Background: As nationwide government-led whole-genome sequencing (WGS) projects progress, optimizing the clinical integration of large-scale WGS results is crucial. We explored how the initial analysis from Korea’s First WGS Pilot Study for Rare Diseases was applied in clinical practice, and then we reanalyzed the data comprehensively at Samsung Medical Center (SMC) Seoul, Korea. Methods: A prospective cohort study designed to collect WGS data under a Korean national initiative was conducted from August 2020 to December 2021. We focused on patients with rare diseases recruited from 16 university hospitals. The participants included 5,000 individuals (2,200 probands and 2,800 family members). The initial WGS data and diagnostic reference reports (from 682 probands and 484 family members), generated based on the First Korean WGS Pilot Study for Rare Diseases, were subsequently reanalyzed by SMC. Results: The initial analysis of the First Korean WGS Pilot Study data revealed a diagnostic rate of 17%. Upon receiving these results, the SMC conducted two rounds of reanalysis, increasing the diagnostic rate from 15% in the first analysis, to 18% in the second, and finally to 24% in the third (P = 1.6 × 10 −5 ). Key factors in improving the genetic diagnosis included increased detection of novel (likely) pathogenic variants (P = 1.0 × 10 −4 ), improved diagnostic rates with larger family recruitment (P = 0.004), and refined clinical information for more precise genotype–phenotype correlation analysis (40%). Conclusions Although national WGS projects lay a foundation for rare disease diagnosis, hospital-level reanalysis and multidisciplinary collaborations are crucial for optimizing diagnostic outcomes.

Purpose: Molecular characteristics of synchronous colorectal cancers (SCRCs) remain incompletely elucidated, despite their importance in targeted therapy selection. We compared the molecular characteristics and somatic mutations between SCRCs. Materials and Methods: This retrospective study (2012-2014) included 98 consecutive patients with surgically resected SCRCs. Molecular characteristics, including microsatellite instability (MSI) and tumor-infiltrating lymphocytes (TILs), were analyzed for all cancer lesions. The intertumoral heterogeneity of SCRCs was evaluated using whole-exome sequencing (WES) for 18 cancers from nine patients with at least one MSI-high (MSI-H) tumor. Results: Twelve patients had at least one MSI-H tumor; five showed discordant MSI status. Mucinous adenocarcinoma frequency and TIL density were higher in patients with at least one MSI-H tumor than in those with only microsatellite-stable tumors. WES revealed that, except one patient (6.5%), most synchronous cancers shared few variants in each patient (0.09%-0.36%). The concordance rates for BRAF, KRAS, NRAS, and PIK3CA, in synchronous cancers from each patient were 66.7%, 66.7%, 66.7%, and 55.6%, respectively. Conclusion Although synchronous cancers shared a mutated gene, the mutation subtypes differed. SCRCs exhibited 5.1% MSI status discordance rate and a high discordance rate in somatic mutational variants. As intertumoral heterogeneity may affect the targeted therapy response, molecular analysis of all tumors is recommended for patients with SCRCs.

Purpose: To develop and validate an artificial intelligence (AI)-based personalized outcome prediction model for upper-urinary tract urothelial carcinoma patients undergoing radical nephroureterectomy. Materials and Methods: Data from patients who underwent radical nephroureterectomy between 2010 and 2020 across three hospitals were retrospectively analyzed. A model was developed using one tertiary center’s data and externally validated with data from two other hospitals. An AI model using XGBoost as risk estimator and bootstrapped Weibull Accelerated Failure Time model for 10-year survival probability was employed. Hyperparameter tuning used Optuna method. Model efficacy was assessed using concordance index, average Brier score, D-calibration, and six-month interval time-dependent area under the curve (AUC). Results: Of 1,039 patients, 627 qualified after excluding 50 with neoadjuvant chemotherapy. Model development used 564 patients (507 training, 57 test) with 9:1 stratified random split, plus 63 for internal validation and 362 for external validation. Significant parameters included preoperative glomerular filtration rate (p<0.001), hydroureteronephrosis (p=0.013), pathological N stage (p<0.001), concurrent carcinoma in situ (p<0.001), disease progression (p<0.001), and survival rate (p<0.001). Disease-free survival (DFS) model’s concordance index: internal validation 0.789, external validations 0.734 and 0.771. Overall survival (OS) model’s concordance index: internal validation 0.819, external validations 0.780 and 0.771. Mean time-dependent AUC was 0.66–0.77 for DFS and 0.67–0.80 for OS during 10-year periods. Conclusions AI-based model effectively predicts disease-free and OS outcomes for upper-urinary tract urothelial carcinoma patients with post-radical nephroureterectomy, showcasing robust performance across multicenter settings.

