Journal of Pathology and Translational Medicine

Sung-Min Chun

3 Articles

BRCA-mutated gastric adenocarcinomas are associated with chromosomal instability and responsiveness to platinum-based chemotherapy: Ji Hyun Oh, Chang Ohk Sung, Hyung-Don Kim, Sung-Min Chun, Jihun Kim; J Pathol Transl Med. 2023;57(6):323-331. Published online November 14, 2023; DOI: https://doi.org/10.4132/jptm.2023.10.22

1,003 View
180 Download

Abstract PDF Supplementary Material: Background
Homologous recombination defect is an important biomarker of chemotherapy in certain tumor types, and the presence of pathogenic or likely pathogenic mutations involving BRCA1 or BRCA2 (p-BRCA) mutations is the most well-established marker for the homologous recombination defect. Gastric cancer, one of the most prevalent tumor types in Asia, also harbors p-BRCA mutations.
Methods
To investigate the clinical significance of p-BRCA mutations, we analyzed 366 gastric cancer cases through next-generation sequencing. We determined the zygosity of p-BRCA mutations based on the calculated tumor purity through variant allelic fraction patterns and investigated whether the presence of p-BRCA mutations is associated with platinum-based chemotherapy and a certain molecular subtype.
Results
Biallelic p-BRCA mutation was associated with better response to platinum-based chemotherapy than heterozygous p-BRCA mutation or wild type BRCA genes. The biallelic p-BRCA mutations was observed only in the chromosomal instability subtype, while all p-BRCA mutations were heterozygous in microsatellite instability subtype.
Conclusions
In conclusion, patients with gastric cancer harboring biallelic p-BRCA mutations were associated with a good initial response to platinum-based chemotherapy and those tumors were exclusively chromosomal instability subtype. Further investigation for potential association with homologous recombination defect is warranted.

Clinical Utility of a Fully Automated Microsatellite Instability Test with Minimal Hands-on Time: Miseon Lee, Sung-Min Chun, Chang Ohk Sung, Sun Y. Kim, Tae W. Kim, Se Jin Jang, Jihun Kim; J Pathol Transl Med. 2019;53(6):386-392. Published online October 11, 2019; DOI: https://doi.org/10.4132/jptm.2019.09.25

6,894 View
218 Download
16 Web of Science
14 Crossref

Background
Microsatellite instability (MSI) analysis is becoming increasingly important in many types of tumor including colorectal cancer (CRC). The commonly used MSI tests are either time-consuming or labor-intensive. A fully automated MSI test, the Idylla MSI assay, has recently been introduced. However, its diagnostic performance has not been extensively validated in clinical CRC samples.
Methods
We evaluated 133 samples whose MSI status had been rigorously validated by standard polymerase chain reaction (PCR), clinical nextgeneration sequencing (NGS) cancer panel test, or both. We evaluated the diagnostic performance of the Idylla MSI assay in terms of sensitivity, specificity, and positive and negative predictive values, as well as various sample requirements, such as minimum tumor purity and the quality of paraffin blocks.
Results
Compared with the gold standard results confirmed through both PCR MSI test and NGS, the Idylla MSI assay showed 99.05% accuracy (104/105), 100% sensitivity (11/11), 98.94% specificity (93/94), 91.67% positive predictive value (11/12), and 100% negative predictive value (93/93). In addition, the Idylla MSI assay did not require macro-dissection in most samples and reliably detected MSI-high in samples with approximately 10% tumor purity. The total turnaround time was about 150 minutes and the hands-on time was less than 2 minutes.
Conclusions
The Idylla MSI assay shows good diagnostic performance that is sufficient for its implementation in the clinic to determine the MSI status of at least the CRC samples. In addition, the fully automated procedure requires only a few slices of formalin-fixed paraffin-embedded tissue and might greatly save time and labor.

