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Lee H, Chae SW, Cho SI, Lee JS, Kim MJ, Seong MW. Utility of Next-Generation Sequencing-Based Chimerism Analysis for Early Relapse Prediction following Allogenic Hematopoietic Cell Transplantation. Int J Mol Sci 2024; 25:2811. [PMID: 38474058 DOI: 10.3390/ijms25052811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Chimerism monitoring following allogeneic hematopoietic cell transplantation (HCT) plays a pivotal role in evaluating engraftment status and identifying early indicators of relapse. Recent advancements in next-generation sequencing (NGS) technology have introduced AlloSeq HCT as a more sensitive alternative to short tandem repeat (STR) analysis. This study aimed to compare AlloSeq HCT with STR, focusing on the prediction of early relapse post-allogeneic HCT. Chimerism levels in 29 HCT recipients were assessed using both STR and NGS, employing a total of 125 whole blood or bone marrow aspirate samples (68 post-HCT and 57 pre-HCT samples from recipients or donors). AlloSeq HCT exhibited high concordance with STR and demonstrated the potential for early detection of chimeric changes, particularly at extremely low levels. The combined advantages of high sensitivity and automated data analysis offered by AlloSeq HCT substantiate its clinical adoption for effective chimerism monitoring.
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Affiliation(s)
- Heerah Lee
- Department of Laboratory Medicine, Chosun University Hospital, Gwangju 61453, Republic of Korea
| | - Seung-Won Chae
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Moon-Woo Seong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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2
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Kim MJ, Kim B, Lee H, Lee JS, Chae SW, Shin HS, Cho SI, Kim SY, Moon J, Lim BC, Ko JM, Chae JH, Park SS, Seong MW. The Korean Genetic Diagnosis Program for Rare Disease Phase II: outcomes of a 6-year national project. Eur J Hum Genet 2023; 31:1147-1153. [PMID: 37414863 PMCID: PMC10545669 DOI: 10.1038/s41431-023-01415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/28/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023] Open
Abstract
The Korean Genetic Diagnosis Program for Rare Disease (KGDP) enrolled 1890 patients with rare diseases between March 2017 and October 2022. Children and adolescents accounted for the majority of the patients, and systemic disease was the most common presenting symptom. The exome-based virtual disease-specific multigene panel was the most frequently used analytical method, with an overall diagnostic yield of 33.3%. A total of 629 positive cases were diagnosed, involving 297 genes. All 297 genes identified in these cases were confirmed to be known genes listed in the OMIM database. The nationwide KGDP network and its cooperation with the Korean Undiagnosed Diseases Program (KUDP) provide a more comprehensive genetic analysis of undiagnosed cases. The partnership between the KGDP and KUDP has the potential to improve the diagnosis and treatment options for patients. In conclusion, KGDP serves as the primary access point or gateway to KUDP.
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Affiliation(s)
- Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Heerah Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Won Chae
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jangsup Moon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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3
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Lee S, Sun CH, Jang H, Kim D, Yoon SS, Koh Y, Na SC, Cho SI, Kim MJ, Seong MW, Byun JM, Yun H. ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application. BMC Bioinformatics 2023; 24:62. [PMID: 36823555 PMCID: PMC9951415 DOI: 10.1186/s12859-023-05173-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
Internal tandem duplication (ITD) of the FMS-like tyrosine kinase (FLT3) gene is associated with poor clinical outcomes in patients with acute myeloid leukemia. Although recent methods for detecting FLT3-ITD from next-generation sequencing (NGS) data have replaced traditional ITD detection approaches such as conventional PCR or fragment analysis, their use in the clinical field is still limited and requires further information. Here, we introduce ITDetect, an efficient FLT3-ITD detection approach that uses NGS data. Our proposed method allows for more precise detection and provides more detailed information than existing in silico methods. Further, it enables FLT3-ITD detection from exome sequencing or targeted panel sequencing data, thereby improving its clinical application. We validated the performance of ITDetect using NGS-based and experimental ITD detection methods and successfully demonstrated that ITDetect provides the highest concordance with the experimental methods. The program and data underlying this study are available in a public repository.
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Affiliation(s)
- Sungyoung Lee
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XCenter for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Choong-Hyun Sun
- GenomeOpinion Inc., 117-3 Hoegiro, Dongdaemoon-gu, Seoul, Republic of Korea
| | - Heejun Jang
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Daeyoon Kim
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Youngil Koh
- grid.31501.360000 0004 0470 5905Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea ,grid.412484.f0000 0001 0302 820XDepartment of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seung Chan Na
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Im Cho
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- grid.412484.f0000 0001 0302 820XDepartment of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- grid.412484.f0000 0001 0302 820XDepartment of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ja Min Byun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea. .,Center for Precision Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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4
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Lee JS, Yun KW, Jeong H, Kim B, Kim MJ, Park JH, Shin HS, Oh HS, Sung H, Song MG, Cho SI, Kim SY, Kang CK, Choe PG, Park WB, Kim NJ, Oh MD, Choi EH, Park S, Kim TS, Lee JH, Sung H, Park SS, Seong MW. SARS-CoV-2 shedding dynamics and transmission in immunosuppressed patients. Virulence 2022; 13:1242-1251. [PMID: 35891618 PMCID: PMC9336477 DOI: 10.1080/21505594.2022.2101198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern have been emerging. However, knowledge of temporal and spatial dynamics of SARS-CoV-2 is limited. This study characterized SARS-CoV-2 evolution in immunosuppressed patients with long-term SARS-CoV-2 shedding for 73–250 days, without specific treatment. We conducted whole-genome sequencing of 27 serial samples, including 26 serial samples collected from various anatomic sites of two patients and the first positive sample from patient 2‘s mother. We analysed the intrahost temporal dynamics and genomic diversity of the viral population within different sample types. Intrahost variants emerging during infection showed diversity between individual hosts. Remarkably, N501Y, P681R, and E484K, key substitutions within spike protein, emerged in vivo during infection and became the dominant population. P681R, which had not yet been detected in the publicly available genome in Korea, appeared within patient 1 during infection. Mutually exclusive substitutions at residues R346 (R346S and R346I) and E484 (E484K and E484A) of spike protein and continuous turnover of these substitutions occurred. Unique genetic changes were observed in urine samples. A household transmission from patient 2 to his mother, at least 38 days after the diagnosis, was characterized. Viruses may differently mutate and adjust to the host selective pressure, which could enable the virus to replicate efficiently for fitness in each host. Intrahost variants could be candidate variants likely to spread to the population eventually. Our findings may provide new insights into the dynamics of SARS-CoV-2 in response to interactions between the virus and host.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ki Wook Yun
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyeonju Jeong
- Department of Internal Medicine, Gyeonggi Provincial Medical Center, Ansung Hospital, Anseong Gyeonggi-do, Republic of Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyeon Sae Oh
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hobin Sung
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Myung Gi Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seungman Park
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hee Lee
- Department of Haematology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
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5
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Lee JS, Han Y, Yun WG, Kwon W, Kim H, Jeong H, Seo MS, Park Y, Cho SI, Kim H, Kim JY, Seong MW, Jang JY, Park SS. Parallel Analysis of Pre- and Postoperative Circulating Tumor DNA and Matched Tumor Tissues in Resectable Pancreatic Ductal Adenocarcinoma: A Prospective Cohort Study. Clin Chem 2022; 68:1509-1518. [PMID: 36177751 DOI: 10.1093/clinchem/hvac153] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is a promising biomarker for early tumor detection and minimal residual disease (MRD) assessment in early-stage cancer, but quantifying minute amounts of ctDNA is challenging and well-designed studies on ctDNA in early-stage cancer are still lacking. Here, we adapted a sensitive next-generation sequencing (NGS) technology and performed parallel analysis of pre- and postoperative ctDNA and matched tumor tissues in a prospective cohort of patients with resectable pancreatic ductal adenocarcinoma (PDAC). METHODS In total, 70 consecutive patients undergoing curative resection for resectable PDAC were enrolled. We performed integrated digital error suppression-enhanced cancer personalized profiling by deep sequencing NGS of triple-matched samples (pre/postoperative plasma cell-free DNA [cfDNA], tumor tissue, and genomic DNA) targeting 77 genes. RESULTS Preoperative ctDNA was detected in 37.7% of the evaluable patients, with a median variant allele frequency of 0.09%. Twelve additional oncogenic mutations were detected exclusively in preoperative ctDNA but not in tissue. When quantitative concentrations of ctDNA were estimated in haploid genome equivalents per milliliter (hGE/mL), the risk of early recurrence was high in patients with postoperative ctDNA >1 hGE/mL. cfDNA variants from 24.5% of patients had features compatible with clonal hematopoiesis. CONCLUSIONS An optimized NGS approach might add value beyond tissue analysis through the highly sensitive detection of minute amounts of ctDNA in resectable PDAC. Postoperative ctDNA concentration could be a tool for MRD assessment. Moreover, parallel analyses of matched tissues and leukocytes might be required to accurately detect clinically relevant ctDNA.
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Affiliation(s)
- Jee Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngmin Han
- Department of Surgery and Cancer Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Won Gun Yun
- Department of Surgery and Cancer Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Wooil Kwon
- Department of Surgery and Cancer Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hongbeom Kim
- Department of Surgery and Cancer Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyeonju Jeong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Myoung-Seock Seo
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yongsook Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Haeryoung Kim
- Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jin-Young Jang
- Department of Surgery and Cancer Research Institute, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
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6
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Yang D, Cho S, Cho SI, Kim M, Seong MW, Park SS. Genetic mutation spectrum of pantothenate kinase-associated neurodegeneration expanded by breakpoint sequencing in pantothenate kinase 2 gene. Orphanet J Rare Dis 2022; 17:111. [PMID: 35246191 PMCID: PMC8896100 DOI: 10.1186/s13023-022-02251-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neurodegeneration with brain iron accumulation describes a group of rare heterogeneous progressive neurodegenerative disorders characterized by excessive iron accumulation in the basal ganglia region. Pantothenate kinase-associated neurodegeneration (PKAN) is a major form of this disease. RESULTS A total of 7 unrelated patients were diagnosed with PKAN in a single tertiary center from August 2009 to February 2018. Ten variants in PANK2 including three novel sequence variants and one large exonic deletion were detected. Sequencing of the breakpoint was performed to predict the mechanism of large deletion and AluSx3 and AluSz6 were found with approximately 97.3% sequence homology. CONCLUSION The findings support the disease-causing role of PANK2 and indicate the possibility that exonic deletion of PANK2 found in PKAN is mediated through Alu-mediated homologous recombination.