Purpose: To assess the accuracy of supraspinatus muscle fat fraction and atrophy measured on the Y-view compared with the newly proposed fossa-view sagittal MRI plane. Materials and Methods: This study included 84 patients (36 male; mean age, 65.1 ± 10.1 years) who underwent shoulder MRI with extended oblique sagittal T1-weighted and three-dimensional (3D) six-echo Dixon imaging between December 2020 and November 2022. The reference fat fraction was calculated by integrating voxel-wise Dixon values, while supraspinatus muscle volume was quantified using a 3D nnU-Net algorithm and normalized to the scapular volume to derive the standardized muscle index (SMI). Fat fraction and cross-sectional area were quantified on the Y-view and fossaview and compared with the reference values. Subgroup analyses were performed using fatty degeneration and retraction grades. Results: Agreement with the reference fat fraction was significantly higher for the fossa-view (intraclass correlation coefficient [ICC], 0.923) than for the Y-view (ICC, 0.822;p = 0.006). The fossa-view showed smaller deviations and narrower limits of agreement.For SMI, the Y-view (ICC, 0.782) showed higher agreement than the fossa-view (ICC, 0.694), although the difference was not statistically significant (p = 0.219). Subgroup analyses showed better Y-view performance at lower retraction grades and better fossa-view performance at higher grades, although the differences were not statistically significant (all p > 0.05). Conclusion Both planes reliably quantified the fat fraction with greater accuracy in the fossa-view. However, single-plane assessment of muscle atrophy was less reliable, underscoring the need for MRI evaluation of the entire muscle.

Acanthamoeba is an opportunistic pathogen responsible for granulomatous amoebic encephalitis and amoebic keratitis. Despite its clinical significance, effective treatments remain challenging due to a limited understanding of its pathogenic mechanism. This study developed a genetic manipulation system in Acanthamoeba to facilitate gene function and drug screening studies. We applied the Cre/loxP system to integrate the gene encoding the tdTomato fluorescent protein into the genome of Acanthamoeba castellanii via homologous recombination. The polyubiquitin gene and its untranslated regions were identified and verified, after which the tdTomato gene was cloned between the untranslated regions of the polyubiquitin gene. The construct was then introduced into the Acanthamoeba genome using a modified pLPBLP vector containing loxP sites. Cre recombinase was utilized to remove the neomycin resistance cassette flanked by loxP sites, and genetically modified cells were selected by clonal dilution. The integration of the tdTomato gene, confirmed through PCR and fluorescence microscopy, showed stable expression in both trophozoites and cysts without the need for antibiotic selection. We demonstrated the feasibility of antibiotic-free reporter gene expression in Acanthamoeba. The system provides a valuable tool for functional genomics, allowing us to explore gene functions in Acanthamoeba and develop reliable drug screening models. Furthermore, the ability to express genes without the continuous use of selection markers opens up new possibilities for studying the pathobiology of this pathogen and advancing the development of novel therapeutic strategies against Acanthamoeba infections.

Purpose: Adjuvant chemotherapy (AC) is recommended for muscle-invasive or lymph node-positive upper urinary tract urothelial carcinoma (UTUC) after radical nephroureterectomy (RNU). However, disease recurrences are frequently observed in pT1 disease, and AC may increase the risk of overtreatment in pT2 UTUC patients. This study aimed to validate a risk-adapted scoring model for selecting UTUC patients with ≤pT2 disease who would benefit from AC. Materials and Methods: We retrospectively analyzed 443 ≤pT2 UTUC patients who underwent RNU. A risk-adapted scoring model was applied, categorizing patients into low- or high-risk groups. Recurrence-free survival (RFS) and cancer-specific survival (CSS) were analyzed according to risk group. Results: Overall, 355 patients (80.1%) and 88 patients (19.9%) were categorized into the low- and high-risk groups, respectively, with the latter having higher pathological stages, concurrent carcinoma in situ, and synchronous bladder tumors. Disease recurrence occurred in 45 patients (10.2%), among whom 19 (5.4%) and 26 (29.5%) belonged to the low- and high-risk groups, respectively (p<0.001). High-risk patients had significantly shorter RFS (64.3% vs. 93.6% at 60 months; hazard ratio [HR] 13.66; p<0.001) and worse CSS (80.7% vs. 91.5% at 60 months; HR 4.25; p=0.002). Multivariate analysis confirmed that pT2 stage and the high-risk group were independent predictors of recurrence and cancer-specific death (p<0.001). Decision curve analysis for RFS showed larger net benefits with our model than with the T stage model. Conclusions The risk-adapted scoring model effectively predicts recurrence and identifies optimal candidates for AC post RNU in non-metastatic UTUC.

