1.Target-Enhanced Whole-Genome Sequencing Shows Clinical Validity Equivalent to Commercially Available Targeted Oncology Panel
Sangmoon LEE ; Jin ROH ; Jun Sung PARK ; Islam Oguz TUNCAY ; Wonchul LEE ; Jung-Ah KIM ; Brian Baek-Lok OH ; Jong-Yeon SHIN ; Jeong Seok LEE ; Young Seok JU ; Ryul KIM ; Seongyeol PARK ; Jaemo KOO ; Hansol PARK ; Joonoh LIM ; Erin CONNOLLY-STRONG ; Tae-Hwan KIM ; Yong Won CHOI ; Mi Sun AHN ; Hyun Woo LEE ; Seokhwi KIM ; Jang-Hee KIM ; Minsuk KWON
Cancer Research and Treatment 2025;57(2):350-361
Purpose:
Cancer poses a significant global health challenge, demanding precise genomic testing for individualized treatment strategies. Targeted-panel sequencing (TPS) has improved personalized oncology but often lacks comprehensive coverage of crucial cancer alterations. Whole-genome sequencing (WGS) addresses this gap, offering extensive genomic testing. This study demonstrates the medical potential of WGS.
Materials and Methods:
This study evaluates target-enhanced WGS (TE-WGS), a clinical-grade WGS method sequencing both cancer and matched normal tissues. Forty-nine patients with various solid cancer types underwent both TE-WGS and TruSight Oncology 500 (TSO500), one of the mainstream TPS approaches.
Results:
TE-WGS detected all variants reported by TSO500 (100%, 498/498). A high correlation in variant allele fractions was observed between TE-WGS and TSO500 (r=0.978). Notably, 223 variants (44.8%) within the common set were discerned exclusively by TE-WGS in peripheral blood, suggesting their germline origin. Conversely, the remaining subset of 275 variants (55.2%) were not detected in peripheral blood using the TE-WGS, signifying them as bona fide somatic variants. Further, TE-WGS provided accurate copy number profiles, fusion genes, microsatellite instability, and homologous recombination deficiency scores, which were essential for clinical decision-making.
Conclusion
TE-WGS is a comprehensive approach in personalized oncology, matching TSO500’s key biomarker detection capabilities. It uniquely identifies germline variants and genomic instability markers, offering additional clinical actions. Its adaptability and cost-effectiveness underscore its clinical utility, making TE-WGS a valuable tool in personalized cancer treatment.
2.Target-Enhanced Whole-Genome Sequencing Shows Clinical Validity Equivalent to Commercially Available Targeted Oncology Panel
Sangmoon LEE ; Jin ROH ; Jun Sung PARK ; Islam Oguz TUNCAY ; Wonchul LEE ; Jung-Ah KIM ; Brian Baek-Lok OH ; Jong-Yeon SHIN ; Jeong Seok LEE ; Young Seok JU ; Ryul KIM ; Seongyeol PARK ; Jaemo KOO ; Hansol PARK ; Joonoh LIM ; Erin CONNOLLY-STRONG ; Tae-Hwan KIM ; Yong Won CHOI ; Mi Sun AHN ; Hyun Woo LEE ; Seokhwi KIM ; Jang-Hee KIM ; Minsuk KWON
Cancer Research and Treatment 2025;57(2):350-361
Purpose:
Cancer poses a significant global health challenge, demanding precise genomic testing for individualized treatment strategies. Targeted-panel sequencing (TPS) has improved personalized oncology but often lacks comprehensive coverage of crucial cancer alterations. Whole-genome sequencing (WGS) addresses this gap, offering extensive genomic testing. This study demonstrates the medical potential of WGS.
Materials and Methods:
This study evaluates target-enhanced WGS (TE-WGS), a clinical-grade WGS method sequencing both cancer and matched normal tissues. Forty-nine patients with various solid cancer types underwent both TE-WGS and TruSight Oncology 500 (TSO500), one of the mainstream TPS approaches.