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Affiliation(s)
- Dahae Yang
- Department of Laboratory Medicine, Kosin Gospel University Hospital, Busan, Korea
| | - Sanghyun Cho
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Manjin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea. .,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.
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7
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Kim B, Park Y, Cho SI, Kim MJ, Chae JH, Kim JY, Seong MW, Park SS. Clinical Utility of Methylation-Specific Multiplex Ligation-Dependent Probe Amplification for the Diagnosis of Prader-Willi Syndrome and Angelman Syndrome. Ann Lab Med 2022; 42:79-88. [PMID: 34374352 PMCID: PMC8368237 DOI: 10.3343/alm.2022.42.1.79] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/17/2020] [Accepted: 07/06/2021] [Indexed: 12/17/2022] Open
Abstract
Background Prader–Willi syndrome (PWS) and Angelman syndrome (AS) are genomic imprinting disorders that are mainly caused by a deletion on 15q11-q13, the uniparental disomy of chromosome 15, or an imprinting defect. We evaluated the utility of methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) as a diagnostic tool and for demonstrating the relationship between molecular mechanisms and clinical presentation. Methods We performed MS-MLPA using DNA samples from 93 subjects (45 PWS, 24 AS, and 24 non-PWS/AS controls) who had previously undergone MS-PCR for the diagnosis of PWS/AS. We compared the results of both assays, and patients’ clinical phenotypes were reviewed retrospectively. Results MS-MLPA showed a 100% concordance rate with MS-PCR. Among the 45 PWS patients, 26 (57.8%) had a deletion of 15q11-q13, and the others (42.2%) had uniparental disomy 15 or an imprinting defect. Among the 24 AS patients, 16 (66.7%) had a deletion of 15q11-q13, 7 AS patients (29.2%) had uniparental disomy 15 or an imprinting defect, and one AS patient (4.2%) showed an imprinting center deletion. Conclusions MS-MLPA has clinical utility for the diagnosis of PWS/AS, and it is superior to MS-PCR in that it can identify the molecular mechanism underlying the disease.
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Affiliation(s)
- Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yongsook Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical research Institute, Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical research Institute, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical research Institute, Seoul National University Hospital, Seoul, Korea
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8
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Kim MJ, Lee S, Yun H, Cho SI, Kim B, Lee JS, Chae JH, Sun C, Park SS, Seong MW. Consistent count region-copy number variation (CCR-CNV): an expandable and robust tool for clinical diagnosis of copy number variation at the exon level using next-generation sequencing data. Genet Med 2021; 24:663-672. [PMID: 34906491 DOI: 10.1016/j.gim.2021.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Despite the importance of exonic copy number variations (CNVs) in human genetic diseases, reliable next-generation sequencing-based methods for detecting them are unavailable. We developed an expandable and robust exonic CNV detection tool called consistent count region (CCR)-CNV. METHODS In total, about 1000 samples of the truth set were used for validating CCR-CNV. We compared CCR-CNV performance with 2 well-known CNV tools. Finally, to overcome the limitations of CCR-CNV, we devised a combined approach. RESULTS The mean sensitivity and specificity of CCR-CNV alone were above 95%, which was superior to that of other CNV tools, such as DECoN and Atlas-CNV. However, low covered region and positive predictive value and high false discovery rate act as obstacles to its use in clinical settings. The combined approach showed much improved performance than CCR-CNV alone. CONCLUSION In this study, we present a novel diagnostic tool that allows the identification of exonic CNVs with high confidence using various reagents and clinical next-generation sequencing platforms. We validated this method using the largest multiple ligation-dependent probe amplification-confirmed data set, including sufficient copy normal control data. The approach, combined with existing CNV tools, allows the implementation of CCR-CNV in clinical settings.
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Affiliation(s)
- Man Jin Kim
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sungyoung Lee
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Boram Kim
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea; Department of Pediatrics, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | | | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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9
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Lee JS, Kim SY, Kim TS, Hong KH, Ryoo NH, Lee J, Park JH, Cho SI, Kim MJ, Kim YG, Kim B, Shin HS, Oh HS, Seo MS, Gwon TR, Kim Y, Park JS, Chin BS, Park WB, Park SS, Seong MW. Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection After Recovery from Mild Coronavirus Disease 2019. Clin Infect Dis 2021; 73:e3002-e3008. [PMID: 33219681 PMCID: PMC7890673 DOI: 10.1093/cid/ciaa1421] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Positive results from real-time reverse-transcription polymerase chain reaction (rRT-PCR) in recovered patients raise concern that patients who recover from coronavirus disease 2019 (COVID-19) may be at risk of reinfection. Currently, however, evidence that supports reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has not been reported. METHODS We conducted whole-genome sequencing of the viral RNA from clinical specimens at the initial infection and at the positive retest from 6 patients who recovered from COVID-19 and retested positive for SARS-CoV-2 via rRT-PCR after recovery. A total of 13 viral RNAs from the patients' respiratory specimens were consecutively obtained, which enabled us to characterize the difference in viral genomes between initial infection and positive retest. RESULTS At the time of the positive retest, we were able to acquire a complete genome sequence from patient 1, a 21-year-old previously healthy woman. In this patient, through the phylogenetic analysis, we confirmed that the viral RNA of positive retest was clustered into a subgroup distinct from that of the initial infection, suggesting that there was a reinfection of SARS-CoV-2 with a subtype that was different from that of the primary strain. The spike protein D614G substitution that defines the clade "G" emerged in reinfection, while mutations that characterize the clade "V" (ie, nsp6 L37F and ORF3a G251V) were present at initial infection. CONCLUSIONS Reinfection with a genetically distinct SARS-CoV-2 strain may occur in an immunocompetent patient shortly after recovery from mild COVID-19. SARS-CoV-2 infection may not confer immunity against a different SARS-CoV-2 strain.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, South Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, South Korea
| | - Nam-Hee Ryoo
- Department of Laboratory Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Jaehyeon Lee
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, South Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Young-gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeon Sae Oh
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Myoung-Seock Seo
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Tae-Rin Gwon
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Yeonjae Kim
- Department of Infectious Disease, National Medical Center, Seoul, South Korea
| | - Jun-Sun Park
- Research Institute of Public Health, National Medical Center, Seoul, South Korea
| | - Bum Sik Chin
- Department of Infectious Disease, National Medical Center, Seoul, South Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
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10
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Yang JH, Cho SI, Kim DH, Yoon JY, Moon J, Kim JW, Choi S, Suh DH. Pilot study of fractional microneedling radiofrequency for hidradenitis suppurativa assessed by clinical response and histology. Clin Exp Dermatol 2021; 47:335-342. [PMID: 34431555 DOI: 10.1111/ced.14905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Hidradenitis suppurativa (HS) is a devastating chronic inflammatory skin disease with frequent recurrences. Various systemic treatments and procedures have been used but the efficacy of fractional microneedling radiofrequency (FMR) has not been reported. AIM To evaluate the clinical and histological efficacy of FMR in the treatment of HS lesions. METHODS An 8-week, prospective, split-body, unblinded study was conducted, which enrolled 10 adult patients with mild to moderate HS to receive 3 sessions of FMR treatment biweekly. HS severity was assessed using the number and type of lesions, HS Physician Global Assessment (HS-PGA) and the modified Sartorius score (mSS). Skin biopsies were performed on participants to assess change in inflammation before and after FMR. RESULTS Severity of HS was significantly reduced on the FMR-treated side of the body, but not on the control side. Inflammatory HS lesions were significantly reduced after 4 weeks, while HS-PGA and mSS were significantly decreased after 6 weeks. Immunohistochemistry staining showed decreased expression of inflammatory markers including neutrophil elastases, interleukin (IL)-8 and IL-17, tumour necrosis factor-α, transforming growth factor-β1 and matrix metalloproteinases. CONCLUSION FMR may be a viable treatment option for mild to moderate HS.
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Affiliation(s)
- J H Yang
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea.,Acne, Rosacea, Seborrheic Dermatitis and Hidradenitis Suppurativa Research Laboratory, Seoul National University Hospital, Seoul, South Korea
| | - S I Cho
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - D H Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - J Y Yoon
- Acne, Rosacea, Seborrheic Dermatitis and Hidradenitis Suppurativa Research Laboratory, Seoul National University Hospital, Seoul, South Korea
| | - J Moon
- Reone Skin Clinic, Seoul, South Korea
| | - J W Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - S Choi
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - D H Suh
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea.,Acne, Rosacea, Seborrheic Dermatitis and Hidradenitis Suppurativa Research Laboratory, Seoul National University Hospital, Seoul, South Korea
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11
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Gu H, Kim MJ, Yang D, Song JY, Cho SI, Park SS, Seong MW. Accuracy and Performance Evaluation of Triplet Repeat Primed PCR as an Alternative to Conventional Diagnostic Methods for Fragile X Syndrome. Ann Lab Med 2021; 41:394-400. [PMID: 33536358 PMCID: PMC7884195 DOI: 10.3343/alm.2021.41.4.394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 11/26/2022] Open
Abstract
Background Conventional diagnosis of fragile X syndrome (FXS) is based on a combination of fragment analysis (FA) and Southern blotting (SB); however, this diagnostic approach is time- and labor-intensive and has pitfalls such as the possibility of missing large number alleles. Triplet repeat primed PCR (TP-PCR) is a current alternative used to overcome these limitations. We evaluated the diagnostic usefulness of TP-PCR compared with the conventional diagnostic protocol consisting of FA and/or SB in terms of allele categorization, repeat number correlation, and zygosity concordance in female genetic carriers. Methods From November 2013 to March 2018, 458 patients (326 males, 132 females) were simultaneously examined using FA and/or SB and TP-PCR by detecting CGG repeat numbers in FMR1 gene and diagnosed as per American College of Medical Genetics guidelines. Results The TP-PCR results showed high concordance with the FA and/or SB results for all three aspects (allele categorization, repeat number correlation, and zygosity concordance in female genetic carriers). TP-PCR detected CGG expansions ≥200 in all full mutation (FM) allele cases in male patients, as well as both the normal allele (NL) and FM allele in female carriers. In premutation (PM) allele carriers, the TP-PCR results were consistent with the FA and/or SB results. In terms of zygosity concordance in female genetic carriers, 12 NL cases detected by TP-PCR showed a merged peak consisting of two close heterozygous peaks; however, this issue was resolved using a 10-fold dilution. Conclusions TP-PCR may serve as a reliable alternative method for FXS diagnosis.
