same time. In addition, we evaluated the impact of capture region, which might lead to different values of TMB; the evaluation of capture region was based on the size of NGS and target sequencing panels. In this pilot study, TMB was evaluated by LDT and WES by using duplicated reference samples; the results of TMB showed high concordance rate (R² = 0.887). This was also reflected in clinical samples (n = 100), which showed R² of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated that the LDT panel identified a relatively higher number of mutations. It was feasible to calculate TMB with LDT panel, which can be useful in clinical practice. Furthermore, a customized approach must be developed for calculating TMB, which differs according to cancer types and specific clinical settings.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.23
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• pp.10525-10529
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• 2015

Objective: To investigate the relationship between the perception of cancer risk and likelihood of having undergone cancer screening. Materials and Methods: We used data from the Korean Health Panel Survey from December 2011 onward. Of 3,390 patients who visited a hospital during the previous year, we included data from 2,466 individuals; 924 samples were excluded due to missing data. Logistic regression analysis and the chi square test were used to investigate the association between perceived cancer risk and the likelihood of having undergone cancer screening. Results: For patients who perceived their risk of developing cancer during the next 10 years to be 30-40%, the odds ratio was increased 1.65 fold (95%CI: 1.223, 2.234) compared with those who perceived their risk to be almost zero. Although the difference was not statistically significant, perceiving cancer risk as either extremely low or extremely high appears to be associated with a reduced likelihood of having undergone cancer screening, resulting in an inverted U-shaped relationship. Conclusions: Physicians and researchers should be aware of the importance of the affective component of risk perception. Policies addressing the influence of cancer risk perception should be implemented in South Korea and worldwide.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2619-2624
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• 2016

Background: Cancer is a worldwide health problem. Arabic countries are also concerned and the burden linked to the pain related to cancer is dsiquieting. The aim of this study is to set the panel of valid tools for assessing the multiple dimensions of pain in arabic speaking countries. Materials and Methods: A systematic review on PubMed, Scopus, and Science Direct databases was conducted using as key words cancer, pain and arabic speaking population. The content of 51 articles was studied and nine articles were retained for their relevance for the issue. Results: We founf eight different questionnaires. MSAS-Leb, EORTC-C30, EORTC-BR23, MDASI, FLIC, and COOP/WONCA are dedicated to physical and psychological dimensions of pain. BPI is centered on direct items for measuring pain accurately. ABQ-II is the unique tool focusing on barriers to cancer pain control. All tools are confirmed valid and reliable in the context studied for assessing pain and disconfort linked to cancer. Conclusions: This panel of questionnaires covers all relevant aims for assessing pain in diferent arabic speaking countries with the recommendation of a cultural adaptation to local arabic languages.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2713-2717
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• 2014

Background: Cancer imposes significant economic challenges for individuals, families, and society. Households of cancer patients often experience income loss due to change in job status and/or excessive medical expenses. Thus, we examined whether changes in economic status for such households is affected by catastrophic health expenditures. Materials and Methods: We used the Korea Health Panel Survey (KHPS) Panel $1^{st}-4^{th}$ (2008-2011 subjects) data and extracted records from 211 out of 5,332 households in the database for this study. To identify factors associated with catastrophic health expenditures and, in particular, to examine the relationship between change in economic status and catastrophic health expenditures, we conducted a generalized linear model analysis. Results: Among 211 households with cancer patients, 84 (39.8%) experienced catastrophic health expenditures, while 127 (40.2%) did not show evidence of catastrophic medical costs. If a change in economic status results from a change in job status for head of household (job loss), these households are more likely to incur catastrophic health expenditure than households who have not experienced a change in job status (odds ratios (ORs)=2.17, 2.63, respectively). A comparison between households with a newly-diagnosed patient versus households with patients having lived with cancer for one or two years, showed the longer patients had cancer, the more likely their households incurred catastrophic medical costs (OR=1.78, 1.36, respectively). Conclusions: Change in economic status of households in which the cancer patient was the head of household was associated with a greater likelihood that the household would incur catastrophic health costs. It is imperative that the Korean government connect health and labor policies in order to develop economic programs to assist households with cancer patients.

• Journal of Korean Medical Science
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• v.33 no.53
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• pp.342.1-342.6
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• 2018

We validated the diagnostic performance of a previously developed blood-based 7-protein biomarker panel, $AptoDetect^{TM}$-Lung (Aptamer Sciences Inc., Pohang, Korea) using modified aptamer-based proteomic technology for lung cancer detection. Non-small cell lung cancer (NSCLC), 200 patients and benign nodule controls, 200 participants were enrolled. In a high-risk population corresponding to ${\geq}55years$ of age and ${\geq}30pack-years$, the diagnostic performance was improved, showing 73.3% sensitivity and 90.5% specificity with an area under the curve of 0.88. $AptoDetect^{TM}$-Lung (Aptamer Sciences Inc.) offers the best validated performance to discriminate NSCLC from benign nodule controls in a high-risk population and could play a complementary role in lung cancer screening.