1.Mock communities to assess biases in nextgeneration sequencing of bacterial species representation
Younjee HWANG ; Ju Yeong KIM ; Se Il KIM ; Ji Yeon SUNG ; Hye Su MOON ; Tai-Soon YONG ; Ki Ho HONG ; Hyukmin LEE ; Dongeun YONG
Annals of Clinical Microbiology 2025;28(1):3-
Background:
The 16S rRNA-targeted next-generation sequencing (NGS) has been widely used as the primary tool for microbiome analysis. However, whether the sequenced microbial diversity absolutely represents the original sample composition remains unclear. This study aimed to evaluate whether 16S rRNA gene-targeted NGS accurately captures bacterial community composition.
Methods:
Mock communities were constructed using equal amounts of DNA from 18 bacterial strains in three formats: genomic DNA, recombinant plasmids, and polymerase chain reaction (PCR) templates. The V3V4 region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq.
Results:
Data regression analysis revealed that the recombinant plasmid produced more accurate and precise correlation curve than that by the gDNA and PCR products, with a slope closest to 1 (1.0082) and the highest R² value (0.9975). Despite the same input amount of bacterial DNA, the NGS read distribution varied across all three mock communities. Using multiple regression analysis, we found that the guanine-cytosine (GC) content of the V3V4 region, 16S rRNA gene, size of gDNA, and copy number of 16S rRNA were significantly associated with the NGS output of each bacterial species.
Conclusion
This study demonstrated that recombinant plasmids are the preferred option for quality control and that NGS output is biased owing to certain bacterial characteristics, such as %GC content, gDNA size, and 16S rRNA gene copy number. Further research is required to develop a system that compensates for NGS process biases using mock communities.
2.The 2024 Korean Enhanced Recovery After Surgery (ERAS) guidelines for colorectal cancer: a secondary publication
Kil-yong LEE ; Soo Young LEE ; Miyoung CHOI ; Moonjin KIM ; Ji Hong KIM ; Ju Myung SONG ; Seung Yoon YANG ; In Jun YANG ; Moon Suk CHOI ; Seung Rim HAN ; Eon Chul HAN ; Sang Hyun HONG ; Do Joong PARK ; Sang-Jae PARK ;
Annals of Coloproctology 2025;41(1):3-26
The Korean Enhanced Recovery After Surgery (ERAS) Committee within the Korean Society of Surgical Metabolism and Nutrition was established to develop ERAS guidelines tailored to the Korean context. This guideline focuses on creating the most current evidence-based practice guidelines for ERAS purposes, based on systematic reviews. All key questions targeted randomized controlled trials exclusively, and if fewer than 2 were available, studies employing propensity score matching were also included. Recommendations for each key question were marked with strength of recommendation and level of evidence following internal and external review processes by the committee.
3.Harnessing Institutionally Developed Clinical Targeted Sequencing to Improve Patient Survival in Breast Cancer: A Seven-Year Experience
Jiwon KOH ; Jinyong KIM ; Go-Un WOO ; Hanbaek YI ; So Yean KWON ; Jeongmin SEO ; Jeong Mo BAE ; Jung Ho KIM ; Jae Kyung WON ; Han Suk RYU ; Yoon Kyung JEON ; Dae-Won LEE ; Miso KIM ; Tae-Yong KIM ; Kyung-Hun LEE ; Tae-You KIM ; Jee-Soo LEE ; Moon-Woo SEONG ; Sheehyun KIM ; Sungyoung LEE ; Hongseok YUN ; Myung Geun SONG ; Jaeyong CHOI ; Jong-Il KIM ; Seock-Ah IM
Cancer Research and Treatment 2025;57(2):443-456
Purpose:
Considering the high disease burden and unique features of Asian patients with breast cancer (BC), it is essential to have a comprehensive view of genetic characteristics in this population. An institutional targeted sequencing platform was developed through the Korea Research-Driven Hospitals project and was incorporated into clinical practice. This study explores the use of targeted next-generation sequencing (NGS) and its outcomes in patients with advanced/metastatic BC in the real world.
Materials and Methods:
We reviewed the results of NGS tests administered to BC patients using a customized sequencing platform—FiRST Cancer Panel (FCP)—over 7 years. We systematically described clinical translation of FCP for precise diagnostics, personalized therapeutic strategies, and unraveling disease pathogenesis.
Results:
NGS tests were conducted on 548 samples from 522 patients with BC. Ninety-seven point six percentage of tested samples harbored at least one pathogenic alteration. The common alterations included mutations in TP53 (56.2%), PIK3CA (31.2%), GATA3 (13.8%), BRCA2 (10.2%), and amplifications of CCND1 (10.8%), FGF19 (10.0%), and ERBB2 (9.5%). NGS analysis of ERBB2 amplification correlated well with human epidermal growth factor receptor 2 immunohistochemistry and in situ hybridization. RNA panel analyses found potentially actionable and prognostic fusion genes. FCP effectively screened for potentially germline pathogenic/likely pathogenic mutation. Ten point three percent of BC patients received matched therapy guided by NGS, resulting in a significant overall survival advantage (p=0.022), especially for metastatic BCs.