OBJECTIVES: This study aimed to compare maternal outcomes and the home environment between non‑vulnerable families with children under 2 receiving universal home visiting services and vulnerable families receiving sustained home visiting services. METHODS: This study was conducted in Seoul, Korea, where the country’s first nurse‑led early childhood home visiting program was introduced. A total of 551 mother‑child dyads participated in cross‑sectional surveys conducted at various child ages (6±2 weeks, 6±1 months, 12±1 months, and 24±1 months). Universal home visiting services were provided within six weeks postpartum to non‑vulnerable families, while vulnerable families received sustained services consisting of 25 visits over 24 months. Maternal knowledge of sudden infant death syndrome (SIDS) and childcare, maternal distress, and the Korean Infant‑Toddler Home Observation for Measurement of Environment (K‑IT‑HOME) were assessed. RESULTS: Overall, the universal home visitation group demonstrated higher levels of maternal knowledge regarding SIDS and childcare compared to the sustained home visitation group (all p-values <0.05), while the sustained home visitation group reported higher levels of maternal distress (p<0.001). The total K‑IT‑HOME score was 1.47 points higher in the universal home visitation group than in the sustained home visitation group (p<0.001). No significant differences were observed in the acceptance, organization, or involvement subscales of the K‑IT‑HOME (all p-values >0.05). CONCLUSIONS This study demonstrated that disparities in maternal outcomes and home environments persisted in early childhood between the sustained and universal home visitation groups.

OBJECTIVES: This study aimed to compare maternal outcomes and the home environment between non‑vulnerable families with children under 2 receiving universal home visiting services and vulnerable families receiving sustained home visiting services. METHODS: This study was conducted in Seoul, Korea, where the country’s first nurse‑led early childhood home visiting program was introduced. A total of 551 mother‑child dyads participated in cross‑sectional surveys conducted at various child ages (6±2 weeks, 6±1 months, 12±1 months, and 24±1 months). Universal home visiting services were provided within six weeks postpartum to non‑vulnerable families, while vulnerable families received sustained services consisting of 25 visits over 24 months. Maternal knowledge of sudden infant death syndrome (SIDS) and childcare, maternal distress, and the Korean Infant‑Toddler Home Observation for Measurement of Environment (K‑IT‑HOME) were assessed. RESULTS: Overall, the universal home visitation group demonstrated higher levels of maternal knowledge regarding SIDS and childcare compared to the sustained home visitation group (all p-values <0.05), while the sustained home visitation group reported higher levels of maternal distress (p<0.001). The total K‑IT‑HOME score was 1.47 points higher in the universal home visitation group than in the sustained home visitation group (p<0.001). No significant differences were observed in the acceptance, organization, or involvement subscales of the K‑IT‑HOME (all p-values >0.05). CONCLUSIONS This study demonstrated that disparities in maternal outcomes and home environments persisted in early childhood between the sustained and universal home visitation groups.

Acanthamoeba is an opportunistic pathogen responsible for granulomatous amoebic encephalitis and amoebic keratitis. Despite its clinical significance, effective treatments remain challenging due to a limited understanding of its pathogenic mechanism. This study developed a genetic manipulation system in Acanthamoeba to facilitate gene function and drug screening studies. We applied the Cre/loxP system to integrate the gene encoding the tdTomato fluorescent protein into the genome of Acanthamoeba castellanii via homologous recombination. The polyubiquitin gene and its untranslated regions were identified and verified, after which the tdTomato gene was cloned between the untranslated regions of the polyubiquitin gene. The construct was then introduced into the Acanthamoeba genome using a modified pLPBLP vector containing loxP sites. Cre recombinase was utilized to remove the neomycin resistance cassette flanked by loxP sites, and genetically modified cells were selected by clonal dilution. The integration of the tdTomato gene, confirmed through PCR and fluorescence microscopy, showed stable expression in both trophozoites and cysts without the need for antibiotic selection. We demonstrated the feasibility of antibiotic-free reporter gene expression in Acanthamoeba. The system provides a valuable tool for functional genomics, allowing us to explore gene functions in Acanthamoeba and develop reliable drug screening models. Furthermore, the ability to express genes without the continuous use of selection markers opens up new possibilities for studying the pathobiology of this pathogen and advancing the development of novel therapeutic strategies against Acanthamoeba infections.

OBJECTIVES: This study aimed to compare maternal outcomes and the home environment between non‑vulnerable families with children under 2 receiving universal home visiting services and vulnerable families receiving sustained home visiting services. METHODS: This study was conducted in Seoul, Korea, where the country’s first nurse‑led early childhood home visiting program was introduced. A total of 551 mother‑child dyads participated in cross‑sectional surveys conducted at various child ages (6±2 weeks, 6±1 months, 12±1 months, and 24±1 months). Universal home visiting services were provided within six weeks postpartum to non‑vulnerable families, while vulnerable families received sustained services consisting of 25 visits over 24 months. Maternal knowledge of sudden infant death syndrome (SIDS) and childcare, maternal distress, and the Korean Infant‑Toddler Home Observation for Measurement of Environment (K‑IT‑HOME) were assessed. RESULTS: Overall, the universal home visitation group demonstrated higher levels of maternal knowledge regarding SIDS and childcare compared to the sustained home visitation group (all p-values <0.05), while the sustained home visitation group reported higher levels of maternal distress (p<0.001). The total K‑IT‑HOME score was 1.47 points higher in the universal home visitation group than in the sustained home visitation group (p<0.001). No significant differences were observed in the acceptance, organization, or involvement subscales of the K‑IT‑HOME (all p-values >0.05). CONCLUSIONS This study demonstrated that disparities in maternal outcomes and home environments persisted in early childhood between the sustained and universal home visitation groups.