Results:
TE-WGS detected all variants reported by TSO500 (100%, 498/498). A high correlation in variant allele fractions was observed between TE-WGS and TSO500 (r=0.978). Notably, 223 variants (44.8%) within the common set were discerned exclusively by TE-WGS in peripheral blood, suggesting their germline origin. Conversely, the remaining subset of 275 variants (55.2%) were not detected in peripheral blood using the TE-WGS, signifying them as bona fide somatic variants. Further, TE-WGS provided accurate copy number profiles, fusion genes, microsatellite instability, and homologous recombination deficiency scores, which were essential for clinical decision-making.
Conclusion
TE-WGS is a comprehensive approach in personalized oncology, matching TSO500’s key biomarker detection capabilities. It uniquely identifies germline variants and genomic instability markers, offering additional clinical actions. Its adaptability and cost-effectiveness underscore its clinical utility, making TE-WGS a valuable tool in personalized cancer treatment.
3.Target-Enhanced Whole-Genome Sequencing Shows Clinical Validity Equivalent to Commercially Available Targeted Oncology Panel
Sangmoon LEE ; Jin ROH ; Jun Sung PARK ; Islam Oguz TUNCAY ; Wonchul LEE ; Jung-Ah KIM ; Brian Baek-Lok OH ; Jong-Yeon SHIN ; Jeong Seok LEE ; Young Seok JU ; Ryul KIM ; Seongyeol PARK ; Jaemo KOO ; Hansol PARK ; Joonoh LIM ; Erin CONNOLLY-STRONG ; Tae-Hwan KIM ; Yong Won CHOI ; Mi Sun AHN ; Hyun Woo LEE ; Seokhwi KIM ; Jang-Hee KIM ; Minsuk KWON
Cancer Research and Treatment 2025;57(2):350-361
Purpose:
Cancer poses a significant global health challenge, demanding precise genomic testing for individualized treatment strategies. Targeted-panel sequencing (TPS) has improved personalized oncology but often lacks comprehensive coverage of crucial cancer alterations. Whole-genome sequencing (WGS) addresses this gap, offering extensive genomic testing. This study demonstrates the medical potential of WGS.
Materials and Methods:
This study evaluates target-enhanced WGS (TE-WGS), a clinical-grade WGS method sequencing both cancer and matched normal tissues. Forty-nine patients with various solid cancer types underwent both TE-WGS and TruSight Oncology 500 (TSO500), one of the mainstream TPS approaches.
Results:
TE-WGS detected all variants reported by TSO500 (100%, 498/498). A high correlation in variant allele fractions was observed between TE-WGS and TSO500 (r=0.978). Notably, 223 variants (44.8%) within the common set were discerned exclusively by TE-WGS in peripheral blood, suggesting their germline origin. Conversely, the remaining subset of 275 variants (55.2%) were not detected in peripheral blood using the TE-WGS, signifying them as bona fide somatic variants. Further, TE-WGS provided accurate copy number profiles, fusion genes, microsatellite instability, and homologous recombination deficiency scores, which were essential for clinical decision-making.
Conclusion
TE-WGS is a comprehensive approach in personalized oncology, matching TSO500’s key biomarker detection capabilities. It uniquely identifies germline variants and genomic instability markers, offering additional clinical actions. Its adaptability and cost-effectiveness underscore its clinical utility, making TE-WGS a valuable tool in personalized cancer treatment.
