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.Exploratory Clinical Trial of a Depression Diagnostic Software That Integrates Stress Biomarkers and Composite Psychometrics
Sooah JANG ; In-Young KIM ; Sun-Woo CHOI ; Anna LEE ; Ju-Yeal LEE ; Hyunkyung SHIN ; Junwoo LEE ; Mikyeong LEE ; Kyoung-Ryul LEE ; Saeeun JUNG ; Jin Sun RYU ; Jihee OH ; Manjae KWON ; Joohan KIM ; Ryunsup AHN ; Young-Chul JUNG ; Jeong-Ho SEOK
Psychiatry Investigation 2024;21(3):230-241
Objective:
This study evaluated the clinical effectiveness of Minds.NAVI, a depression screening kit combining psychometric measures and stress hormone biomarkers, in a prospective clinical trial. The objective was to assess its potential as a depression screening tool and investigate the associations between psychological assessments, salivary hormone staging, and depression severity.
Methods:
Thirty-five participants with major depressive disorder and 12 healthy controls (HCs) were included. The Minds.NAVI software, utilizing the PROtective and Vulnerable factors battEry Test (PROVE) and salivary cortisol/dehydroepiandrosterone (DHEA) analysis, was employed. The PROVE test is a comprehensive self-report questionnaire that assesses depressive symptoms, suicide risk, attachment style, adverse childhood experiences, mentalization capacity, and resilience. In addition, salivary cortisol and DHEA levels were measured to evaluate the functional stage of the hypothalamic–pituitary–adrenal (HPA) axis.
Results:
Minds.NAVI exhibited 100% sensitivity, 91.7% specificity, and 97.9% accuracy in distinguishing depression from HCs within an exploratory small group. Salivary stress hormone phases showed changes with depression stage (p=0.030), and the proportion of patients with “adrenal exhaustion stage” was higher in the moderate/severe depression group (p=0.038). Protective/vulnerable factors differed significantly between controls and depressed groups (p<0.001). Cortisol awakening response inversely correlated with depressive symptom severity (r=-0.31, p=0.034).
Conclusion
This study suggested possible clinical effectiveness of Minds.NAVI, a depression screening tool that integrates psychometric measures and stress hormone biomarkers. The findings support the potential association between depression, chronic stress, and HPA axis hyporesponsiveness.
5.Safety and Efficacy of Everolimus-Eluting Bioresorbable Vascular Scaffold Versus Second-Generation Drug-Eluting Stents in Real-World Practice
Joo Myung LEE ; Hyun Sung JOH ; Ki Hong CHOI ; David HONG ; Taek Kyu PARK ; Jeong Hoon YANG ; Young Bin SONG ; Jin-Ho CHOI ; Seung-Hyuk CHOI ; Jin-Ok JEONG ; Jong-Young LEE ; Young Jin CHOI ; Jei-Keon CHAE ; Seung-Ho HUR ; Jang-Whan BAE ; Ju-Hyeon OH ; Kook-Jin CHUN ; Hyun-Joong KIM ; Byung Ryul CHO ; Doosup SHIN ; Seung Hun LEE ; Doyeon HWANG ; Hyun-Jong LEE ; Ho-Jun JANG ; Hyun Kuk KIM ; Sang Jin HA ; Eun-Seok SHIN ; Joon-Hyung DOH ; Joo-Yong HAHN ; Hyeon-Cheol GWON ; On behalf of the SMART-REWARD Investigators
Journal of Korean Medical Science 2023;38(5):e34-
Background:
The risk of device thrombosis and device-oriented clinical outcomes with bioresorbable vascular scaffold (BVS) was reported to be significantly higher than with contemporary drug-eluting stents (DESs). However, optimal device implantation may improve clinical outcomes in patients receiving BVS. The current study evaluated mid-term safety and efficacy of Absorb BVS with meticulous device optimization under intravascular imaging guidance.
Methods:
The SMART-REWARD and PERSPECTIVE-PCI registries in Korea prospectively enrolled 390 patients with BVS and 675 patients with DES, respectively. The primary endpoint was target vessel failure (TVF) at 2 years and the secondary major endpoint was patientoriented composite outcome (POCO) at 2 years.