Citations

Citations to this article as recorded by

Integration of rapid PCR testing as an adjunct to NGS in diagnostic pathology services within the UK: evidence from a case series of non-squamous, non-small cell lung cancer (NSCLC) patients with follow-up
Alison Finall, Gareth Davies, Trevor Jones, Gwion Emlyn, Pearl Huey, Anna Mullard
Journal of Clinical Pathology.2023; 76(6): 391. CrossRef
Analytical Validation and Clinical Utilization of the Oncomine Comprehensive Assay Plus Panel for Comprehensive Genomic Profiling in Solid Tumors
Catherine I. Dumur, Ramakrishnan Krishnan, Jorge A. Almenara, Kathleen E. Brown, Kailyn R. Dugan, Christiana Farni, Fatima Z. Ibrahim, Naomi A. Sanchez, Sumra Rathore, Dinesh Pradhan, Jonathan H. Hughes
Journal of Molecular Pathology.2023; 4(2): 109. CrossRef
Performance of Immunohistochemical and Molecular Methods in Detecting Microsatellite Instability in Gastric Cancer: A Multicenter Study
Diogo Sousa Marques, Irene Gullo, Luís Mascarenhas-Lemos, João Ricardo Silva, Catarina Neto do Nascimento, Patrícia Pontes, Lídia Pinho, Luis Cirnes, Xiaogang Wen, Marília Cravo, Fátima Carneiro
Pathobiology.2023; 90(6): 389. CrossRef
Diagnostic mutationnel rapide Idylla™ : applications théranostiques actuelles et futures
Amélie Bourhis, Annabelle Remoué, Laura Samaison, Arnaud Uguen
Annales de Pathologie.2022; 42(4): 329. CrossRef
Comparison of the Idylla™ MSI assay with the Promega™ MSI Analysis System and immunohistochemistry on formalin-fixed paraffin-embedded tissue of endometrial carcinoma: results from an international, multicenter study
Sonia Gatius, Ana Velasco, Mar Varela, Miriam Cuatrecasas, Pedro Jares, Lisa Setaffy, Benjamin Bonhomme, Almudena Santon, Kristina Lindemann, Sabrina Croce, Ben Davidson, Sigurd Lax, Jose Palacios, Xavier Matias-Guiu
Virchows Archiv.2022; 480(5): 1031. CrossRef
Idylla MSI test combined with immunohistochemistry is a valuable and cost effective strategy to search for microsatellite instable tumors of noncolorectal origin
Laura Samaison, Arnaud Uguen
Pathology International.2022; 72(4): 234. CrossRef
Detection of microsatellite instability in a panel of solid tumours with the Idylla MSI Test using extracted DNA
Adrien Pécriaux, Loetitia Favre, Julien Calderaro, Cécile Charpy, Jonathan Derman, Anaïs Pujals
Journal of Clinical Pathology.2021; 74(1): 36. CrossRef
Idylla microsatellite instability assay versus mismatch repair immunohistochemistry: a retrospective comparison in gastric adenocarcinoma
Luke Farmkiss, Ilona Hopkins, Mary Jones
Journal of Clinical Pathology.2021; 74(9): 604. CrossRef
Multi-center real-world comparison of the fully automated Idylla™ microsatellite instability assay with routine molecular methods and immunohistochemistry on formalin-fixed paraffin-embedded tissue of colorectal cancer
Ana Velasco, Fatma Tokat, Jesper Bonde, Nicola Trim, Elisabeth Bauer, Adam Meeney, Wendy de Leng, George Chong, Véronique Dalstein, Lorand L. Kis, Jon A. Lorentzen, Snjezana Tomić, Keeley Thwaites, Martina Putzová, Astrid Birnbaum, Romena Qazi, Vanessa Pr
Virchows Archiv.2021; 478(5): 851. CrossRef
Detection of microsatellite instability with Idylla MSI assay in colorectal and endometrial cancer
Iiris Ukkola, Pirjo Nummela, Annukka Pasanen, Mia Kero, Anna Lepistö, Soili Kytölä, Ralf Bützow, Ari Ristimäki
Virchows Archiv.2021; 479(3): 471. CrossRef
Managing Difficulties of Microsatellite Instability Testing in Endometrial Cancer-Limitations and Advantages of Four Different PCR-Based Approaches
Janna Siemanowski, Birgid Schömig-Markiefka, Theresa Buhl, Anja Haak, Udo Siebolts, Wolfgang Dietmaier, Norbert Arens, Nina Pauly, Beyhan Ataseven, Reinhard Büttner, Sabine Merkelbach-Bruse
Cancers.2021; 13(6): 1268. CrossRef
Evaluation of Micro Satellite Instability and Mismatch Repair Status in Different Solid Tumors: A Multicenter Analysis in a Real World Setting
Umberto Malapelle, Paola Parente, Francesco Pepe, Caterina De Luca, Pasquale Pisapia, Roberta Sgariglia, Mariantonia Nacchio, Gianluca Gragnano, Gianluca Russo, Floriana Conticelli, Claudio Bellevicine, Elena Vigliar, Antonino Iaccarino, Claudia Covelli,
Cells.2021; 10(8): 1878. CrossRef
Novel Biocartis Idylla™ cartridge-based assay for detection of microsatellite instability in colorectal cancer tissues
Andres E. Mindiola-RomeroMD, Donald C. GreenBS, M. Rabie Al-TurkmaniPhD, Kelley N. GodwinBS, Anna C. MackayBS, Laura J. TafeMD, Bing RenMD, Gregory J. TsongalisPhD
Experimental and Molecular Pathology.2020; 116: 104519. CrossRef
Evaluation of 3 molecular-based assays for microsatellite instability detection in formalin-fixed tissues of patients with endometrial and colorectal cancers
Pauline Gilson, Julien Levy, Marie Rouyer, Jessica Demange, Marie Husson, Céline Bonnet, Julia Salleron, Agnès Leroux, Jean-Louis Merlin, Alexandre Harlé
Scientific Reports.2020;[Epub] CrossRef