4.Factors related to lung function outcomes in critically ill COVID-19 patients in South Korea
Tae Hun KIM ; Myung Jin SONG ; Sung Yoon LIM ; Yeon Joo LEE ; Young-Jae CHO
Acute and Critical Care 2024;39(1):100-107
New variants of the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic continue to emerge. However, little is known about the effect of these variants on clinical outcomes. This study evaluated the risk factors for poor pulmonary lung function test (PFT). Methods: The study retrospectively analyzed 87 patients in a single hospital and followed up by performing PFTs at an outpatient clinic from January 2020 to December 2021. COVID-19 variants were categorized as either a non-delta variant (November 13, 2020–July 6, 2021) or the delta variant (July 7, 2021–January 29, 2022). Results: The median age of the patients was 62 years, and 56 patients (64.4%) were male. Mechanical ventilation (MV) was provided for 52 patients, and 36 (41.4%) had restrictive lung defects. Forced vital capacity (FVC) and diffusion capacity of the lung for carbon monoxide (DLCO ) were lower in patients on MV. Male sex (odds ratio [OR], 0.228) and MV (OR, 4.663) were significant factors for decreased DLCO . The duration of MV was associated with decreased FVC and DLCO . However, the type of variant did not affect the decrease in FVC (P=0.750) and DLCO (P=0.639). Conclusions: Among critically ill COVID-19 patients, 40% had restrictive patterns with decreased DLCO . The reduction of PFT was associated with MV, type of variants.
5.Factors related to lung function outcomes in critically ill COVID-19 patients in South Korea
Tae Hun KIM ; Myung Jin SONG ; Sung Yoon LIM ; Yeon Joo LEE ; Young-Jae CHO
Acute and Critical Care 2024;39(1):100-107
New variants of the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic continue to emerge. However, little is known about the effect of these variants on clinical outcomes. This study evaluated the risk factors for poor pulmonary lung function test (PFT). Methods: The study retrospectively analyzed 87 patients in a single hospital and followed up by performing PFTs at an outpatient clinic from January 2020 to December 2021. COVID-19 variants were categorized as either a non-delta variant (November 13, 2020–July 6, 2021) or the delta variant (July 7, 2021–January 29, 2022). Results: The median age of the patients was 62 years, and 56 patients (64.4%) were male. Mechanical ventilation (MV) was provided for 52 patients, and 36 (41.4%) had restrictive lung defects. Forced vital capacity (FVC) and diffusion capacity of the lung for carbon monoxide (DLCO ) were lower in patients on MV. Male sex (odds ratio [OR], 0.228) and MV (OR, 4.663) were significant factors for decreased DLCO . The duration of MV was associated with decreased FVC and DLCO . However, the type of variant did not affect the decrease in FVC (P=0.750) and DLCO (P=0.639). Conclusions: Among critically ill COVID-19 patients, 40% had restrictive patterns with decreased DLCO . The reduction of PFT was associated with MV, type of variants.
6.Factors related to lung function outcomes in critically ill COVID-19 patients in South Korea
Tae Hun KIM ; Myung Jin SONG ; Sung Yoon LIM ; Yeon Joo LEE ; Young-Jae CHO
Acute and Critical Care 2024;39(1):100-107
New variants of the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic continue to emerge. However, little is known about the effect of these variants on clinical outcomes. This study evaluated the risk factors for poor pulmonary lung function test (PFT). Methods: The study retrospectively analyzed 87 patients in a single hospital and followed up by performing PFTs at an outpatient clinic from January 2020 to December 2021. COVID-19 variants were categorized as either a non-delta variant (November 13, 2020–July 6, 2021) or the delta variant (July 7, 2021–January 29, 2022). Results: The median age of the patients was 62 years, and 56 patients (64.4%) were male. Mechanical ventilation (MV) was provided for 52 patients, and 36 (41.4%) had restrictive lung defects. Forced vital capacity (FVC) and diffusion capacity of the lung for carbon monoxide (DLCO ) were lower in patients on MV. Male sex (odds ratio [OR], 0.228) and MV (OR, 4.663) were significant factors for decreased DLCO . The duration of MV was associated with decreased FVC and DLCO . However, the type of variant did not affect the decrease in FVC (P=0.750) and DLCO (P=0.639). Conclusions: Among critically ill COVID-19 patients, 40% had restrictive patterns with decreased DLCO . The reduction of PFT was associated with MV, type of variants.