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Affiliation(s)
- Hyunjung Gu
- Department of Laboratory Medicine, Graduate School, Kyung Hee University, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Dahae Yang
- Department of Laboratory Medicine, Kosin University Gospel Hospital, Busan, Korea
| | - Ji Yun Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
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12
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Lee JS, Han D, Kim SY, Hong KH, Jang MJ, Kim MJ, Kim YG, Park JH, Cho SI, Park WB, Lee KB, Shin HS, Oh HS, Kim TS, Park SS, Seong MW. Longitudinal proteomic profiling provides insights into host response and proteome dynamics in COVID-19 progression. Proteomics 2021; 21:e2000278. [PMID: 33945677 PMCID: PMC8206655 DOI: 10.1002/pmic.202000278] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/21/2022]
Abstract
In managing patients with coronavirus disease 2019 (COVID‐19), early identification of those at high risk and real‐time monitoring of disease progression to severe COVID‐19 is a major challenge. We aimed to identify potential early prognostic protein markers and to expand understanding of proteome dynamics during clinical progression of the disease. We performed in‐depth proteome profiling on 137 sera, longitudinally collected from 25 patients with COVID‐19 (non‐severe patients, n = 13; patients who progressed to severe COVID‐19, n = 12). We identified 11 potential biomarkers, including the novel markers IGLV3‐19 and BNC2, as early potential prognostic indicators of severe COVID‐19. These potential biomarkers are mainly involved in biological processes associated with humoral immune response, interferon signalling, acute phase response, lipid metabolism, and platelet degranulation. We further revealed that the longitudinal changes of 40 proteins persistently increased or decreased as the disease progressed to severe COVID‐19. These 40 potential biomarkers could effectively reflect the clinical progression of the disease. Our findings provide some new insights into host response to SARS‐CoV‐2 infection, which are valuable for understanding of COVID‐19 disease progression. This study also identified potential biomarkers that could be further validated, which may support better predicting and monitoring progression to severe COVID‐19.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, South Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, South Korea
| | - Myoung-Jin Jang
- Medical Research Collaborating Center, Seoul National University Hospital
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Kyung Bok Lee
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeon Sae Oh
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea
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13
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Abstract
Thalassemia is characterized by the impaired synthesis of globin chains due to disease-causing variants in α- or β-globin genes. In this review, we provide an overview of the molecular basis underlying α- and β-thalassemia, and of the current technologies used to characterize these disease-causing variants for the diagnosis of thalassemia. Understanding these molecular basis and technologies will prove to be beneficial for the accurate diagnosis of thalassemia.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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14
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Kim MJ, Shin HS, Oh HS, Cho SI, Kim YG, Lee JS, Park SS, Seong MW. FMS-like Tyrosine Kinase 3-Internal Tandem Duplication Allele Concentrations Should Be Determined in a Mutation-Type-Specific Manner. Clin Chem 2021; 67:691-693. [PMID: 33686396 DOI: 10.1093/clinchem/hvab019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Rare Disease Center, Seoul National University Hospital, Seoul, Korea
| | - Ho Seob Shin
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyeon Sae Oh
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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15
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Kim JY, Yang HK, Kim N, Kim MJ, Cho SI, Seong M, Park SS, Hwang J. Strabismus in chronic progressive external ophthalmoplegia. Acta Ophthalmol 2021; 99:e274-e280. [PMID: 33191655 DOI: 10.1111/aos.14558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/02/2020] [Indexed: 11/28/2022]
Abstract
PURPOSE To elucidate the patterns of strabismus and ophthalmoplegia associated with chronic progressive external ophthalmoplegia (CPEO) confirmed by mitochondrial DNA (mtDNA) deletions in Asians. METHODS A total of 10 patients confirmed to have mtDNA deletion associated with CPEO were included. Long-range PCR encompassing the entire mtDNA was carried out. In the cases with mtDNA deletion, the exact deletion ranges of mtDNA were identified by sequencing. A full ophthalmologic examination including prism and alternate cover test in the primary position, evaluation of ductions and versions, and binocularity was performed in 10 patients with confirmed mtDNA deletions associated with CPEO. RESULTS All of the patients showed ophthalmoplegia as well as ptosis, even after eyelid surgeries. Ophthalmoplegia was symmetric between both eyes in nine patients (90%) while one patient (10%) showed asymmetric ophthalmoplegia with esotropia and left hypotropia. Among the nine patients with symmetric involvement, four patients (44%) showed exotropia, three (33%) had exotropia with vertical deviation, and the remaining two patients (22%) showed orthotropia. Five out of 10 patients (50%) complained of diplopia associated with strabismus, four of whom (80%) had vertical deviation. Three out of five patients (60%) without diplopia showed exotropia of 20 prism diopters (PD) to 50 PD. CONCLUSIONS Exotropia with/without vertical deviation is the most common form of strabismus in Asian patients with CPEO and only one of them showed a small angle of esotropia. Ophthalmoplegia could be asymmetric in 10% of CPEO patients.
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Affiliation(s)
- Ji Yeon Kim
- Biomedical Research Institute Seoul National University Hospital Seoul Korea
| | - Hee Kyung Yang
- Department of Ophthalmology Seoul National University College of MedicineSeoul National University Bundang Hospital Seongnam Korea
| | - Namju Kim
- Department of Ophthalmology Seoul National University College of MedicineSeoul National University Bundang Hospital Seongnam Korea
| | - Man Jin Kim
- Department of Laboratory Medicine Seoul National University HospitalSeoul National University College of Medicine Seoul Korea
| | - Sung Im Cho
- Department of Laboratory Medicine Seoul National University HospitalSeoul National University College of Medicine Seoul Korea
| | - Moon‐Woo Seong
- Biomedical Research Institute Seoul National University Hospital Seoul Korea
- Department of Laboratory Medicine Seoul National University HospitalSeoul National University College of Medicine Seoul Korea
| | - Sung Sup Park
- Biomedical Research Institute Seoul National University Hospital Seoul Korea
- Department of Laboratory Medicine Seoul National University HospitalSeoul National University College of Medicine Seoul Korea
| | - Jeong‐Min Hwang
- Department of Ophthalmology Seoul National University College of MedicineSeoul National University Bundang Hospital Seongnam Korea
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16
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Han H, Byun JM, Shin DY, Yoon SS, Koh Y, Hong J, Kim I, Lee C, Yoo H, Yun H, Kim MJ, Cho SI, Seong MW, Park SS. Leukemic stem cell phenotype is associated with mutational profile in acute myeloid leukemia. Korean J Intern Med 2021; 36:401-412. [PMID: 32811132 PMCID: PMC7969060 DOI: 10.3904/kjim.2020.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND/AIMS Understanding leukemic stem cell (LSC) is important for acute myeloid leukemia (AML) treatment. However, association of LSC with patient prognosis and genetic information in AML patients is unclear. METHODS Here we investigated the associations between genetic information and the various LSC phenotypes, namely multipotent progenitor (MPP)-like, lymphoid primed multipotent progenitor (LMPP)-like and granulocyte-macrophage progenitors (GMP)-like LSC in 52 AML patients. RESULTS In secondary AML patients, MPP-like LSC was significantly higher than de novo AML (p = 0.0037). The proportion of MPP-like LSC was especially high in post-myeloproliferative neoplasm AML (p = 0.0485). There was no correlation between age and LSC phenotype. Mutations of KRAS and NRAS were observed in MPP-like LSC dominant patients, TP53 and ASXL1 mutations in LMPP-like LSC dominant patients, and CEBPA, DNMT3A and IDH1 mutations in GMP-like LSC dominant patients. Furthermore, KRAS mutation was significantly associated with MPP-like LSC expression (p = 0.0540), and TP53 mutation with LMPP-like LSC expression (p = 0.0276). When the patients were separated according to the combined risk including next generation sequencing data, the poorer the prognosis, the higher the LMPP-like LSC expression (p = 0.0052). This suggests that the dominant phenotype of LSC is one of the important factors in predicting the prognosis and treatment of AML. CONCLUSION LSC phenotype in AML is closely associated with the recurrent mutations which has prognostic implication. Further research to confirm the meaning of LSC phenotype in the context of genetic aberration is warranted.
