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.

Background: Retinitis pigmentosa (RP) comprises a heterogeneous group of inherited retinal dystrophies. The genetic landscape of RP has been characterized; however, knowledge gaps regarding age-specific genetic variation trends in Korean patients remain. We comprehensively characterized the age-stratified genetic landscape of RP in Korean patients, with a focus on identifying novel mutational trends and clinically actionable insights. Methods: We performed targeted next-generation sequencing of 199 genes associated with RP and related disorders in a cohort of 403 unrelated patients clinically diagnosed as having RP. We analyzed the inheritance patterns, variation spectrum, and prevalence of pathogenic variants, stratifying the results by age, and conducted copy number variation (CNV) analysis. Results: A genetic diagnosis was achieved for 193 of the 403 patients (48%). The diagnostic yield was highest in patients diagnosed before 20 yrs of age (60%), with lower yields in older age groups. Although USH2A and EYS, the most common causative genes in autosomal recessive inheritance, were frequently identified, RPGR pathogenic variants accounted for a significantly larger proportion of genetically solved cases diagnosed before the age of 20 yrs (27%–28%) than in those with later-onset disease (9%–15%). CNVs were identified in 4% of genetically solved cases. Conclusions The results underscore distinct, age-related genetic contributions to RP in Korean patients, with RPGR variants demonstrating relevance in early-onset disease, and provide diagnostic insights to improve current practices. These findings can aid in prioritizing gene therapy targets and refining screening strategies.

Although venous invasion (VI) is associated with distant metastasis and observed in >50% of pT2–4 colorectal cancers (CRCs), the role of VI in pT1 CRCs is not well-defined. Methods: Thirty-four surgically resected pT1 CRCs were reevaluated for 2-dimensional (2D) VI using hematoxylin and eosin (H&E)–stained slides with additional elastic and desmin immunohistochemical staining (cohort A). Additionally, 27 pT1 CRCs without knowing VI status were selected for 3-dimensional (3D) VI evaluation only (cohort B). All 61 cases (cohorts A and B) were studied in 3D using tissue clearing. Results: VI was detected more commonly in 3D (17/34, 50.0%) than in 2D H&E slide evaluation (9/34, 26.5%, p = .047). When VI was identified in 3D (27/61, 44.3%), the most common phase was that of intraluminal growth (22/27, 81.5%), followed by intravasation (7/27, 25.9%) and extravasation (5/27, 18.5%). E-cadherin expression was characterized in 3D in foci of VI and varied in each phase of invasion. Conclusions: All three phases were observed in VI of pT1 CRCs. The extravasation of neoplastic cells from foci of VI in pT1 CRC suggests that VI could be a route of intratumoral spreading in a subset of pT1 CRCs.

Purpose: While TP53 mutations are well known to be associated with adverse prognosis in hematological diseases, their functional impact remains incompletely understood. This study examines the spectrum of TP53 mutations across various hematologic malignancies and evaluates their functional impact. Materials and Methods: Using targeted sequencing panels, we analyzed TP53 mutations in the bone marrow aspiration samples of a retrospective cohort of 856 patients diagnosed with hematologic malignancies. To assess the impact of TP53 mutations, we applied the evolutionary action (EAp53) score and the relative fitness score (RFS), previously proposed functional scoring methods. The effects of variant allele frequency (VAF), disruptive mutations, EAp53 score, and RFS on overall survival (OS) were evaluated. Results: TP53 mutations were associated with inferior OS compared with wildtype TP53 (median OS 10.0 months versus not estimable; hazard ratio (HR) 4.6; p<0.001). In the acute myeloid leukemia, multiple myeloma, and myelodysplastic syndrome subgroups, TP53 mutations had a significant adverse impact on OS. (HRs 3.8, 4.2, 6.0, respectively; p<0.001, p=0.005, p<0.001, respectively). Patients with VAF >50% had significantly poorer OS compared to those with VAF ≤50% (median OS 7.5 months versus 22.8 months; HR 2.2, p=0.016). Moreover, patients in the high-risk RFS group (RFS >0.22) had significantly worse OS compared to those in the low-risk RFS group (RFS ≤0.22) (median OS 5.6 months versus 16.3 months; HR 2.2, p=0.041). However, no significant survival difference was observed between the EAp53 high-risk (>75) and low-risk (≤75) groups, or between patients with disruptive and non-disruptive mutations. Conclusion Our findings highlight VAF and RFS as valuable tools for stratifying TP53-mutant patients into high-risk and low-risk groups.

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: Radical cystectomy (RC) is associated with substantial postoperative morbidity, and unplanned readmission remains common despite advances in perioperative management. However, the association between postoperative readmission due to complications and oncologic outcomes after RC for bladder cancer has not been clearly defined. We evaluated the impact of postoperative readmission on overall survival (OS) and cancer-specific survival (CSS) after RC for bladder cancer. Materials and Methods: We retrospectively analyzed 3,972 patients who underwent RC for bladder cancer in a multicenter cohort. Postoperative readmission was defined as unplanned hospitalization within 90 days postsurgery due to surgery-related complications. Survival outcomes were assessed using the Kaplan-Meier method and compared using the log-rank test. Univariable and multivariable Cox proportional hazards regression analyses were performed to identify independent predictors of OS and CSS. Results: Among the study population, 916 patients (23.1%) experienced postoperative readmission. Baseline and perioperative characteristics were generally comparable between patients with and without readmission. Kaplan-Meier analyses demonstrated significantly worse OS and CSS among patients who experienced postoperative readmission (both log-rank p<0.001). In multivariable analyses adjusting for clinicopathological factors, postoperative readmission remained independently associated with worse OS (hazard ratio [HR], 1.654; 95% confidence interval [CI], 1.464–1.868; p<0.001) and CSS (HR, 1.761; 95% CI, 1.509–2.055; p<0.001). Conclusion Postoperative readmission within 90 days after RC was independently associated with inferior long-term oncologic outcomes. These findings suggest the importance of strategies aimed at preventing postoperative complications and subsequent readmission.

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.

Background: Sleep disorders and insomnia are prevalent worldwide, with negative health outcomes. The Pittsburgh Sleep Quality Index (PSQI) is a widely used self-report assessment tool for evaluating sleep quality, comprising seven subdomains. The Korean version of the PSQI (PSQI-K) has been tested for reliability and validity in small sample sizes but lacks large-scale validation using objective measures. Methods: This study was conducted with 268 Korean adults attending health check programs. Participants completed the PSQI-K questionnaire and wore Fitbit devices (Fitbit Inc., USA) to ascertain sleep parameters. Reliability was analyzed using the Cronbach’s α coefficient, and construct validity was determined through factor analysis. Criteria validity was assessed by correlating their index scores with Fitbit sleep parameters. We identified the optimal cutoff for detecting sleep disorders. Results: The Cronbach’s α coefficient was 0.61, indicating adequate internal consistency. Factor analysis revealed three factors, explaining 48.2% of sleep quality variance. The index scores were negatively correlated with Fitbit sleep efficiency, total sleep time, and number of awakenings (P<0.05). The optimal cutoff point for identifying sleep disorder groups was ≥6. Conclusion The PSQI-K demonstrated good reliability and validity when correlated with Fitbit sleep parameters, offering a practical screening tool for identifying sleep disorders among Korean adults. Cutoff scores can help identify patients for sleep interventions. However, further large-scale studies are required to validate these findings.

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.