7.Factors related to lung function outcomes in critically ill COVID-19 patients in South Korea
Tae Hun KIM ; Myung Jin SONG ; Sung Yoon LIM ; Yeon Joo LEE ; Young-Jae CHO
Acute and Critical Care 2024;39(1):100-107
New variants of the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic continue to emerge. However, little is known about the effect of these variants on clinical outcomes. This study evaluated the risk factors for poor pulmonary lung function test (PFT). Methods: The study retrospectively analyzed 87 patients in a single hospital and followed up by performing PFTs at an outpatient clinic from January 2020 to December 2021. COVID-19 variants were categorized as either a non-delta variant (November 13, 2020–July 6, 2021) or the delta variant (July 7, 2021–January 29, 2022). Results: The median age of the patients was 62 years, and 56 patients (64.4%) were male. Mechanical ventilation (MV) was provided for 52 patients, and 36 (41.4%) had restrictive lung defects. Forced vital capacity (FVC) and diffusion capacity of the lung for carbon monoxide (DLCO ) were lower in patients on MV. Male sex (odds ratio [OR], 0.228) and MV (OR, 4.663) were significant factors for decreased DLCO . The duration of MV was associated with decreased FVC and DLCO . However, the type of variant did not affect the decrease in FVC (P=0.750) and DLCO (P=0.639). Conclusions: Among critically ill COVID-19 patients, 40% had restrictive patterns with decreased DLCO . The reduction of PFT was associated with MV, type of variants.
8.Toxicological properties of Technekitty injection (Tc-99m) in diagnosing feline hyperthyroidism
Jae Cheong LIM ; So-Young LEE ; Eun Ha CHO ; Yu Mi JUNG ; Ki Hwan PARK ; Young Uk PARK ; Sung Soo NAM ; Tae Hoon LEE ; Jae Won LEE ; Yiseul CHOI ; Inki LEE ; Yeon CHAE ; Byeong-Teck KANG
Journal of Biomedical and Translational Research 2024;25(4):201-210
Following the previous study, which investigated the pharmacological properties of the Technekitty injection (Tc-99m), the toxicity of a single intravenous administration of the Technekittyinjection (Tc-99m) and the side effects that may occur at the diagnostic dose were confirmed.The Technekitty injection (Tc-99m) was administered intravenously once at a dose of 0, 0.67, 2.0, and 6.0 mCi/kg to 5 male and female rats per group. Mortality, general symptom obser-vation, and weight measurement were performed for 2 weeks, followed by observation of autopsy findings. There were no deaths, and no statistically significant weight change was observed. No abnormal systemic signs related to the Technekitty injection (Tc-99m) were observed. These results confirmed that Technekitty injection (Tc-99m) can be safely admin-istered intravenously at doses up to 6.0 mCi/kg. Additionally, technetium-99m at an average dose of 2 mCi (74 MBq) has been verified as a diagnostic dose without adverse effects, al-lowing the Technekitty injection (Tc-99m) to be used safely without side effects at this dosage.This study demonstrates that the Technekitty injection (Tc-99m) has a wide safety margin, supporting its potential for clinical application. Moreover, these findings align with the nonclin-ical safety standards for radiopharmaceuticals, reinforcing its utility in veterinary medicine.The Technekitty injection (Tc-99m) is expected to be applicable for clinical diagnosis as a vet-erinary drug in Korea.