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Affiliation(s)
- Heejoo Han
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ja Min Byun
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Dong-Yeop Shin
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Correspondence to Dong-Yeop Shin, M.D. Department of Internal Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Korea Tel: +82-2-2072-2228 Fax: +82-2-762-9662 E-mail:
| | - Sung-Soo Yoon
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Cancer Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Youngil Koh
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Junshik Hong
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Inho Kim
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Chansup Lee
- Cancer Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Hyeonjoo Yoo
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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17
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Lee JS, Seo MS, Gwon TR, Cho SI, Kim YG, Kim MJ, Park JH, Kang CK, Choe PG, Park WB, Kim NJ, Oh MD, Kim TS, Park SS, Seong MW. Communication: Comparison of Respiratory Specimens for the Detection of SARS-CoV-2. Ann Clin Lab Sci 2021; 51:140-144. [PMID: 33653794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We compared SARS-CoV-2 detection rate of different respiratory specimens (nasopharyngeal swab [NPS], n=92; oropharyngeal swab [OPS], n=18; sputum, n=11). We also compared cycle threshold (Ct) values of paired specimen types obtained from the same patient on the same day. Then we characterized viral load kinetics of NPS (n=142), OPS (n=126), and sputum (n=75), during disease course. Sputum samples showed higher detection rate than NPS, and OPS exhibited the lowest detection rate. The median Ct values in NPS were significantly lower than in paired OPS, and higher than in paired sputum, respectively (P<0.05). During the disease course, viral load was the lowest in OPS and the highest in sputum samples.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Myoung-Seock Seo
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Tae-Rin Gwon
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Nam-Joong Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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18
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Han MS, Seong MW, Heo EY, Park JH, Kim N, Shin S, Cho SI, Park SS, Choi EH. Sequential Analysis of Viral Load in a Neonate and Her Mother Infected With Severe Acute Respiratory Syndrome Coronavirus 2. Clin Infect Dis 2020; 71:2236-2239. [PMID: 32297925 PMCID: PMC7184375 DOI: 10.1093/cid/ciaa447] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 04/15/2020] [Indexed: 01/06/2023] Open
Abstract
We report changes in viral load over time in a 27-day-old neonate with coronavirus disease 2019 who presented with fever, cough, and vomiting. Severe acute respiratory syndrome coronavirus 2 RNA was detected in the nasopharynx, oropharynx, stool, saliva, plasma, and urine. The highest viral RNA copies in nasopharynx decreased over time while viral load in stool remained high.
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Affiliation(s)
- Mi Seon Han
- Department of Pediatrics, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eun Young Heo
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Ji Hong Park
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Namhee Kim
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea.,Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
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Seo SH, Kim JH, Kim MJ, Cho SI, Kim SJ, Kang H, Shin CS, Park SS, Lee KE, Seong MW. Whole Exome Sequencing Identifies Novel Genetic Alterations in Patients with Pheochromocytoma/Paraganglioma. Endocrinol Metab (Seoul) 2020; 35:909-917. [PMID: 33397043 PMCID: PMC7803589 DOI: 10.3803/enm.2020.756] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/03/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Pheochromocytoma and paragangliomas (PPGL) are known as tumors with the highest level of heritability, approximately 30% of all cases. Clinical practice guidelines of PPGL recommend genetic testing for germline variants in all patients. In this study, we used whole exome sequencing to identify novel causative variants associated with PPGL to improve the detection of rare genetic variants in our cohort. METHODS Thirty-six tested negative for pathogenic variants in previous Sanger sequencing or targeted gene panel testing for PPGL underwent whole exome sequencing. Whole exome sequencing was performed using DNA samples enriched using TruSeq Custom Enrichment Kit and sequenced with MiSeq (Illumina Inc.). Sequencing alignment and variant calling were performed using SAMtools. RESULTS Among previously mutation undetected 36 patients, two likely pathogenic variants and 13 variants of uncertain significance (VUS) were detected in 32 pheochromocytoma-related genes. SDHA c.778G>A (p.Gly260Arg) was detected in a patient with head and neck paraganglioma, and KIF1B c.2787-2A>C in a patient with a bladder paraganglioma. Additionally, a likely pathogenic variant in BRCA2, VUS in TP53, and VUS in NFU1 were detected. CONCLUSION Exome sequencing further identified genetic alterations by 5.6% in previously mutation undetected patients in PPGL. Implementation of targeted gene sequencing consisted of extended genes of PPGL in routine clinical screening can support the level of comprehensive patient assessment.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Seoul,
Korea
| | - Jung Hee Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul,
Korea
| | - Man Jin Kim
- Laboratory Medicine, Seoul National University College of Medicine, Seoul,
Korea
| | - Sung Im Cho
- Laboratory Medicine, Seoul National University College of Medicine, Seoul,
Korea
| | - Su Jin Kim
- Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul,
Korea
| | - Hyein Kang
- Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul,
Korea
| | - Chan Soo Shin
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul,
Korea
| | - Sung Sup Park
- Laboratory Medicine, Seoul National University College of Medicine, Seoul,
Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul,
Korea
| | - Kyu Eun Lee
- Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul,
Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul,
Korea
| | - Moon-Woo Seong
- Laboratory Medicine, Seoul National University College of Medicine, Seoul,
Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul,
Korea
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20
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Kim YG, Kim MJ, Lee JS, Lee JA, Song JY, Cho SI, Park SS, Seong MW. SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use. J Mol Diagn 2020; 23:140-148. [PMID: 33246077 DOI: 10.1016/j.jmoldx.2020.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/23/2020] [Accepted: 11/10/2020] [Indexed: 01/03/2023] Open
Abstract
Despite the wide application of next-generation sequencing, Sanger sequencing still plays a necessary role in clinical laboratories. However, recent developments in the field of bioinformatics have focused mostly on next-generation sequencing, while tools for Sanger sequencing have shown little progress. In this study, SnackVar (https://github.com/Young-gonKim/SnackVar, last accessed June 22, 2020), a novel graphical user interface-based software for Sanger sequencing, was developed. All types of variants, including heterozygous insertion/deletion variants, can be identified by SnackVar with minimal user effort. The featured reference sequences of all of the genes are prestored in SnackVar, allowing for detected variants to be precisely described based on coding DNA references according to the nomenclature of the Human Genome Variation Society. Among 88 previously reported variants from four insertion/deletion-rich genes (BRCA1, APC, CALR, and CEBPA), the result of SnackVar agreed with reported results in 87 variants [98.9% (93.0%; 99.9%)]. The cause of one incorrect variant calling was proven to be erroneous base callings from poor-quality trace files. Compared with commercial software, SnackVar required less than one-half of the time taken for the analysis of a selected set of test cases. We expect SnackVar to be a cost-effective option for clinical laboratories performing Sanger sequencing.
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Affiliation(s)
- Young-Gon Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jung Ae Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ji Yun Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
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21
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Cho SI, Kim YE, Jo SJ. Association of COVID-19 with skin diseases and relevant biologics: a cross-sectional study using nationwide claim data in South Korea. Br J Dermatol 2020; 184:296-303. [PMID: 32875557 PMCID: PMC9213995 DOI: 10.1111/bjd.19507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
Background As the coronavirus disease 2019 (COVID‐19) pandemic has spread, information about COVID‐19 and skin disease or related biologics is still lacking. Objectives To identify the association between COVID‐19 and skin diseases or biologics. Methods A nationwide claim dataset relevant to COVID‐19 in South Korea was analysed. This dataset included insurance claim data before and during COVID‐19 treatment and clinical outcomes. Claim data related to skin diseases and relevant biologics were analysed to determine the association of COVID‐19 with skin diseases and relevant biologics. Results The dataset contained a total of 234 427 individuals (111 947 male and 122 480 female) who underwent COVID‐19 testing. Of them, 7590 (3·2%) were confirmed as having COVID‐19, and 227 (3·0%) confirmed patients died. Among various skin diseases and biologics, no significant increase in the presence of specific skin diseases or exposure to biologics was observed in the COVID‐19‐positive group, even after adjusting for or matching covariates. The presence of skin diseases and exposure to biologics also did not seem to affect clinical outcomes including mortality. Conclusions Underlying skin diseases did not appear to increase susceptibility to COVID‐19 or mortality from COVID‐19. Considering the risks and benefits, biologics for dermatological conditions might be continuously used during the COVID‐19 pandemic.
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Affiliation(s)
- S I Cho
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - Y E Kim
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
| | - S J Jo
- Department of Dermatology, Seoul National University College of Medicine, Seoul, South Korea
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22
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Cho SI, Han B, Hur K, Mun JH. Perceptions and attitudes of medical students regarding artificial intelligence in dermatology. J Eur Acad Dermatol Venereol 2020; 35:e72-e73. [PMID: 32852856 DOI: 10.1111/jdv.16812] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/24/2020] [Accepted: 06/30/2020] [Indexed: 12/21/2022]
Affiliation(s)
- S I Cho
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea
| | - B Han
- Seoul National University College of Medicine, Seoul, Korea
| | - K Hur
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea
| | - J-H Mun
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea.,Institute of Human-Environment Interface Biology, Seoul National University, Seoul, Korea
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23
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Han MS, Seong MW, Kim N, Shin S, Cho SI, Park H, Kim TS, Park SS, Choi EH. Viral RNA Load in Mildly Symptomatic and Asymptomatic Children with COVID-19, Seoul, South Korea. Emerg Infect Dis 2020; 26:2497-2499. [PMID: 32497001 PMCID: PMC7510743 DOI: 10.3201/eid2610.202449] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Along with positive SARS-CoV-2 RNA in nasopharyngeal swabs, viral RNA was detectable at high concentration for >3 weeks in fecal samples from 12 mildly symptomatic and asymptomatic children with COVID-19 in Seoul, South Korea. Saliva also tested positive during the early phase of infection. If proven infectious, feces and saliva could serve as transmission sources.
