https://ir.ymlib.yonsei.ac.kr/handle/22282913/168814 2026-05-12T23:12:36Z 2026-05-12T23:12:36Z Kang, Yehyun Lee, Hyeonah Park, Yu Jin Lee, Seung-Tae Choi, Jong Rak Shin, Saeam https://ir.ymlib.yonsei.ac.kr/handle/22282913/212030 2026-04-30T03:08:34Z 2026-04-01T00:00:00Z

Title: Comparative evaluation of two NGS-based assays for somatic hypermutation analysis of IGHV genes in chronic lymphocytic leukemia Authors: Kang, Yehyun; Lee, Hyeonah; Park, Yu Jin; Lee, Seung-Tae; Choi, Jong Rak; Shin, Saeam Abstract: PurposeSomatic hypermutation (SHM) of the immunoglobulin heavy chain variable (IGHV) region is a key prognostic marker in chronic lymphocytic leukemia (CLL). Traditionally, SHM status has been determined using Sanger sequencing (SS); however, next-generation sequencing (NGS) provides an alternative method for assessing both SHM status and clonal rearrangements. This study aimed to compare the performance of two commercially available NGS assays for evaluating IGH clonality and SHM status in CLL.MethodsIn this retrospective study, 42 samples from patients diagnosed with CLL were analyzed. Genomic DNA extracted from peripheral blood or bone marrow aspirates was analyzed using two commercial NGS assays: the LymphoTrack (R) IGHV Leader (Leader) and IGH FR1 (FR1) assays (Invivoscribe, CA, USA). SS was performed as the reference method for SHM assessment.ResultsThe Leader assay identified clonality in 95.2% of cases, whereas the FR1 assay detected clonality in 88.1%. Conclusive SHM status was determined in 90.5% of samples using the Leader assay and in 76.2% using the FR1 assay; when results from both assays were combined, the rate increased to 92.9%. Among samples with conclusive results by both SS and each NGS assay, the Leader assay demonstrated higher concordance with SS (97.1%, 34/35) than the FR1 assay (86.2%, 25/29). Greater variability in clonal detection was observed with the FR1 assay.ConclusionThese findings indicate that the Leader assay provides a more reliable assessment of SHM status, with higher concordance with SS. Although the FR1 assay may offer additional information regarding clonal patterns, its results should be interpreted cautiously. Given the limited sample size, further studies are warranted to validate these findings. Overall, the Leader assay appears to be more suitable as a primary tool for SHM evaluation, with FR1 results serving a complementary role when interpreted in clinical context.

2026-04-01T00:00:00Z Jhang, Jin Ho Ahn, Kwangjin Kim, Dokyun Jeong, Seok Hoon Kim, Hyun Soo Kim, Young Ree Kim, Young Ah Shin, Kyeong Seob Shin, Jeong Hwan Park, Jeong Su Park, Kyoung Un Kwon, Yong Jun Kim, Soo Hyun Shin, Jong Hee Ahn, Soon Young Lee, Sung Young Bae, Song-mee Yoo, Jung Sik Uh, Young https://ir.ymlib.yonsei.ac.kr/handle/22282913/212154 2026-05-12T08:36:03Z 2026-04-01T00:00:00Z

Title: Application of Long-Read Whole-Genome Sequencing to Clarify Genotypic-Phenotypic Discrepancies in Methicillin-Resistant Staphylococcus aureus Authors: Jhang, Jin Ho; Ahn, Kwangjin; Kim, Dokyun; Jeong, Seok Hoon; Kim, Hyun Soo; Kim, Young Ree; Kim, Young Ah; Shin, Kyeong Seob; Shin, Jeong Hwan; Park, Jeong Su; Park, Kyoung Un; Kwon, Yong Jun; Kim, Soo Hyun; Shin, Jong Hee; Ahn, Soon Young; Lee, Sung Young; Bae, Song-mee; Yoo, Jung Sik; Uh, Young Abstract: Background/Objectives: The Korean Global Antimicrobial Resistance Surveillance System monitors bloodstream Staphylococcus aureus infections by combining antimicrobial susceptibility testing (AST) with conventional polymerase chain reaction (PCR). Considering the clinical significance of methicillin-resistant S. aureus (MRSA), we performed an in-depth analysis of isolates showing genotypic-phenotypic discrepancies. Methods: Isolates were collected from designated collection centers in the Republic of Korea between 2017 and 2024. The 30 mu g cefoxitin disk diffusion method was used to define the phenotypes. PCR targeting mecA and the staphylococcal cassette chromosome mec (SCCmec) was used to identify genotypes through gel electrophoresis. Long-read whole-genome sequencing (WGS) was performed using the Revio system (Pacific Biosciences) for isolates exhibiting discrepancies between phenotypes and genotypes. Results: In total, 5808 isolates were screened, and seven cases of genotypic-phenotypic discrepancies were identified, including one infant and six elderly patients with chromosomal SCCmec type IV. Although WGS confirmed intact PCR primer-binding sites, structural alterations were observed: three isolates had normal-length mecA and mecR1, two had partial deletions in mecA, and two featured either mecA or mecR1 split into two proteins. Notably, although the six isolates with intact mecR1 genes matched the nucleotide length of SCCmec type IV, their sequences exhibited high homology with SCCmec type II. Conclusions: Despite the presence of mecA, the non-standard configuration of regulatory genes within the SCCmec elements suppressed actual resistance expression. Because conventional PCR focusing on partial gene segments could overlook such phenotypic traits, the meticulous observation and implementation of WGS are crucial for the accurate characterization of genotypic-phenotypic discrepancies.