9.Pharmacological properties of Technekitty injection (Tc-99m) in diagnosing feline hyperthyroidism
Jae Cheong LIM ; So-Young LEE ; Eun Ha CHO ; Yu Mi JUNG ; Ki Hwan PARK ; Young Uk PARK ; Sung Soo NAM ; Tae Hoon LEE ; Jae Won LEE ; Jisu SUN ; Hye Kyung CHUNG ; Yong Jin LEE ; Yeon CHAE ; Byeong-Teck KANG
Journal of Biomedical and Translational Research 2024;25(4):185-199
Thyroid scanning using technetium-99m ( 99mTc) is the gold standard for diagnosing feline hyperthyroidism. In cats with an overactive thyroid, a thyroid scan is the most appropriate imaging technique to detect and localize any hyperfunctional adenomatous thyroid tissue. In this study, the pharmacological properties of the Technekitty injection (Tc-99m), developed as a diagnostic agent for feline hyperthyroidism using 99mTc as an active ingredient, were tested in FRTL-5 thyroid follicular cell line and ICR mice. The percentage of cell uptake of the Tc-99m in FRTL-5 thyroid cells was 0.182 ± 0.018%, which was about 6 times higher compared to Clone 9 hepatocytes. This uptake decreased by 38.2% due to competitive inhibition by iodine (sodium iodide). In tissue distribution tests by using ICR mice, the highest distribution was observed in the liver, kidneys, spleen, lungs, and femur at 0.083 hours after administration, and this distribution decreased as the compound was excreted through the kidneys, the pri-mary excretory organ. Maximum distribution was confirmed at 1 hour in the small intestine, 6hours in the large intestine, and 2 hours in the thyroid gland. Additionally, the total amount excreted through urine and feces over 48 hours (2 days) was 78.80% of the injected dose, with 37.70% (47.84% of the total excretion) excreted through urine and 41.10% (52.16% of the total excretion) through feces. In conclusion, the Tc-99m has the same mechanism of action, potency, absorption, distribution, metabolism, and excretion characteristics as 99mTc used for feline hyperthyroidism in the United States, Europe, and other countries, because the Technekitty injection (Tc-99m) contains 99mTc as its sole active ingredient. Based on these results, the Technekitty injection (Tc-99m) is expected to be safely used in the clinical diagnosis of feline hyperthyroidism.
10.Occupation classification model based on DistilKoBERT: using the 5th and 6th Korean Working Condition Surveys
Tae-Yeon KIM ; Seong-Uk BAEK ; Myeong-Hun LIM ; Byungyoon YUN ; Domyung PAEK ; Kyung Ehi ZOH ; Kanwoo YOUN ; Yun Keun LEE ; Yangho KIM ; Jungwon KIM ; Eunsuk CHOI ; Mo-Yeol KANG ; YoonHo CHO ; Kyung-Eun LEE ; Juho SIM ; Juyeon OH ; Heejoo PARK ; Jian LEE ; Jong-Uk WON ; Yu-Min LEE ; Jin-Ha YOON
Annals of Occupational and Environmental Medicine 2024;36(1):e19-
Accurate occupation classification is essential in various fields, including policy development and epidemiological studies. This study aims to develop an occupation classification model based on DistilKoBERT. This study used data from the 5th and 6th Korean Working Conditions Surveys conducted in 2017 and 2020, respectively. A total of 99,665 survey participants, who were nationally representative of Korean workers, were included. We used natural language responses regarding their job responsibilities and occupational codes based on the Korean Standard Classification of Occupations (7th version, 3-digit codes). The dataset was randomly split into training and test datasets in a ratio of 7:3. The occupation classification model based on DistilKoBERT was fine-tuned using the training dataset, and the model was evaluated using the test dataset. The accuracy, precision, recall, and F1 score were calculated as evaluation metrics. The final model, which classified 28,996 survey participants in the test dataset into 142 occupational codes, exhibited an accuracy of 84.44%. For the evaluation metrics, the precision, recall, and F1 score of the model, calculated by weighting based on the sample size, were 0.83, 0.84, and 0.83, respectively. The model demonstrated high precision in the classification of service and sales workers yet exhibited low precision in the classification of managers. In addition, it displayed high precision in classifying occupations prominently represented in the training dataset. This study developed an occupation classification system based on DistilKoBERT, which demonstrated reasonable performance. Despite further efforts to enhance the classification accuracy, this automated occupation classification model holds promise for advancing epidemiological studies in the fields of occupational safety and health.

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