Good Laboratory Standards for Clinical Next-Generation Sequencing Cancer Panel Tests: Jihun Kim, Woong-Yang Park, Nayoung K. D. Kim, Se Jin Jang, Sung-Min Chun, Chang-Ohk Sung, Jene Choi, Young-Hyeh Ko, Yoon-La Choi, Hyo Sup Shim, Jae-Kyung Won; J Pathol Transl Med. 2017;51(3):191-204. Published online May 10, 2017; DOI: https://doi.org/10.4132/jptm.2017.03.14

22,948 View
1,056 Download
30 Web of Science
31 Crossref

Abstract PDF

Next-generation sequencing (NGS) has recently emerged as an essential component of personalized cancer medicine due to its high throughput and low per-base cost. However, no sufficient guidelines for implementing NGS as a clinical molecular pathology test are established in Korea. To ensure clinical grade quality without inhibiting adoption of NGS, a taskforce team assembled by the Korean Society of Pathologists developed laboratory guidelines for NGS cancer panel testing procedures and requirements for clinical implementation of NGS. This consensus standard proposal consists of two parts: laboratory guidelines and requirements for clinical NGS laboratories. The laboratory guidelines part addressed several important issues across multistep NGS cancer panel tests including choice of gene panel and platform, sample handling, nucleic acid management, sample identity tracking, library preparation, sequencing, analysis and reporting. Requirements for clinical NGS tests were summarized in terms of documentation, validation, quality management, and other required written policies. Together with appropriate pathologist training and international laboratory standards, these laboratory standards would help molecular pathology laboratories to successfully implement NGS cancer panel tests in clinic. In this way, the oncology community would be able to help patients to benefit more from personalized cancer medicine.