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24
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Lee JS, Lee KB, Song H, Sun C, Kim MJ, Cho SI, Lee YK, Park SS, Seong MW. Direct Haplotyping-Based Noninvasive Prenatal Test for Myotonic Dystrophy Type 1 with Large CTG Expansion. Clin Chem 2020; 66:614-615. [PMID: 32167563 DOI: 10.1093/clinchem/hvaa025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/23/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea
| | - Kyung Bok Lee
- Department of Statistics, Seoul National University, Seoul, Republic of Korea
| | - Han Song
- Genome Opinion Inc., Seongdong-gu, Seoul, Republic of Korea
| | - ChoongHyun Sun
- Genome Opinion Inc., Seongdong-gu, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
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25
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Seong MW, Kim M, Shin HS, Cho SI, Park SS. Three-Year Experience of an External Proficiency Testing Survey for Next-Generation Sequencing-Based Testing for Germline Mutation. ACTA ACUST UNITED AC 2020. [DOI: 10.15263/jlmqa.2020.42.1.48] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Manjin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ho-Seob Shin
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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26
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Seo SH, Bacolla A, Yoo D, Koo YJ, Cho SI, Kim MJ, Seong MW, Kim HJ, Kim JM, Tainer JA, Park SS, Kim JY, Jeon B. Replication-Based Rearrangements Are a Common Mechanism for SNCA Duplication in Parkinson's Disease. Mov Disord 2020; 35:868-876. [PMID: 32039503 DOI: 10.1002/mds.27998] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND SNCA multiplication is a genomic cause of familial PD, showing dosage-dependent toxicity. Until now, nonallelic homologous recombination was suggested as the mechanism of SNCA duplication, based on various types of repetitive elements found in the spanning region of the breakpoints. However, the sequence at the breakpoint was analyzed only for 1 case. OBJECTIVES We have analyzed the breakpoint sequences of 6 patients with PD who had duplicated SNCA using whole-genome sequencing data to elucidate the mechanism of SNCA duplication. METHODS Six patient samples with SNCA duplication underwent whole-genome sequencing. The duplicated regions were defined with nucleotide-resolution breakpoints, which were confirmed by junction polymerase chain reaction and Sanger sequencing. The search for potential non-B DNA-forming sequences and stem-loop structure predictions was conducted. RESULTS Duplicated regions ranged from the smallest region of 718.3 kb to the largest one of 4,162 kb. Repetitive elements were found at 8 of the 12 breakpoint sequences on each side of the junction, but none of the pairs shared overt homologies. Five of these six junctions had microhomologies (2-4 bp) at the breakpoint, and a short stretch of sequences was inserted in 3 cases. All except one junction were located within or next to stem-loop structures. CONCLUSION Our study has determined that homologous recombination mechanisms involving repetitive elements are not the main cause of the duplication of SNCA. The presence of microhomology at the junctions and their position within stem-loop structures suggest that replication-based rearrangements may be a common mechanism for SNCA amplification. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.,Seoul National University College of Medicine, Seoul, Korea
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dallah Yoo
- Department of Neurology, Kyung Hee University Hospital, Seoul, Korea
| | - Yoon Jung Koo
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Han-Joon Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jong-Min Kim
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sung Sup Park
- Seoul National University College of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Beomseok Jeon
- Seoul National University College of Medicine, Seoul, Korea.,Department of Neurology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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27
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Lee JK, Seong MW, Shin D, Kim JI, Han MS, Yeon Y, Cho SI, Park SS, Choi EH. Comparative genomics of Mycoplasma pneumoniae isolated from children with pneumonia: South Korea, 2010-2016. BMC Genomics 2019; 20:910. [PMID: 31783732 PMCID: PMC6884898 DOI: 10.1186/s12864-019-6306-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 11/18/2019] [Indexed: 12/03/2022] Open
Abstract
Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. The phylogenetic tree constructed with 78 genomes including 30 genomes from Korea formed two clusters and further divided into two sub-clusters. eBURST analysis revealed two clonal complexes according to P1 typing results showing higher diversity among P1 type 2 strains. Conclusions The comparative whole genome approach was able to define high genetic identity, unique structural diversity, and phylogenetic associations among the 78 M. pneumoniae strains isolated worldwide.
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Affiliation(s)
- Joon Kee Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea.,Department of Pediatrics, Chungbuk National University Hospital, Cheongju, South Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Dongjin Shin
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea.,Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea.,Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, South Korea
| | - Mi Seon Han
- Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Youbin Yeon
- Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Sung Im Cho
- Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, South Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea. .,Department of Pediatrics, Seoul National University Children's Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
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28
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Cho SI, Sun S, Mun JH, Kim C, Kim SY, Cho S, Youn SW, Kim HC, Chung JH. Dermatologist-level classification of malignant lip diseases using a deep convolutional neural network. Br J Dermatol 2019; 182:1388-1394. [PMID: 31449661 DOI: 10.1111/bjd.18459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Deep convolutional neural networks (DCNNs) can classify skin diseases at a level equivalent to a dermatologist, but their performance in specific areas requires further research. OBJECTIVE To evaluate the performance of a trained DCNN-based algorithm in classifying benign and malignant lip diseases. METHODS A training set of 1629 images (743 malignant, 886 benign) was used with Inception-Resnet-V2. Performance was evaluated using another set of 344 images and 281 images from other hospitals. Classifications by 44 participants (six board-certified dermatologists, 12 dermatology residents, nine medical doctors not specialized in dermatology and 17 medical students) were used for comparison. RESULTS The outcomes based on the area under curve, sensitivity and specificity were 0·827 [95% confidence interval (CI) 0·782-0·873], 0·755 (95% CI 0·673-0·827) and 0·803 (95% CI 0·752-0·855), respectively, for the set of 344 images; and 0·774 (95% CI 0·699-0·849), 0·702 (95% CI 0·579-0·808) and 0·759 (95% CI 0·701-0·813), respectively, for the set of 281 images. The DCNN was equivalent to the dermatologists and superior to the nondermatologists in classifying malignancy. After referencing the DCNN result, the mean ± SD Youden index increased significantly for nondermatologists, from 0·201 ± 0·156 to 0·322 ± 0·141 (P < 0·001). CONCLUSIONS DCNNs can classify lip diseases at a level similar to dermatologists. This will help unskilled physicians discriminate between benign and malignant lip diseases. What's already known about this topic? Deep convolutional neural networks (DCNNs) can classify malignant and benign skin diseases at a level equivalent to dermatologists. The lips are a unique feature in terms of histology and morphology. Previous studies of DCNNs have not investigated tumours on specific locations. What does this study add? This study shows that DCNNs can distinguish rare malignant and benign lip disorders at the same rate as dermatologists. DCNNs can help nondermatologists to distinguish malignant lip diseases. What are the clinical implications of this work? DCNNs can distinguish malignant and benign skin diseases even at specific locations such as the lips, as well as board-certified dermatologists. Malignant lip diseases are rare and difficult for less trained doctors to differentiate them from benign lesions. This study shows that in dermatology, DCNN can help improve decision-making processes for rare skin diseases in specific areas of the body.
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Affiliation(s)
- S I Cho
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea
| | - S Sun
- Interdisciplinary Program, Bioengineering Major, Graduate School, Seoul National University, Seoul, Korea
| | - J-H Mun
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea
| | - C Kim
- Seoul National University College of Medicine, Seoul, Korea
| | - S Y Kim
- Seoul National University College of Medicine, Seoul, Korea
| | - S Cho
- Department of Dermatology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - S W Youn
- Department of Dermatology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - H C Kim
- Interdisciplinary Program, Bioengineering Major, Graduate School, Seoul National University, Seoul, Korea.,Department of Biomedical Engineering, and Medical Research Center, Seoul National University College of Medicine, Seoul, Korea
| | - J H Chung
- Department of Dermatology, Seoul National University College of Medicine, Seoul, Korea
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Yang D, Kim B, Song DY, Kim TY, Kim MJ, Cho SI, Kim H, Seong MW, Park SS. Pitfalls of ABO Genotyping Based on Targeted Single Nucleotide Variant Analysis Due to a Nondeletional O Allele Lacking c.261delG: First Report of ABO*O.09.01 in Korea. Ann Lab Med 2019; 39:599-601. [PMID: 31240894 PMCID: PMC6660326 DOI: 10.3343/alm.2019.39.6.599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/18/2019] [Accepted: 05/17/2019] [Indexed: 11/21/2022] Open
Affiliation(s)
- Dahae Yang
- Department of Laboratory Medicine, Kosin Gospel University Hospital, Busan, Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Da Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Tae Yeul Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hyungsuk Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
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Lee JS, Yoon M, Kim MJ, Cho SI, Seong MW, Park SS, Kim JY. Evaluation of the new Abbott Real-Time EBV assay: fully automated quantification of EBV in whole blood by targeting BLLF1. Diagn Microbiol Infect Dis 2019; 94:135-139. [PMID: 30777343 DOI: 10.1016/j.diagmicrobio.2018.12.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022]
Abstract
The accurate measurement of the Epstein-Barr virus (EBV) DNA level in the blood is required for managing EBV-associated diseases. A new commercial Abbott Real-Time EBV assay, which targets the BLLF1 gene, was evaluated on 120 clinical whole blood samples and the Qnostics EBV analytical panel. The limit of detection of the assay was 48.9 IU/mL (95% confidence interval, 48.1-49.8 IU/mL). The assay was linear from 2 to 5 log10 IU/mL (R2 = 0.997). The within-run coefficients of variation (CVs) ranged from 1.68% to 4.75% and the between-run CVs ranged from 1.73% to 12.83% for samples with high, medium, and low viral loads. EBV DNA loads measured by Abbott EBV assay strongly correlated with the results quantified by another commercial Nanogen EBV Real-Time Alert Q-PCR assay (r = 0.879, P < 0.0001). The fully automated Abbott Real-Time EBV assay targeting BLLF1 reduced both hands-on time and turnaround time and demonstrated a reliable performance for EBV DNA quantification in whole blood.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea; Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Mihye Yoon
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea; Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea.