Conclusion
Clinical NGS provided multifaceted benefits, deepening our understanding of the disease, improving diagnostic precision, and paving the way for targeted therapies. The concrete advantages of FCP highlight the importance of multi-gene testing for BC, especially for metastatic conditions.
4.Alteration in gut microbiota after colonoscopy: proposed mechanisms and the role of probiotic interventions
Hyeong Ho JO ; Moon Young LEE ; Se Eun HA ; Dong Han YEOM ; Yong Sung KIM
Clinical Endoscopy 2025;58(1):25-39
Colonoscopy, a widely used procedure for diagnosing and treating colonic diseases, induces transient gastrointestinal symptoms and alterations in the gut microbiota. This review comprehensively examines the evidence on alterations in the gut microbiota following colonoscopy and their possible mechanisms. Factors such as rapid colonic evacuation, increased osmolality, and mucus thinning caused by bowel preparation and exposure to oxygen during the procedure contribute to these alterations. Typically, the alterations revert to the baseline within a short time. However, their long-term implications remain unclear, necessitating further investigation. Split-dose bowel preparation and CO2 insufflation during the procedure result in fewer alterations in the gut microbiota. Probiotic administration immediately after colonoscopy shows promise in reducing alterations and gastrointestinal symptoms. However, the widespread use of probiotics remains controversial due to the transient nature of both the symptoms and gut microbial alterations following a colonoscopy. Probiotics may offer greater benefits to individuals with preexisting gastrointestinal symptoms. Thus, probiotic administration may be a viable option for selected patients.
5.Primary Cholangiocarcinoma of the Liver Presenting as a Complicated Hepatic Cyst: A Diagnostic Challenge
Chang Won HA ; Sang Deok SHIN ; Myung Ji GOH ; Byeong Geun SONG ; Wonseok KANG ; Dong Hyun SINN ; Geum-Youn GWAK ; Yong-Han PAIK ; Moon Seok CHOI ; Joon Hyeok LEE
The Korean Journal of Gastroenterology 2025;85(1):83-88
Primary cholangiocarcinoma is a rare bile duct epithelial neoplasm that can present with atypical clinical manifestations, complicating its diagnosis. A 62-year-old male showed symptoms suggestive of a complicated hepatic cyst that was later identified as intrahepatic cholangiocarcinoma. The patient presented with abdominal discomfort without fever. Imaging revealed a large cystic lesion in the liver. Despite the initial treatment for a presumed abscess, a biopsy confirmed cholangiocarcinoma. This case highlights the diagnostic challenge of distinguishing between benign complicated hepatic cysts and malignancies, particularly when typical markers of infection are absent. Early biopsy and vigilant assessments are crucial in such presentations to avoid a delayed diagnosis and initiate appropriate treatment.
6.Miliary Tuberculosis Initially Presenting as an Isolated Hepatic Abscess
Chang Won HA ; Sang Deok SHIN ; Myung Ji GOH ; Byeong Geun SONG ; Wonseok KANG ; Dong Hyun SINN ; Geum-Youn GWAK ; Yong-Han PAIK ; Moon Seok CHOI ; Joon Hyeok LEE
The Korean Journal of Gastroenterology 2025;85(1):78-82
Hepatic tuberculosis, typically associated with miliary tuberculosis, can occasionally present as localized liver lesions. This case report describes a 77-year-old male presenting with persistent abdominal pain and fever, following an endoscopic retrograde cholangiopancreatography for bile duct sludge removal. Subsequent computed tomography revealed focal liver lesions. Despite initial treatment with antibiotics for a suspected inflammatory liver abscess, his condition did not improve. A liver biopsy was performed, revealing caseous granulomas, and the tuberculosis polymerase chain reaction result was positive. The patient was diagnosed with primary hepatic tuberculosis, which later disseminated. Oral anti-tuberculosis therapy was initiated and is currently being closely monitored. This case emphasizes the importance of considering hepatic tuberculosis in the differential diagnosis of liver lesions, particularly in cases involving cholestatic liver function tests, and persistent symptoms unresponsive to conventional antibiotics.
7.Do Strength and Anthropometric Size of the Lower Body Correlate with Serum Testosterone Levels?
Tae Yong PARK ; Moon Young CHOI ; Doohwan KONG ; Jeong Kyun YEO ; Min Gu PARK
The World Journal of Men's Health 2025;43(1):205-212
Purpose:
Although lower body strength and size are often regarded as symbols of masculinity, their relationship to testosterone is unclear. This study aimed to determine the correlation between lower body strength, size, and testosterone levels.
Materials and Methods:
Serum testosterone levels, waist circumference, and body mass index (BMI) were measured in 69 men with erectile dysfunction (age >40 years). The circumferences of the thigh and calf were measured, and the muscle strength of the knee joints was evaluated using an isokinetic dynamometer. Patients were classified into three groups according to testosterone levels (group 1, <230 ng/dL; group 2, 230 to 350 ng/dL; group 3, >350 ng/dL). Differences in calf and thigh circumference, bilateral knee extension, and flexion strength between the three groups were investigated using a one-way analysis of variance. Pearson’s chi-square test was used to assess differences in lifestyle habits and underlying diseases. A partial correlation analysis was conducted to determine the association between testosterone levels and lower body size and strength.