Citations

Citations to this article as recorded by

Validation and Clinical Application of ONCOaccuPanel for Targeted Next-Generation Sequencing of Solid Tumors
Moonsik Kim, Changseon Lee, Juyeon Hong, Juhee Kim, Ji Yun Jeong, Nora Jee-Young Park, Ji-Eun Kim, Ji Young Park
Cancer Research and Treatment.2023; 55(2): 429. CrossRef
Establishing molecular pathology curriculum for pathology trainees and continued medical education: a collaborative work from the Molecular Pathology Study Group of the Korean Society of Pathologists
Jiwon Koh, Ha Young Park, Jeong Mo Bae, Jun Kang, Uiju Cho, Seung Eun Lee, Haeyoun Kang, Min Eui Hong, Jae Kyung Won, Youn-La Choi, Wan-Seop Kim, Ahwon Lee
Journal of Pathology and Translational Medicine.2023; 57(5): 265. CrossRef
Clinical applications of next-generation sequencing in the diagnosis of genetic disorders in Korea: a narrative review
Jihoon G. Yoon, Man Jin Kim, Yong Jin Kwon, Jong-Hee Chae
Journal of the Korean Medical Association.2023; 66(10): 613. CrossRef
Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study
Mustafa Umit Oner, Jianbin Chen, Egor Revkov, Anne James, Seow Ye Heng, Arife Neslihan Kaya, Jacob Josiah Santiago Alvarez, Angela Takano, Xin Min Cheng, Tony Kiat Hon Lim, Daniel Shao Weng Tan, Weiwei Zhai, Anders Jacobsen Skanderup, Wing-Kin Sung, Hwee
Patterns.2022; 3(2): 100399. CrossRef
Update on Molecular Diagnosis in Extranodal NK/T-Cell Lymphoma and Its Role in the Era of Personalized Medicine
Ka-Hei (Murphy) Sun, Yin-Ting (Heylie) Wong, Ka-Man (Carmen) Cheung, Carmen (Michelle) Yuen, Yun-Tat (Ted) Chan, Wing-Yan (Jennifer) Lai, Chun (David) Chao, Wing-Sum (Katie) Fan, Yuen-Kiu (Karen) Chow, Man-Fai Law, Ho-Chi (Tommy) Tam
Diagnostics.2022; 12(2): 409. CrossRef
Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data
Chad M. Vanderbilt, Anita S. Bowman, Sumit Middha, Kseniya Petrova-Drus, Yi-Wei Tang, Xin Chen, Youxiang Wang, Jason Chang, Natasha Rekhtman, Klaus J. Busam, Sounak Gupta, Meera Hameed, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Snjezana Dogan, Ahm
The Journal of Molecular Diagnostics.2022; 24(5): 515. CrossRef
Performance Evaluation of Three DNA Sample Tracking Tools in a Whole Exome Sequencing Workflow
Gertjan Wils, Céline Helsmoortel, Pieter-Jan Volders, Inge Vereecke, Mauro Milazzo, Jo Vandesompele, Frauke Coppieters, Kim De Leeneer, Steve Lefever
Molecular Diagnosis & Therapy.2022; 26(4): 411. CrossRef
Clinical Quality Considerations when Using Next-Generation Sequencing (NGS) in Clinical Drug Development
Timothé Ménard, Alaina Barros, Christopher Ganter
Therapeutic Innovation & Regulatory Science.2021; 55(5): 1066. CrossRef
Fast Healthcare Interoperability Resources (FHIR)–Based Quality Information Exchange for Clinical Next-Generation Sequencing Genomic Testing: Implementation Study
Donghyeong Seong, Sungwon Jung, Sungchul Bae, Jongsuk Chung, Dae-Soon Son, Byoung-Kee Yi
Journal of Medical Internet Research.2021; 23(4): e26261. CrossRef
Status of Next-Generation Sequencing-Based Genetic Diagnosis in Hematologic Malignancies in Korea (2017-2018)