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Lee JS, Oh S, Park SK, Lee MH, Lee JW, Kim SW, Son BH, Noh DY, Lee JE, Park HL, Kim MJ, Cho SI, Lee YK, Park SS, Seong MW. Reclassification of BRCA1 and BRCA2 variants of uncertain significance: a multifactorial analysis of multicentre prospective cohort. J Med Genet 2018; 55:794-802. [PMID: 30415210 DOI: 10.1136/jmedgenet-2018-105565] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 11/03/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 (BRCA1/2) variants classified ambiguously as variants of uncertain significance (VUS) are a major challenge for clinical genetic testing in breast cancer; their relevance to the cancer risk is unclear and the association with the response to specific BRCA1/2-targeted agents is uncertain. To minimise the proportion of VUS in BRCA1/2, we performed the multifactorial likelihood analysis and validated this method using an independent cohort of patients with breast cancer. METHODS We used a data set of 2115 patients with breast cancer from the nationwide multicentre prospective Korean Hereditary Breast Cancer study. In total, 83 BRCA1/2 VUSs (BRCA1, n=26; BRCA2, n=57) were analysed. The multifactorial probability was estimated by combining the prior probability with the overall likelihood ratio derived from co-occurrence of each VUS with pathogenic variants, personal and family history, and tumour characteristics. The classification was compared with the interpretation according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG/AMP) guidelines. An external validation was conducted using independent data set of 810 patients. RESULTS We were able to redefine 38 VUSs (BRCA1, n=10; BRCA2, n=28). The revised classification was highly correlated with the ACMG/AMP guideline-based interpretation (BRCA1, p for trend=0.015; BRCA2, p=0.001). Our approach reduced the proportion of VUS from 19% (154/810) to 8.9% (72/810) in the retrospective validation data set. CONCLUSION The classification in this study would minimise the 'uncertainty' in clinical interpretation, and this validated multifactorial model can be used for the reliable annotation of BRCA1/2 VUSs.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sohee Oh
- Department of Biostatistics SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Sue Kyung Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min-Hyuk Lee
- Department of Surgery, College of Medicine, Soonchunhyang University, Seoul, Republic of Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seongnam, Republic of Korea
| | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Byung Ho Son
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seongnam, Republic of Korea
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hai-Lin Park
- Department of Surgery, Kangnam CHA Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea.,Department of Laboratory Medicine, Hallym University College of Medicine, Anyang, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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Lee S, Kim EJ, Cho SI, Park H, Seo SH, Seong MW, Park SS, Jung SE, Lee SC, Park KW, Kim HY. Spectrum of MNX1 Pathogenic Variants and Associated Clinical Features in Korean Patients with Currarino Syndrome. Ann Lab Med 2018; 38:242-248. [PMID: 29401559 PMCID: PMC5820069 DOI: 10.3343/alm.2018.38.3.242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 09/20/2017] [Accepted: 12/11/2017] [Indexed: 12/14/2022] Open
Abstract
Background The major genetic cause of Currarino syndrome (CS), a congenital malformation syndrome typically characterized by sacral agenesis, anorectal malformation, and presence of a pre-sacral mass, is known to be pathogenic variants in motor neuron and pancreas homeobox 1 (MNX1), which exist in almost all familial cases and 30% of sporadic cases. Less commonly, a large deletion or a complex rearrangement involving the 7q36 region is associated with CS. We investigated the spectrum of MNX1 pathogenic variants and associated clinical features in the Korean patients with CS. Methods We enrolled 25 patients with CS, including 24 sporadic cases and one familial case. Direct sequencing of MNX1 and multiplex ligation-dependent probe amplification were performed. We also analyzed clinical phenotypes and evaluated genotype-phenotype correlations. Results We identified six novel variants amongst a total of six null variants, one missense variant, and one large deletion. The null variants included four frameshift variants (p.Gly98Alafs*124, p.Gly145Alafs*77, p.Gly151Leufs*67, and p.Ala216Profs*5) and two nonsense variants (p.Tyr186* and p.Gln212*). The missense variant, p.Lys295Gln, was located in the highly-conserved homeobox domain and was predicted to be deleterious. A large deletion involving the 7q36 region was detected in one patient. Pathogenic variants in MNX1 were detected in 28% of all CS cases and 25% of sporadic cases. The clinical phenotype was variable in patients with and without pathogenic variants; no significant genotype-phenotype correlation was observed. Conclusions This study revealed the spectrum and phenotypic variability of MNX1 pathogenic variants in the Korean population.
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Affiliation(s)
- Seungjun Lee
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Gyeongsang National University Changwon Hospital, Changwon, Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Eun Jung
- Department of Pediatric Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Seong Cheol Lee
- Department of Pediatric Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Kwi Won Park
- Department of Pediatric Surgery, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Young Kim
- Department of Pediatric Surgery, Seoul National University College of Medicine, Seoul, Korea.
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Seo SH, Kim SY, Cho SI, Park H, Lee S, Choi JM, Kim MJ, Lee JS, Ahn KJ, Song MK, Bae EJ, Park SS, Seong MW. Application of Multigene Panel Sequencing in Patients with Prolonged Rate-corrected QT Interval and No Pathogenic Variants Detected in KCNQ1, KCNH2, and SCN5A. Ann Lab Med 2018; 38:54-58. [PMID: 29071820 PMCID: PMC5700148 DOI: 10.3343/alm.2018.38.1.54] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/29/2017] [Accepted: 09/14/2017] [Indexed: 01/08/2023] Open
Abstract
Long QT syndrome (LQTS) is an inherited cardiac disease characterized by a prolonged heart rate-corrected QT (QTc) interval. We investigated the genetic causes in patients with prolonged QTc intervals who were negative for pathogenic variants in three major LQTS-related genes (KCNQ1, KCNH2, and SCN5A). Molecular genetic testing was performed using a panel including 13 LQTS-related genes and 67 additional genes implicated in other cardiac diseases. Overall, putative genetic causes of prolonged QTc interval were identified in three of the 30 patients (10%). Among the LQTS-related genes, we detected a previously reported pathogenic variant, CACNA1C c.1552C>T, responsible for cardiac-only Timothy syndrome. Among the genes related to other cardiac diseases, a likely pathogenic variant, RYR2 c.11995A>G, was identified in a patient with catecholaminergic polymorphic ventricular tachycardia. Another patient who developed dilated cardiomyopathy with prolonged QTc interval was found to carry a likely pathogenic variant, TAZ c.718G>A, associated with infantile dilated cardiomyopathy. Comprehensive screening of genetic variants using multigene panel sequencing enables detection of genetic variants with a possible involvement in QTc interval prolongation, thus uncovering unknown molecular mechanisms underlying LQTS.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - So Yeon Kim
- Department of Laboratory Medicine, National Medical Center, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Gyeongsang National University Changwon Hospital, Changwon, Korea
| | - Seungjun Lee
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong Moon Choi
- Green Cross Genome, Yongin, Korea.,Green Cross Laboratories, Yongin, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jee Soo Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Korea
| | - Kyung Jin Ahn
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Mi Kyoung Song
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Jung Bae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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Abstract
BACKGROUND Studies on the association between depression and risk of tuberculosis (TB) are lacking. OBJECTIVE To determine the association between depression and risk of TB. METHODS From a nationwide database, patients with depression were identified to form the exposure cohort between 2003 and 2013. The control cohort comprised an equivalent number of subjects without any mood disorders, with each subject age- and sex-matched to a patient in the exposure cohort. The incidence of TB was identified in the exposure cohort and control cohort between 2003 and 2013. A multivariable Cox proportional hazards model was used to estimate the association between depression and the subsequent risk of TB. RESULTS A total of 32 372 patients with depression and the same number of controls were identified. The risk of TB in the depression cohort was 2.63-fold (95%CI 1.74-3.96) higher than in the control cohort. When the depression was classified as 'mild' and 'severe', the risk of TB was proportional to depression severity. CONCLUSIONS Patients with depression are at a higher risk for TB, and a dose-response relationship exists between depression and the subsequent risk of TB.
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Affiliation(s)
- K H Oh
- Korean Institute of Tuberculosis, Cheongju, Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - H Choi
- Korean Institute of Tuberculosis, Cheongju
| | - E J Kim
- Graduate School of Public Health, Seoul National University, Seoul, Korea
| | - H J Kim
- Korean Institute of Tuberculosis, Cheongju
| | - S I Cho
- Graduate School of Public Health, Seoul National University, Seoul, Korea
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Park J, Park SW, Cho SI, Park I, Kim YH, Park EY, Oh JK, Kim SJ, Park JH, Lim MK. Planning of national prospective study on tobacco behavior transition among adolescents in Korea. Eur J Public Health 2017. [DOI: 10.1093/eurpub/ckx186.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- J Park
- Graduate School of Cancer Science and Policy, National Cancer Center, Daegu, South Korea
| | - SW Park
- Catholic University of Daegu, School of Medicine, Daegym, South Korea
| | - SI Cho
- Seoul National University, Seoul, South Korea
| | - I Park
- Pukyong National University, Busan, South Korea
| | - YH Kim
- Pukyong National University, Busan, South Korea
| | - EY Park
- National Cancer Center, Goyang, South Korea
| | - JK Oh
- Graduate School of Cancer Science and Policy, National Cancer Center, Daegu, South Korea
| | - SJ Kim
- National Cancer Center, Goyang, South Korea
| | - JH Park
- National Cancer Center, Goyang, South Korea
| | - MK Lim
- Graduate School of Cancer Science and Policy, National Cancer Center, Daegu, South Korea
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Seo SH, Kim MJ, Park SW, Kim JH, Yu YS, Song JY, Cho SI, Ahn JH, Oh YH, Lee JS, Lee S, Seong MW, Park SS, Kim JY. Large Deletions of TSPAN12 Cause Familial Exudative Vitreoretinopathy (FEVR). Invest Ophthalmol Vis Sci 2017; 57:6902-6908. [PMID: 28002565 DOI: 10.1167/iovs.16-20585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Familial exudative vitreoretinopathy (FEVR) is a rare, hereditary visual disorder. The gene TSPAN12 is associated with autosomal dominant inheritance of FEVR. The prevalence and impact of large deletions/duplications of TSPAN12 on FEVR patients is unknown. To glean better insight of TSPAN12 on FEVR pathology, herein, we describe three FEVR patients with TSPAN12 deletions. Methods Thirty-three Korean FEVR patients, who previously screened negative for TSPAN12 mutations, mutations in other FEVR-associated genes such as NDP, FZD4, LRP5, and large deletions and duplications of NDP, FZD4, and LRP5, were selected for TSPAN12 large deletion and duplication analyses. Semiquantitative multiplex PCR for TSPAN12 gene dosage analyses were performed, followed by droplet digital PCR (ddPCR) for validation. Results Among the 33 patients, three patients were confirmed to carry large TSPAN12 deletions. Two of them had whole-gene deletions of TSPAN12, and the other patient possessed a deletion of TSPAN12 in exon 4. FEVR severity detected in these patients was not more severe than in a patient with TSPAN12 point mutation. Conclusions Regarding previously reported proportions of FEVR-associated genes contributing to the disorder's autosomal dominant inheritance pattern in Korea, we determined that patients with TSPAN12 large deletions were more common than patients with single nucleotide variants in TSPAN12. Evaluating TSPAN12 large deletions and duplications should be considered in FEVR screening and diagnosis as well as in routine genetic workups for FEVR patients.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Wook Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Hun Kim
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young Suk Yu
- Department of Ophthalmology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Yun Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Joo Hyun Ahn
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Yeon Hee Oh
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seungjun Lee
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea 5Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
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Hong KH, Hong SK, Cho SI, Ra E, Han KH, Kang SB, Kim EC, Park SS, Seong MW. Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis. Ann Lab Med 2017; 36:441-9. [PMID: 27374709 PMCID: PMC4940487 DOI: 10.3343/alm.2016.36.5.441] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/03/2016] [Accepted: 05/30/2016] [Indexed: 01/30/2023] Open
Abstract
Background Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. Methods In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. Results ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). Conclusions Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.
