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Most patients diagnosed with clear cell renal cell carcinoma (ccRCC) are also detected with small and organ‐confined tumors, and the majority of these are classified as clinical tumor stage 1a (cT1a). A considerable proportion of patients with cT1 RCC shows tumor upstaging to pathological stage 3a (pT3a), and these patients have worse oncological outcomes. The role of circulating tumor DNA (ctDNA) in RCC has been limited to monitoring treatment response and resistance. Therefore, the present study aimed to evaluate the potential of ctDNA in predicting pT3a upstaging in cT1a ccRCC. We sequenced plasma samples preoperatively collected from 48 patients who had undergone partial nephrectomy for cT1a ccRCC using data from a prospective cohort RCC. The ctDNA were profiled and compared with clinicopathological ccRCC features to predict pT3a upstaging. Associations between ctDNA, tumor complexity, and pT3a upstaging were evaluated. Tumor complexity was assessed using the anatomical classification system. Univariate analysis used chi‐squared and Student's t ‐tests; multivariate analysis considered significant factors from univariate analyses. Of the 48 patients with cT1a ccRCC, 12 (25%) were upstaged to pT3a, with ctDNA detected in 10 (20.8%), predominantly in patients with renal sinus fat invasion (SFI; n  = 8). Among the pT3a group, ctDNA was detected in 75%, contrasting with only 2.8% in patients with pT1a (1/36). Detection of ctDNA was the only significant preoperative predictor of pT3a upstaging, especially in SFI. This study is the first to suggest ctDNA as a preoperative predictor of pT3a RCC upstaging from cT1a based on preoperative radiological images.

Radioactive materials were released into the ocean following the Fukushima Daiichi Nuclear Power Plant accident in 2011. Six years after the accident, the radioactive material concentration was markedly increased in the Okhotsk Intermediate Water (OIW) of the Sea of Okhotsk. This material may have been subjected to southward subsurface dispersal by the North Pacific Intermediate Water (NPIW), which originates from the OIW. The spatiotemporal limitations of available methods have made it challenging to track the dispersal paths of radioactive materials in the North Pacific Subpolar region. Here, we performed a tracer experiment using a three-dimensional numerical model to determine the path of 137 Cs from Fukushima to the Sea of Okhotsk via surface subpolar gyre currents and subsurface dispersion by OIW and NPIW. The results showed that the 137 Cs concentration in the Sea of Okhotsk increased via the surface current and moved progressively southward via OIW six years after the accident and eastward via OIW and NPIW nine years after the accident, indicating that 137 Cs transported by NPIW entered the subtropical region. Based on experiments, this temporal change was mainly caused by ocean currents. Thus, subsurface recirculation of radioactive material via the OIW and NPIW should be considered based on the predicted path and travel time of additional materials released from the power plant.

Understanding the variability in material transport from the Taiwan Strait (TS) to the Korean Strait (KS) is crucial for predicting ecological changes and the spread of marine debris in the East Asian Marginal Seas (EAMS). However, the dynamic variability of this transport remains poorly understood. In this study, we investigated the dynamic variability of material transport from the TS to the KS, using a Lagrangian particle-tracking system coupled with a three-dimensional numerical model. The model results showed that particles originating from the TS most frequently passed through the KS in August, with distinct interannual variability. Our findings indicate that southerly winds enhance the sea surface height (SSH) gradient in the southwestern East China Sea (ECS) shelf region through surface Ekman transport, weakening cross-shelf offshore currents and preventing particles from being transported offshore. The interannual variability of southerly winds is associated with variations in SSH in the southwestern shelf region, thereby modulating material transport from the TS to the KS. Furthermore, southerly winds over the EAMS are found to strengthen during negative phases of the Pacific Decadal Oscillation, suggesting a potential linkage between material connectivity in the EAMS and large-scale climate indices. These findings reveal how physical processes govern material transport in the EAMS, offering valuable insights into the prediction of nutrient fluxes and pollutant dispersion.