JinJu Kim, Ja Young Lee, Jungwon Huh, Myung-Hyun Nam, Myungshin Kim, Young-Uk Cho, Sun-Young Kong, Seung-Tae Lee, In-Suk Kim
Laboratory Medicine Online.2021; 11(1): 25. CrossRef
MSI-Testung
Josef Rüschoff, Gustavo Baretton, Hendrik Bläker, Wolfgang Dietmaier, Manfred Dietel, Arndt Hartmann, Lars-Christian Horn, Korinna Jöhrens, Thomas Kirchner, Ruth Knüchel, Doris Mayr, Sabine Merkelbach-Bruse, Hans-Ulrich Schildhaus, Peter Schirmacher, Mark
Der Pathologe.2021; 42(4): 414. CrossRef
Molecular biomarker testing for non–small cell lung cancer: consensus statement of the Korean Cardiopulmonary Pathology Study Group
Sunhee Chang, Hyo Sup Shim, Tae Jung Kim, Yoon-La Choi, Wan Seop Kim, Dong Hoon Shin, Lucia Kim, Heae Surng Park, Geon Kook Lee, Chang Hun Lee
Journal of Pathology and Translational Medicine.2021; 55(3): 181. CrossRef
MSI testing
Josef Rüschoff, Gustavo Baretton, Hendrik Bläker, Wolfgang Dietmaier, Manfred Dietel, Arndt Hartmann, Lars-Christian Horn, Korinna Jöhrens, Thomas Kirchner, Ruth Knüchel, Doris Mayr, Sabine Merkelbach-Bruse, Hans-Ulrich Schildhaus, Peter Schirmacher, Mark
Der Pathologe.2021; 42(S1): 110. CrossRef
16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer
Huisong Lee, Hyeon Kook Lee, Seog Ki Min, Won Hee Lee
World Journal of Surgical Oncology.2020;[Epub] CrossRef
Risk Stratification Using a Novel Genetic Classifier IncludingPLEKHS1Promoter Mutations for Differentiated Thyroid Cancer with Distant Metastasis
Chan Kwon Jung, Seung-Hyun Jung, Sora Jeon, Young Mun Jeong, Yourha Kim, Sohee Lee, Ja-Seong Bae, Yeun-Jun Chung
Thyroid.2020; 30(11): 1589. CrossRef
Biomarker testing for advanced lung cancer by next-generation sequencing; a valid method to achieve a comprehensive glimpse at mutational landscape
Anurag Mehta, Smreti Vasudevan, Sanjeev Kumar Sharma, Manoj Panigrahi, Moushumi Suryavanshi, Mumtaz Saifi, Ullas Batra
Applied Cancer Research.2020;[Epub] CrossRef
Application Areas of Traditional Molecular Genetic Methods and NGS in relation to Hereditary Urological Cancer Diagnosis
Dmitry S. Mikhaylenko, Alexander S. Tanas, Dmitry V. Zaletaev, Marina V. Nemtsova
Journal of Oncology.2020; 2020: 1. CrossRef
Assembling and Validating Bioinformatic Pipelines for Next-Generation Sequencing Clinical Assays
Jeffrey A SoRelle, Megan Wachsmann, Brandi L. Cantarel
Archives of Pathology & Laboratory Medicine.2020; 144(9): 1118. CrossRef
Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples
Erica K. Barnell, Peter Ronning, Katie M. Campbell, Kilannin Krysiak, Benjamin J. Ainscough, Lana M. Sheta, Shahil P. Pema, Alina D. Schmidt, Megan Richters, Kelsy C. Cotto, Arpad M. Danos, Cody Ramirez, Zachary L. Skidmore, Nicholas C. Spies, Jasreet Hun
Genetics in Medicine.2019; 21(4): 972. CrossRef
A DNA pool of FLT3-ITD positive DNA samples can be used efficiently for analytical evaluation of NGS-based FLT3-ITD quantitation - Testing several different ITD sequences and rates, simultaneously
Zoltán A. Mezei, Dávid Tornai, Róza Földesi, László Madar, Andrea Sümegi, Mária Papp, Péter Antal-Szalmás