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Affiliation(s)
- Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea.,Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea
| | - Sung Kuk Hong
- Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea.,Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eunkyung Ra
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kyung Hee Han
- Department of Obstetrics & Gynecology, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Soon Beom Kang
- Department of Obstetrics & Gynecology, Konkuk University Medical Center, Seoul, Korea
| | - Eui Chong Kim
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
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Cho A, Seong MW, Lim BC, Lee HJ, Byeon JH, Kim SS, Kim SY, Choi SA, Wong AL, Lee J, Kim JS, Ryu HW, Lee JS, Kim H, Hwang H, Choi JE, Kim KJ, Hwang YS, Hong KH, Park S, Cho SI, Lee SJ, Park H, Seo SH, Park SS, Chae JH. Consecutive analysis of mutation spectrum in the dystrophin gene of 507 Korean boys with Duchenne/Becker muscular dystrophy in a single center. Muscle Nerve 2017; 55:727-734. [PMID: 27593222 DOI: 10.1002/mus.25396] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 08/18/2016] [Accepted: 08/30/2016] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Duchenne and Becker muscular dystrophies (DMD and BMD) are allelic X-linked recessive muscle diseases caused by mutations in the large and complex dystrophin gene. METHODS We analyzed the dystrophin gene in 507 Korean DMD/BMD patients by multiple ligation-dependent probe amplification and direct sequencing. RESULTS Overall, 117 different deletions, 48 duplications, and 90 pathogenic sequence variations, including 30 novel variations, were identified. Deletions and duplications accounted for 65.4% and 13.3% of Korean dystrophinopathy, respectively, suggesting that the incidence of large rearrangements in dystrophin is similar among different ethnic groups. We also detected sequence variations in >100 probands. The small variations were dispersed across the whole gene, and 12.3% were nonsense mutations. CONCLUSIONS Precise genetic characterization in patients with DMD/BMD is timely and important for implementing nationwide registration systems and future molecular therapeutic trials in Korea and globally. Muscle Nerve 55: 727-734, 2017.
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Affiliation(s)
- Anna Cho
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Ewha Womans University School of Medicine, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea
| | - Byung Chan Lim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hwa Jeen Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea
| | - Jung Hye Byeon
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Seung Soo Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Soonchunhyang University Cheonan Hospital, Chungcheongnam-do, Korea
| | - Soo Yeon Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sun Ah Choi
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ai-Lynn Wong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jeongho Lee
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Jon Soo Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Daejeon Eulji University Hospital, Daejeon, Korea
| | - Hye Won Ryu
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Sook Lee
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Gachon University Gil Medical Center, Incheon, Korea
| | - Hunmin Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Hee Hwang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Ji Eun Choi
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea.,Department of Pediatrics, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Ki Joong Kim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Young Seung Hwang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea
| | | | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea
| | - Seung Jun Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsangnam-do, Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Korea
| | - Jong Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
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Seong MW, Lee SJ, Cho SI, Ko K, Kim MN, Sung H, Kim JS, Ahn JS, Yu BS, Kim TS, Kim EC, Park SS. External Quality Assessment of MERS-CoV Molecular Diagnostics During the 2015 Korean Outbreak. Ann Lab Med 2017; 36:230-4. [PMID: 26915611 PMCID: PMC4773263 DOI: 10.3343/alm.2016.36.3.230] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/11/2015] [Accepted: 01/29/2016] [Indexed: 01/22/2023] Open
Abstract
Background The largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside Middle East Asia in 2015 has necessitated the rapid expansion of laboratories that conduct MERS-CoV molecular testing in Korea, together with external quality assessment (EQA) to evaluate the assays used. Methods The EQA program consisted of two phases; self-validation and blind assessment. For the first EQA phase, in vitro transcribed upstream region of the envelope gene (upE) and the open reading frame (ORF)1a RNAs were used at a concentration of 1,000 copies/µL. The test panel for the second EQA phase consisted of RNA extracts from three samples, which were obtained from two MERS-CoV positive patients and one MERS-CoV negative patient. Results The first EQA phase results for 46 participants showed a linear relationship between the threshold cycle (CT) values of RNA materials and the logarithmic concentrations for both upE and ORF1a gene targets (R2=0.73 and 0.75, respectively). The mean CT value for each concentration was different depending on which commercial kit was used for the assay. Among the three commonly used kits, PowerChek MERS Real-Time PCR kit (KogeneBiotech, Korea) showed the lowest CT values at all concentrations of upE and most concentrations of ORF1a. The second EQA phase results for 47 participants were 100% correct for all tested samples. Conclusions This EQA survey demonstrates that the MERS-CoV molecular testing performed in Korea during the 2015 outbreak is of robust capability. However, careful establishment and validation of a cut-off value are recommended to ensure good analytical sensitivity.
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Affiliation(s)
- Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Seung Jun Lee
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kyungphil Ko
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Mi Na Kim
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Heungsub Sung
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea
| | - Ji Soo Ahn
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Byung Su Yu
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eui Chong Kim
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea.
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Seong MW, Cho SI, Park H, Seo SH, Lee SJ, Kim EC, Park SS. Genotyping Influenza Virus by Next-Generation Deep Sequencing in Clinical Specimens. Ann Lab Med 2017; 36:255-8. [PMID: 26915615 PMCID: PMC4773267 DOI: 10.3343/alm.2016.36.3.255] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/09/2015] [Accepted: 12/21/2015] [Indexed: 12/25/2022] Open
Abstract
Rapid and accurate identification of an influenza outbreak is essential for patient care and treatment. We describe a next-generation sequencing (NGS)-based, unbiased deep sequencing method in clinical specimens to investigate an influenza outbreak. Nasopharyngeal swabs from patients were collected for molecular epidemiological analysis. Total RNA was sequenced by using the NGS technology as paired-end 250 bp reads. Total of 7 to 12 million reads were obtained. After mapping to the human reference genome, we analyzed the 3-4% of reads that originated from a non-human source. A BLAST search of the contigs reconstructed de novo revealed high sequence similarity with that of the pandemic H1N1 virus. In the phylogenetic analysis, the HA gene of our samples clustered closely with that of A/Senegal/VR785/2010(H1N1), A/Wisconsin/11/2013(H1N1), and A/Korea/01/2009(H1N1), and the NA gene of our samples clustered closely with A/Wisconsin/11/2013(H1N1). This study suggests that NGS-based unbiased sequencing can be effectively applied to investigate molecular characteristics of nosocomial influenza outbreak by using clinical specimens such as nasopharyngeal swabs.
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Affiliation(s)
- Moon Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Seung Jun Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eui Chong Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
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Kim SY, Park SJ, Cho SY, Cha RH, Jee HG, Kim G, Shin HS, Kim Y, Jung YM, Yang JS, Kim SS, Cho SI, Kim MJ, Lee JS, Lee SJ, Seo SH, Park SS, Seong MW. Viral RNA in Blood as Indicator of Severe Outcome in Middle East Respiratory Syndrome Coronavirus Infection. Emerg Infect Dis 2016; 22:1813-6. [PMID: 27479636 PMCID: PMC5038397 DOI: 10.3201/eid2210.160218] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We evaluated the diagnostic and clinical usefulness of blood specimens to detect Middle East respiratory syndrome coronavirus infection in 21 patients from the 2015 outbreak in South Korea. Viral RNA was detected in blood from 33% of patients at initial diagnosis, and the detection preceded a worse clinical course.
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Seong MW, Kim SY, Corman VM, Kim TS, Cho SI, Kim MJ, Lee SJ, Lee JS, Seo SH, Ahn JS, Yu BS, Park N, Oh MD, Park WB, Lee JY, Kim G, Joh JS, Jeong I, Kim EC, Drosten C, Park SS. Microevolution of Outbreak-Associated Middle East Respiratory Syndrome Coronavirus, South Korea, 2015. Emerg Infect Dis 2016; 22:327-30. [PMID: 26814649 PMCID: PMC4734539 DOI: 10.3201/eid2202.151700] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
During the 2015 Middle East respiratory syndrome coronavirus outbreak in South Korea, we sequenced full viral genomes of strains isolated from 4 patients early and late during infection. Patients represented at least 4 generations of transmission. We found no evidence of changes in the evolutionary rate and no reason to suspect adaptive changes in viral proteins.