2026-04-01T00:00:00Z Park, Mikyoung Choi, Hyun-Woo Lim, Jihyang Shin, Kyung-Hwa Oh, Eun-Jee Song, Jaewoo Kim, Kyeong-Hee Jeong, In Hwa Park, Joo-Heon Hwang, Sang-Hyun Kang, Eun-Suk https://ir.ymlib.yonsei.ac.kr/handle/22282913/211251 2026-03-16T04:50:10Z 2026-03-01T00:00:00Z

Title: Considerations of Flow Cytometric Lymphocyte Subset Analysis in Korea Based on a Survey of Current Clinical Laboratory Practice Authors: Park, Mikyoung; Choi, Hyun-Woo; Lim, Jihyang; Shin, Kyung-Hwa; Oh, Eun-Jee; Song, Jaewoo; Kim, Kyeong-Hee; Jeong, In Hwa; Park, Joo-Heon; Hwang, Sang-Hyun; Kang, Eun-Suk Abstract: Flow cytometric lymphocyte subset analysis (FCLSA) is essential for assessing immune status across various diseases and clinical settings. We surveyed current clinical laboratory practices related to FCLSA to establish a baseline reference for future standardization in Korea. Nine university hospitals actively performing FCLSA responded to the 22-question survey, which covered seven categories of laboratory practice. These hospitals used commercial reagent antibody kits from either Beckton Dickinson Biosciences (N= 4) or Beckman Coulter Diagnostics (N =5). Most hospitals performed daily instrument setup and scheduled maintenance every 2-6 months. Two levels of commercial quality control materials were routinely used each day. Sample and reagent antibody volumes varied across hospitals, even when the same reagent kit was used. Acquired cell counts ranged from 5 & times; 103 to 5 & times; 104 cells, with two hospitals adjusting counts based on the cell type analyzed. Most laboratories reported percentages and general opinions; some additionally reported white blood cell and lymphocyte counts, along with lymphocyte percentages. This is the first comprehensive survey on the clinical laboratory practice of FCLSA in Korea. Standardization of FCLSA should be accelerated to ensure reliable and reproducible results.

2026-03-01T00:00:00Z Kim, Young Ah Kim, Hyunsoo Seo, Young Hee Lee, Kyungwon https://ir.ymlib.yonsei.ac.kr/handle/22282913/211260 2026-03-16T04:50:14Z 2026-03-01T00:00:00Z

Title: Prevalence and Molecular Epidemiology of Extended-Spectrum β-Lactamase-Producing Escherichia coli and Effects of Antimicrobial Use in Multiple Pig Industry Sectors in Korea Authors: Kim, Young Ah; Kim, Hyunsoo; Seo, Young Hee; Lee, Kyungwon Abstract: Background: The spread of antimicrobial-resistant bacteria has close relationships among humans, animals, and the environment, necessitating the implementation of the "One Health" approach. In previous study, the prevalence and molecular epidemiology of extended-spectrum (3-lactamase-producing Escherichia coli (ESBL-EC) were investigated across multiple pig industry sectors in Korea. In this study, animal developmental stages and antimicrobial usage policies on farms were also considered. Methods: A total of 6,288 non-duplicated samples were collected from pig farms, slaughterhouses, and their personnel from three provinces in Korea between 2020 and 2022. Antimicrobial susceptibility and ESBL gene characterization were performed on the samples. Results: Overall, 1,084 ESBL-EC isolates were collected, with positivity detection rates of 24.7%, 23.3%, 12.7%, 3.9%, 17.2% in pigs, workers, the environment, meat, and total samples, respectively. Common ESBL types were blaCTX-M-55 (N = 628), blaCTX-M-15 (N = 204), and blaCTX-M-14 (N =127). Pig-derived E. coli isolates had antimicrobial resistance (AMR) rates of 80.4%, 47.2%, 32.6%, 36.7%, 43.4%, 62.4%, and 72.1% to ampicillin, piperacillin, cefazoline, ciprofloxacin, cotrimoxazole, chloramphenicol, and tetracycline, respectively. AMR rates were lower in the finishing stage pigs than in the lactating stage pigs and tended to decrease during animal development for most antimicrobials. AMR rates were higher in pigfarms with a customary antimicrobial use policy than in those with a low-level antimicrobial use policy. Conclusions: The findings highlight the significance of elucidating AMR networks among humans, animals, and the environment. Prudent antimicrobial usage and continuous AMR monitoring in the pig industry are crucial to safeguard food safety.

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