Results:
Patient-level pooled analysis evaluated 1,003 patients (377 patients with BVS and 626 patients with DES). Mean scaffold diameter per lesion was 3.24 ± 0.30 mm in BVS group.Most BVSs were implanted with pre-dilatation (90.9%), intravascular imaging guidance (74.9%), and post-dilatation (73.1%) at proximal to mid segment (81.9%) in target vessel.Patients treated with BVS showed comparable risks of 2-year TVF (2.9% vs. 3.7%, adjusted hazard ratio [HR], 1.283, 95% confidence interval [CI], 0.487–3.378, P = 0.615) and 2-year POCO (4.5% vs. 5.9%, adjusted HR, 1.413, 95% CI, 0.663–3.012,P = 0.370) than those with DES. The rate of 2-year definite or probable device thrombosis (0.3% vs. 0.5%, P = 0.424) was also similar. The sensitivity analyses consistently showed comparable risk of TVF and POCO between the 2 groups.
Conclusion
With meticulous device optimization under imaging guidance and avoidance of implantation in small vessels, BVS showed comparable risks of 2-year TVF and device thrombosis with DES.
6.A case of acute kidney injury caused by dapsone-induced methemoglobinemia in a patient with chronic kidney disease
Minsoo KIM ; Su Ik KIM ; Jeong Ryul JO ; Ju Hwan OH ; A Young CHO ; Kwang Young LEE ; In O SUN
Journal of the Korean Society of Emergency Medicine 2023;34(4):379-382
Methemoglobinemia (MetHb), which is characterized by an increased methemoglobin level, is a rare but potentially fatal disorder caused by congenital enzyme deficiencies or exposure to oxidizing agents, including dapsone. Elevation in the methemoglobin level impairs the oxygen-carrying capacity of hemoglobin, produces functional anemia, and induces tissue hypoxia. Such hypoxia results in microcirculation injury and hypoperfusion in the tissue and organs, including the kidney, and is a risk factor for acute kidney injury (AKI). This paper reports a case of AKI caused by dapsone-induced MetHb in a patient with chronic kidney disease, in which the patient ingested approximately 1,500 mg of dapsone in a suicide attempt, which was treated with aggressive management, including methylene blue, ascorbic acid, and transfusion.
7.Phosphodiesterase-5 Inhibitor Attenuates Anxious Phenotypes and Movement Disorder Induced by Mild Ischemic Stroke in Rats
Yeon Hee YU ; Seong-Wook KIM ; Juhyeon KANG ; Yejin SONG ; Hyuna IM ; Seo Jeong KIM ; Dae Young YOO ; Man-Ryul LEE ; Dae-Kyoon PARK ; Jae Sang OH ; Duk-Soo KIM
Journal of Korean Neurosurgical Society 2022;65(5):665-679
Objective:
: Patients with mild ischemic stroke experience various sequela and residual symptoms, such as anxious behavior and deficits in movement. Few approaches have been proved to be effective and safe therapeutic approaches for patients with mild ischemic stroke by acute stroke. Sildenafil (SIL), a phosphodiesterase-5 inhibitor (PDE5i), is a known remedy for neurodegenerative disorders and vascular dementia through its angiogenesis and neurogenesis effects. In this study, we investigated the efficacy of PDE5i in the emotional and behavioral abnormalities in rats with mild ischemic stroke.
Methods:
: We divided the rats into four groups as follows (n=20, respectively) : group 1, naïve; group 2, middle cerebral artery occlusion (MCAo30); group 3, MCAo30+SIL-pre; and group 4, MCAo30+SIL-post. In the case of drug administration groups, single dose of PDE5i (sildenafil citrate, 20 mg/kg) was given at 30-minute before and after reperfusion of MCAo in rats. After surgery, we investigated and confirmed the therapeutic effect of sildenafil on histology, immunofluorescence, behavioral assays and neural oscillations.
Results:
: Sildenafil alleviated a neuronal loss and reduced the infarction volume. And results of behavior task and immunofluorescence shown possibility that anti-inflammation process and improve motor deficits sildenafil treatment after mild ischemic stroke. Furthermore, sildenafil treatment attenuated the alteration of theta-frequency rhythm in the CA1 region of the hippocampus, a known neural oscillatory marker for anxiety disorder in rodents, induced by mild ischemic stroke.
Conclusion
: PDE5i as effective therapeutic agents for anxiety and movement disorders and provide robust preclinical evidence to support the development and use of PDE5i for the treatment of mild ischemic stroke residual disorders.
8.Birt-Hogg-Dubé Syndrome Associated with a Renal Tumor
Su Jin OH ; Ki Eun HWANG ; Eun Taik JEONG ; Hak Ryul KIM ; Keum Ha CHOI ; Dae Woong RYU
Korean Journal of Medicine 2019;94(4):379-382
Birt-Hogg-Dubé syndrome (BHD) is a rare autosomal dominant disorder characterized by the formation of hair follicle tumors, kidney tumors, and pulmonary cysts with recurrent spontaneous pneumothorax. A 44-year-old woman visited Wonkwang University Hospital with mild dyspnea. A chest X-ray on admission revealed pneumothorax in both lung fields. Chest computed tomography (CT) revealed both pneumothorax and multiple, irregularly shaped, variable-sized cysts in both lung fields. Upon physical examination, white dome-shaped papules were observed on the face. Histological examination of the skin lesion confirmed fibrofolliculoma, and genetic studies revealed a folliculin gene mutation. Abdominal CT revealed a 1-cm small solid renal mass at the lower pole of the right kidney. We surgically removed the renal tumor, and a histological diagnosis of oncocytoma was made. Here, we report a case of BHD that demonstrated all three clinical manifestations; this is the first case report of its kind in Korea.