Results:
There was no difference in BMI among the three groups, but waist circumference was significantly larger in group 1 than in groups 2 and 3. When comparing weight-adjusted values, bilateral thigh circumference showed a significant difference among the three groups. There was also a significant difference between the three groups in the weight-adjusted left calf circumference and in the weight-adjusted right knee extension strength. The partial correlation test showed a significant positive correlation between thigh and calf circumference values adjusted for weight and serum testosterone levels. Weight-adjusted knee extension strength demonstrated a significant positive correlation with serum testosterone levels.
Conclusions
Weight-adjusted thigh and calf circumferences, along with the thigh-to-waist ratio, showed a positive correlation with testosterone levels. Weight-adjusted knee extension strength was positively correlated with testosterone levels. Therefore, a robust thigh and strong lower body are related to testosterone.
8.18F-FDOPA PET/CT in Oncology: Procedural Guideline by the KoreanSociety of Nuclear Medicine
Yong-Jin PARK ; Joon Ho CHOI ; Hyunjong LEE ; Seung Hwan MOON ; Inki LEE ; Joohee LEE ; Jang YOO ; Joon Young CHOI ;
Nuclear Medicine and Molecular Imaging 2025;59(1):41-49
This guideline outlines the use of 3,4-dihydroxy-6- 18F-fluoro-L-phenylalanine positron emission tomography / computed tomography for the diagnosis and management of neuroendocrine tumors, brain tumors, and other tumorous conditions. It provides detailed recommendations on patient preparation, imaging procedures, and result interpretation. Based on inter-national standards and adapted to local clinical practices, the guideline emphasizes safety, quality control, and the effec-tive application of 3,4-dihydroxy-6- 18F-fluoro-L-phenylalanine positron emission tomography / computed tomography for various tumors such as insulinomas, pheochromocytomas, and medullary thyroid carcinoma. It also addresses the use of premedication with carbidopa, fasting protocols, and optimal imaging techniques. The aim is to assist nuclear medicine professionals in delivering precise diagnoses, improving patient outcomes, and accommodating evolving medical knowl-edge and technology. This comprehensive document serves as a practical resource to enhance the accuracy, quality, and safety of 3,4-dihydroxy-6- 18F-fluoro-L-phenylalanine positron emission tomography / computed tomography in oncology.
9.Primary Cholangiocarcinoma of the Liver Presenting as a Complicated Hepatic Cyst: A Diagnostic Challenge
Chang Won HA ; Sang Deok SHIN ; Myung Ji GOH ; Byeong Geun SONG ; Wonseok KANG ; Dong Hyun SINN ; Geum-Youn GWAK ; Yong-Han PAIK ; Moon Seok CHOI ; Joon Hyeok LEE
The Korean Journal of Gastroenterology 2025;85(1):83-88
Primary cholangiocarcinoma is a rare bile duct epithelial neoplasm that can present with atypical clinical manifestations, complicating its diagnosis. A 62-year-old male showed symptoms suggestive of a complicated hepatic cyst that was later identified as intrahepatic cholangiocarcinoma. The patient presented with abdominal discomfort without fever. Imaging revealed a large cystic lesion in the liver. Despite the initial treatment for a presumed abscess, a biopsy confirmed cholangiocarcinoma. This case highlights the diagnostic challenge of distinguishing between benign complicated hepatic cysts and malignancies, particularly when typical markers of infection are absent. Early biopsy and vigilant assessments are crucial in such presentations to avoid a delayed diagnosis and initiate appropriate treatment.
10.Miliary Tuberculosis Initially Presenting as an Isolated Hepatic Abscess
Chang Won HA ; Sang Deok SHIN ; Myung Ji GOH ; Byeong Geun SONG ; Wonseok KANG ; Dong Hyun SINN ; Geum-Youn GWAK ; Yong-Han PAIK ; Moon Seok CHOI ; Joon Hyeok LEE
The Korean Journal of Gastroenterology 2025;85(1):78-82
Hepatic tuberculosis, typically associated with miliary tuberculosis, can occasionally present as localized liver lesions. This case report describes a 77-year-old male presenting with persistent abdominal pain and fever, following an endoscopic retrograde cholangiopancreatography for bile duct sludge removal. Subsequent computed tomography revealed focal liver lesions. Despite initial treatment with antibiotics for a suspected inflammatory liver abscess, his condition did not improve. A liver biopsy was performed, revealing caseous granulomas, and the tuberculosis polymerase chain reaction result was positive. The patient was diagnosed with primary hepatic tuberculosis, which later disseminated. Oral anti-tuberculosis therapy was initiated and is currently being closely monitored. This case emphasizes the importance of considering hepatic tuberculosis in the differential diagnosis of liver lesions, particularly in cases involving cholestatic liver function tests, and persistent symptoms unresponsive to conventional antibiotics.

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