Acute myeloid leukemia (AML) is one of the most common types of leukemia. With the recent advances in sequencing technology and the growing body of knowledge on the genetics of AML, there is increasing concern about cancer predisposing germline mutations as well as somatic mutations. As familial cases sharing germline mutations are constantly reported, germline predisposition gene mutations in patients with AML are gaining attention. We performed genomic sequencing of Korean patients diagnosed with AML to identify the prevalence and characteristics of germline predisposition mutations. Among 180 patients, germline predisposition mutations were identified in 13 patients (13/180, 7.2%, eight adults and five children). Germline mutations of BLM , BRCA1 , BRCA2 , CTC1 , DDX41 , ERCC4 , ERCC6 , FANCI , FANCM , PALB2 , and SBDS were identified. Most of the mutations are in genes involved in DNA repair and genomic stability maintenance. Patients harboring germline mutations tended to have earlier onset of AML ( p  = 0.005), however, the presence of germline mutations did not showed significant association with other clinical characteristics or treatment outcome. Since each mutation was rare, further study with a larger number of cases would be needed to establish the effect of the mutations.

PPM1D (Protein phosphatase magnesium-dependent 1δ) is known as a damage response regulator, a part of the p53 negative feedback loop. Truncating mutations of PPM1D, resulting in overexpression, are frequently found in the blood of patients with breast or ovarian cancer. To identify whether the PPM1D mutation predisposes patients to such cancers or if it results from the cancer and therapy, somatic PPM1D mutations in association with previous cancer and chemotherapy need to be explored. We performed next-generation sequencing (NGS) analysis of blood samples from patients suspected to have hereditary cancer. We grouped the patients according to their diagnoses and history of chemotherapy. For the patients with PPM1D mutations in blood, tumor tissue specimens were examined for the PPM1D mutation using conventional sequencing. A total of 1,195 patients, including 719 patients with breast cancer and 240 with ovarian cancer, were tested, and four (~0.3%) had the truncating mutation in PPM1D. All truncating mutations were in exon 6, in mosaic form, with a mean allele fraction of 11.15%. While 395 out of the 1,195 patients had undergone chemotherapy, the four with the truncating mutation had a history of cisplatin-based chemotherapy. No corresponding mutations were identified in the tumor tissues. We investigated the frequency of the somatic mosaic PPM1D mutation, in patients with breast or ovarian cancer, which is suggested to be low and related to a history of cisplatin-based chemotherapy. It may be a marker of previous exposure to selective pressure for cells with an impaired DNA damage response.

Background BCR::ABL1 fusion has significant prognostic value and is screened for chronic myeloid leukemia (CML) disease monitoring as a part of routine molecular testing. To overcome the limitations of the current standard real-time quantitative polymerase chain reaction (RQ-PCR), we designed and validated a next-generation sequencing (NGS)-based assay to quantify BCR::ABL1 and ABL1 transcript copy numbers. Methods After PCR amplification of the target sequence, deep sequencing was performed using an Illumina Nextseq 550Dx sequencer and in-house–designed bioinformatics pipeline. The Next-generation Quantitative sequencing (NQ-seq) assay was validated for its analytical performance, including precision, linearity, and limit of detection, using serially diluted control materials. A comparison with conventional RQ-PCR was performed with 145 clinical samples from 77 patients. Results The limit of detection of the NQ-seq was the molecular response (MR) 5.6 [ BCR::ABL1 0.00028% international scale (IS)]. The NQ-seq exhibited excellent precision and linear range from MR 2.0 to 5.0. The IS value from the NQ-seq was highly correlated with conventional RQ-PCR. Conclusions We conclude that the NQ-seq is an effective tool for monitoring BCR::ABL1 transcripts in CML patients with high sensitivity and reliability. Prospective assessment of the unselected large series is required to validate the clinical impact of this NGS-based monitoring strategy.

Prosthetic joint infection (PJI) is a severe complication of hip or knee arthroplasty, often necessitating invasive intervention and posing a high risk of adverse outcomes. Early diagnosis and tailored antibiotic therapy are critical for the effective management of PJI. This study evaluated the utility of cell-free deoxyribonucleic acid (cfDNA) extracted from synovial fluid to diagnose PJI and identify the causative pathogens. This prospective, single-center study included a PJI group consisting of patients with confirmed infections based on the European Bone and Joint Infection Society criteria and a non-PJI group comprising patients without suspected PJIs who underwent joint surgery or aspiration. Synovial fluid samples were collected from all patients, and various culture methods, including conventional synovial fluid, sonication, and tissue and blood cultures, were applied along with cfDNA analysis. A total of 35 patients were included, with 20 diagnosed with PJI and 15 classified as non-PJI. The median cfDNA concentration in synovial fluid was significantly higher in the PJI group (4.560 ng/μl, interquartile range (IQR) [3.320-6.348]) compared with the non-PJI group (0.028 ng/μl, IQR [0.009-0.273]) ( < 0.001). The Youden index identified a cfDNA concentration ≥ 1.59 ng/μl as strong likelihood of PJI. Culture positivity rates in the PJI group were as follows: synovial culture (10/20, 50.0%), sonication culture (8/9, 88.9%), tissue culture (2/8, 25.0%), and blood culture (2/12, 16.7%). The bacterial detection rate of cfDNA was 65.0% (13/20). cfDNA concentration was significantly higher in the PJI group, with synovial cultures showing substantial agreement. Additionally, cfDNA sequencing detected pathogens in patients who had received prior antibiotic therapy and identified multiple pathogens in polymicrobial infections. These findings highlight cfDNA analysis as a valuable diagnostic tool for PJI, with the potential to enhance current diagnostic approaches.