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Loerbroks A, Cho SI, Dollard M, Zou J, Fischer JE, Jiang Y, Angerer P, Herr R, Li J. Associations between work stress and suicidal ideation: pooled findings from six cross-sectional studies. Gesundheitswesen 2016. [DOI: 10.1055/s-0036-1586558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Seo SH, Lee SJ, Park S, Kim MJ, Song JY, Ra EK, Cho SI, Kim HK, Yang MG, Kim JY, Park SS, Seong MW. Performance of two commercially available BCR-ABL1 quantification assays that use an international reporting scale. Clin Chem Lab Med 2016; 54:1157-60. [PMID: 26587743 DOI: 10.1515/cclm-2015-0611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/17/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND Quantifying the BCR-ABL1 rearrangement is important for monitoring chronic myelogenous leukemia (CML). To standardize BCR-ABL1 quantification, the World Health Organization (WHO) established the first international genetic reference panel. Here, we compared the BCR-ABL1 levels determined using international scale (IS)-based commercially available assays. METHODS BCR-ABL1 transcripts were quantified using two IS-based assays. 10-1, 10-2, 10-3, 10-4, 10-5 and 10-6 dilutions of the b3a2 positive RNA were used for evaluating linearity, precision, and limit of detection. Correlation of the assay was evaluated by using DNA obtained from CML patients carrying the BCR-ABL1 b3a2 and b2a2 types. RESULTS Both Ipsogen and Asuragen assays showed fine linearity with reasonable %CV. LOD of each assay was calculated as 0.003% for Ipsogen, and 0.005% for Asuragen. By comparing the results that were lower than 10% by either one of the assay, Ipsogen and Asuragen results showed an overall good linear correlation with a tendency for the Ipsogen assay to show slightly higher levels than the Asuragen assay for b3a2 transcript. For b2a2, the tendency was opposite, with Asuragen showing higher values than the Ipsogen. CONCLUSIONS Two commercially available IS-based BCR-ABL1 assays showed an overall good quantitative correlation. It should be taken into consideration that each assay tended to produce higher values than the other, depending on the BCR-ABL1 subtypes, suggesting that a separate conversion factor for each subtype can be more helpful when BCR-ABL1 transcript levels are converted into IS.
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Abstract
Agastachis Herba is one of the well-known medicinal herbs in Korean traditional medicine. This study was taken up to examine the beneficial effects of Agastachis Herba on a mice model of asthma. BALB/c mice were sensitized and challenged with ovalbumin to produce a murine model of asthma. Methanol extracts of Agastachis Herba were orally administered to the ovalbumin-induced asthmatic mice. The effects of methanol extract of Agastachis Herba on airway hyper responsiveness, immune cell distributions in bronchoalveolar lavage fluid, ovalbumin-specific immunoglobulin E in serum, and histopathological changes were evaluated. Mice treated with the methanol extract of Agastachis Herba showed reduction of airway hyper responsiveness as well as inhibited immune cell infiltration in bronchoalveolar region. Also ovalbumin-specific immunoglobulin E levels in bronchoalveolar lavage fluid significantly decreased in extract treated mice. Histopathological findings showed significant beneficial changes in inflammatory cell infiltration.
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Affiliation(s)
- C Y Lim
- College of Medicine, Dongguk University, Ilsan, Gyounggi-do, Korea
| | - B Y Kim
- Herbal Medicine Research Division, Korea Institute of Oriental Medicine, Daejeon, Korea
| | - S H Lim
- School of Public Health, Far East University, Chungbuk, Korea
| | - S I Cho
- School of Korean Medicine, Pusan National University, Yangsan, Korea
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Je UK, Cho HM, Hong DK, Cho HS, Park YO, Park CK, Kim KS, Lim HW, Kim GA, Park SY, Woo TH, Cho SI. 3D reconstruction based on compressed-sensing (CS)-based framework by using a dental panoramic detector. Phys Med 2015; 32:213-7. [PMID: 26494155 DOI: 10.1016/j.ejmp.2015.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/22/2015] [Accepted: 09/24/2015] [Indexed: 10/22/2022] Open
Abstract
In this work, we propose a practical method that can combine the two functionalities of dental panoramic and cone-beam CT (CBCT) features in one by using a single panoramic detector. We implemented a CS-based reconstruction algorithm for the proposed method and performed a systematic simulation to demonstrate its viability for 3D dental X-ray imaging. We successfully reconstructed volumetric images of considerably high accuracy by using a panoramic detector having an active area of 198.4 mm × 6.4 mm and evaluated the reconstruction quality as a function of the pitch (p) and the angle step (Δθ). Our simulation results indicate that the CS-based reconstruction almost completely recovered the phantom structures, as in CBCT, for p≤2.0 and θ≤6°, indicating that it seems very promising for accurate image reconstruction even for large-pitch and few-view data. We expect the proposed method to be applicable to developing a cost-effective, volumetric dental X-ray imaging system.
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Affiliation(s)
- U K Je
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - H M Cho
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - D K Hong
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - H S Cho
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea.
| | - Y O Park
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - C K Park
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - K S Kim
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - H W Lim
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - G A Kim
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - S Y Park
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - T H Woo
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
| | - S I Cho
- Department of Radiation Convergence Engineering, iTOMO Research Group, Yonsei University, Wonju 220-710, Republic of Korea
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Seo SH, Yu YS, Park SW, Kim JH, Kim HK, Cho SI, Park H, Lee SJ, Seong MW, Park SS, Kim JY. Molecular Characterization ofFZD4,LRP5, andTSPAN12in Familial Exudative Vitreoretinopathy. ACTA ACUST UNITED AC 2015; 56:5143-51. [DOI: 10.1167/iovs.14-15680] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea
| | - Young Suk Yu
- Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Sung Wook Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Hun Kim
- Department of Ophthalmology, Seoul National University Hospital, Seoul, Korea
| | - Hyun Kyung Kim
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea
| | - Seung Jun Lee
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine Seoul National University Hospital, Seoul, Korea 4Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Ji Yeon Kim
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
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Seong MW, Cho A, Park HW, Seo SH, Lim BC, Seol D, Cho SI, Park SS, Chae JH. Clinical applications of next-generation sequencing-based gene panel in patients with muscular dystrophy: Korean experience. Clin Genet 2015; 89:484-488. [PMID: 26060040 DOI: 10.1111/cge.12621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 06/01/2015] [Accepted: 06/03/2015] [Indexed: 11/30/2022]
Abstract
Muscular dystrophy (MD) is a genetically and clinically heterogeneous group of disorders. Here, we performed targeted sequencing of 18 limb-girdle MD (LGMD)-related genes in 35 patients who were highly suspected of having MD. We identified one or more pathogenic variants in 23 of 35 patients (65.7%), and a genetic diagnosis was performed in 20 patients (57.1%). LGMD2B was the most common LGMD type, followed by LGMD1B, LGMD2A, and LGMD2G. Among the three major LGMD types in this group, LGMD1B was correlated with the lowest creatine kinase (CK) levels and the earliest onset, whereas LGMD2B was correlated with the highest CK levels and the latest onset. Thus, next-generation sequencing-based gene panels can be a helpful tool for the diagnosis of MDs, particularly in young children and those displaying atypical symptoms.
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Affiliation(s)
- M-W Seong
- Departments of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - A Cho
- Department of Pediatrics, College of Medicine, Ewha Womans University, Seoul, Korea
| | - H W Park
- Departments of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - S H Seo
- Departments of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - B C Lim
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - D Seol
- Departments of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - S I Cho
- Departments of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - S S Park
- Departments of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - J H Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul National University College of Medicine, Seoul, Korea
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Park H, Hong S, Cho SI, Cho TJ, Choi IH, Jin DK, Sohn YB, Park SW, Cho HH, Cheon JE, Kim SY, Kim JY, Park SS, Seong MW. Case of mild Schmid-type metaphyseal chondrodysplasia with novel sequence variation involving an unusual mutational site of the COL10A1 gene. Eur J Med Genet 2015; 58:175-9. [DOI: 10.1016/j.ejmg.2014.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
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50
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Lee SJ, Chae JH, Lee JA, Cho SI, Seo SH, Park H, Seong MW, Park SS. Non-homologous end joining repair mechanism-mediated deletion of CHD7 gene in a patient with typical CHARGE syndrome. Ann Lab Med 2015; 35:141-5. [PMID: 25553296 PMCID: PMC4272946 DOI: 10.3343/alm.2015.35.1.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 08/28/2014] [Accepted: 10/28/2014] [Indexed: 12/14/2022] Open
Abstract
CHARGE syndrome MIM #214800 is an autosomal dominant syndrome involving multiple congenital malformations. Clinical symptoms include coloboma, heart defects, choanal atresia, retardation of growth or development, genital hypoplasia, and ear anomalies or deafness. Mutations in the chromodomain helicase DNA binding protein 7 (CHD7) gene have been found in 65-70% of CHARGE syndrome patients. Here, we describe a 16-month-old boy with typical CHARGE syndrome, who was referred for CHD7 gene analysis. Sequence analysis and multiplex ligation-dependent probe amplification were performed. A heterozygous 38,304-bp deletion encompassing exon 3 with a 4-bp insertion was identified. There were no Alu sequences adjacent to the breakpoints, and no sequence microhomology was observed at the junction. Therefore, this large deletion may have been mediated by non-homologous end joining. The mechanism of the deletion in the current case differs from the previously suggested mechanisms underlying large deletions or complex genomic rearrangements in the CHD7 gene, and this is the first report of CHD7 deletion by this mechanism worldwide.
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Affiliation(s)
- Seung Jun Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jong Hee Chae
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Jung Ae Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
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