Journal of Biotechnology.2019; 303: 25. CrossRef
Pharmacogenomic Testing: Clinical Evidence and Implementation Challenges
Hippman, Nislow
Journal of Personalized Medicine.2019; 9(3): 40. CrossRef
Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study
Dohee Kwon, Binnari Kim, Hyeong Chan Shin, Eun Ji Kim, Sang Yun Ha, Kee-Taek Jang, Seung Tae Kim, Jeeyun Lee, Won Ki Kang, Joon Oh Park, Kyoung-Mee Kim
Translational Oncology.2019; 12(11): 1488. CrossRef
Analytical Evaluation of an NGS Testing Method for Routine Molecular Diagnostics on Melanoma Formalin-Fixed, Paraffin-Embedded Tumor-Derived DNA
Mancini, Simi, Salvianti, Castiglione, Sonnati, Pinzani
Diagnostics.2019; 9(3): 117. CrossRef
Benchmark Database for Process Optimization and Quality Control of Clinical Cancer Panel Sequencing
Donghyeong Seong, Jongsuk Chung, Ki-Wook Lee, Sook-Young Kim, Byung-Suk Kim, Jung-Keun Song, Sungwon Jung, Taeseob Lee, Donghyun Park, Byoung-Kee Yi, Woong-Yang Park, Dae-Soon Son
Biotechnology and Bioprocess Engineering.2019; 24(5): 793. CrossRef
Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients
Simon Heeke, Véronique Hofman, Elodie Long-Mira, Virginie Lespinet, Salomé Lalvée, Olivier Bordone, Camille Ribeyre, Virginie Tanga, Jonathan Benzaquen, Sylvie Leroy, Charlotte Cohen, Jérôme Mouroux, Charles Marquette, Marius Ilié, Paul Hofman
Cancers.2018; 10(4): 88. CrossRef
Use of the Ion AmpliSeq Cancer Hotspot Panel in clinical molecular pathology laboratories for analysis of solid tumours: With emphasis on validation with relevant single molecular pathology tests and the Oncomine Focus Assay
Ahwon Lee, Sung-Hak Lee, Chan Kwon Jung, Gyungsin Park, Kyo Young Lee, Hyun Joo Choi, Ki Ouk Min, Tae Jung Kim, Eun Jung Lee, Youn Soo Lee
Pathology - Research and Practice.2018; 214(5): 713. CrossRef
Recent Advancement of the Molecular Diagnosis in Pediatric Brain Tumor
Jeong-Mo Bae, Jae-Kyung Won, Sung-Hye Park
Journal of Korean Neurosurgical Society.2018; 61(3): 376. CrossRef
The long tail of molecular alterations in non-small cell lung cancer: a single-institution experience of next-generation sequencing in clinical molecular diagnostics
Caterina Fumagalli, Davide Vacirca, Alessandra Rappa, Antonio Passaro, Juliana Guarize, Paola Rafaniello Raviele, Filippo de Marinis, Lorenzo Spaggiari, Chiara Casadio, Giuseppe Viale, Massimo Barberis, Elena Guerini-Rocco
Journal of Clinical Pathology.2018; 71(9): 767. CrossRef
Clinical laboratory utilization management and improved healthcare performance
Christopher Naugler, Deirdre L. Church
Critical Reviews in Clinical Laboratory Sciences.2018; 55(8): 535. CrossRef
Development of HLA-A, -B and -DR Typing Method Using Next-Generation Sequencing
Dong Hee Seo, Jeong Min Lee, Mi Ok Park, Hyun Ju Lee, Seo Yoon Moon, Mijin Oh, So Young Kim, Sang-Heon Lee, Ki-Eun Hyeong, Hae-Jin Hu, Dae-Yeon Cho
The Korean Journal of Blood Transfusion.2018; 29(3): 310. CrossRef
Value-based genomics
Jun Gong, Kathy Pan, Marwan Fakih, Sumanta Pal, Ravi Salgia
Oncotarget.2018; 9(21): 15792. CrossRef

Author index