9.Birt-Hogg-Dubé Syndrome Associated with a Renal Tumor
Su Jin OH ; Ki Eun HWANG ; Eun Taik JEONG ; Hak Ryul KIM ; Keum Ha CHOI ; Dae Woong RYU
Korean Journal of Medicine 2019;94(4):379-382
Birt-Hogg-Dubé syndrome (BHD) is a rare autosomal dominant disorder characterized by the formation of hair follicle tumors, kidney tumors, and pulmonary cysts with recurrent spontaneous pneumothorax. A 44-year-old woman visited Wonkwang University Hospital with mild dyspnea. A chest X-ray on admission revealed pneumothorax in both lung fields. Chest computed tomography (CT) revealed both pneumothorax and multiple, irregularly shaped, variable-sized cysts in both lung fields. Upon physical examination, white dome-shaped papules were observed on the face. Histological examination of the skin lesion confirmed fibrofolliculoma, and genetic studies revealed a folliculin gene mutation. Abdominal CT revealed a 1-cm small solid renal mass at the lower pole of the right kidney. We surgically removed the renal tumor, and a histological diagnosis of oncocytoma was made. Here, we report a case of BHD that demonstrated all three clinical manifestations; this is the first case report of its kind in Korea.
Adenoma, Oxyphilic
;
Adult
;
Birt-Hogg-Dube Syndrome
;
Diagnosis
;
Dyspnea
;
Estrone
;
Female
;
Hair Follicle
;
Humans
;
Kidney
;
Kidney Neoplasms
;
Korea
;
Lung
;
Physical Examination
;
Pneumothorax
;
Skin
;
Thorax
;
Tomography, X-Ray Computed
10.Computed tomography morphologic features of pulmonary adenocarcinoma with brain/bone metastasis.
Ki Eun HWANG ; Su Jin OH ; Chul PARK ; Se Jeong JEON ; Jeong Mi LEE ; Byong Ki CHA ; Kwon Ha YOON ; Eun Taik JEONG ; Hak Ryul KIM
The Korean Journal of Internal Medicine 2018;33(2):340-346
BACKGROUND/AIMS: Brain and bone metastases are common in patients with lung cancer. The development of metastasis is associated with poor survival in lung cancer patients. Although tumor morphologic features on radiographs are routinely assessed for differentiation between benign and malignant lung nodules, they are not used to predict metastasis. We assessed morphologic features of pulmonary adenocarcinomas with brain/bone metastasis on computed tomography (CT) to identify related factors for metastasis. METHODS: We performed a retrospective analysis of initial chest CT findings (size, type of contour, percentage of necrosis, enhancement, presence or absence of calcification, and air cavity) from 2009 to 2010 of patients with brain or bone metastasis and compared the findings with those of patients without metastases. RESULTS: In total, 128 patients were included (78 men, 52 women; mean age 69 years; range, 36 to 87). Nineteen patients had brain metastases and 32 had bone metastases. Morphologic features associated with brain metastasis included size ≥ 50 mm (odds ratio [OR], 3.37; 95% confidence interval [CI], 1.24 to 9.17; p = 0.013), necrosis ≥ 30% (OR, 4.51; 95% CI, 1.62 to 12.55; p =0.002), and presence of calcification (OR, 3.97; 95% CI, 1.16 to 13.55; p = 0.035). Morphologic features associated with bone metastasis included necrosis ≥ 30% (OR, 4.639; 95% CI, 1.98 to 10.82; p < 0.001) and T 3 to 4 stage (OR, 2.53; 95% CI, 1.07 to 6.00; p = 0.031). CONCLUSIONS: We found that necrosis ≥ 30% was associated with pulmonary adenocarcinoma with brain and bone metastasis at initial chest CT morphologic feature. To validate these results, further research should be conducted.
Adenocarcinoma*
;
Brain
;
Female
;
Humans
;
Lung
;
Lung Neoplasms
;
Male
;
Necrosis
;
Neoplasm Metastasis*
;
Retrospective Studies
;
Tomography, X-Ray Computed

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