Purpose Somatic 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. Methods In 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® IGHV Leader (Leader) and IGH FR1 (FR1) assays (Invivoscribe, CA, USA). SS was performed as the reference method for SHM assessment. Results The 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. Conclusion These 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.

Background Approximately 50%–60% of secondary resistance to primary EGFR - tyrosine kinase inhibitors (TKI) therapy is caused by acquired p.Thr790Met (T790M) mutation; however, highly fragmented, low-quantity circulating tumor DNA is an obstacle for detecting mutations. Therefore, more sensitive mutation detection techniques are required. Here, we report a new mutant enrichment technology, the CRISPR system combined with post-polymerase chain reaction (PCR) cell-free DNA (cfDNA) (CRISPR-CPPC) to detect the T790M mutation using droplet digital PCR (ddPCR) from cfDNA. Methods The CRISPR-CPPC process comprises the following three steps: (1) cfDNA PCR, (2) assembly of post-PCR cfDNA and CRISPR/CRISPR associated protein 9 complex, and (3) enrichment of the target DNA template. After CRISPR-CPPC, the target DNA was detected using ddPCR. We optimized and validated CRISPR-CPPC using reference cfDNA standards and cfDNA from patients with non-small cell lung cancer who underwent TKI therapy. We then compared the detection sensitivity of CRISPR-CPPC assay with the results of real-time PCR and those of ddPCR. Results CRISPR-CPPC aided detection of T790M with 93.9% sensitivity and 100% specificity. T790M mutant copies were sensitively detected achieving an approximately 13-fold increase in the detected allele frequency. Furthermore, positive rate of detecting a low T790M copy number (< 10 copies/mL) were 93.8% (15/16) and 43.8% (7/16) for CRISPR-CPPC assay and ddPCR, respectively. Conclusions CRISPR-CPPC is a useful mutant enrichment tool for the sensitive detection of target mutation. When tested in patients with progressive disease, the diagnostic performance of CRISPR-CPPC assay is exceptionally better than that of any other currently available methods.

Background The prognosis of a plasma cell neoplasm (PCN) varies depending on the presence of genetic abnormalities. However, detecting sensitive genetic mutations poses challenges due to the heterogeneous nature of the cell population in bone marrow aspiration. The established gold standard for cell sorting is fluorescence-activated cell sorting (FACS), which is associated with lengthy processing times, substantial cell quantities, and expensive equipment. Magnetic-activated cell sorting (MACS) can be performed without the need for FACS equipment and allows for rapid sorting of many cells, making it a practical alternative. Our objective is to conduct a comparative analysis of these two sorting techniques to assess whether MACS can viably replace FACS in clinical applications. Methods Plasma cell purity, fluorescence in situ hybridization (FISH), and next-generation sequencing analyses were performed on FACS- and MACS-sorted bone marrow samples from 31 PCN patients. Results The MACS-sorted samples yielded a higher percentage of plasma cells than FACS-sorted samples under microscopy ( p  = 0.0156) and flow cytometry ( p  = 0.0313). FISH performed by two methods in 10 samples showed the same results, and the proportion of abnormal cells was significantly higher in MACS than in FACS ( p  = 0.001). Wilcoxon matched-pairs signed rank test analysis showed that the median of differences of variant allele frequency (VAF) of two methods (VAF of MACS minus VAF of FACS) in the DNMT3A , TET2 , and ASXL1 (DTA) group was − 0.006555 ( p  = 0.0020), while that in the non-DTA group was 0.002805 ( p  = 0.0019). Ten copy number variants (CNVs) were found in both FACS- and MACS-sorted samples, eight were identified only in MACS-sorted samples, and one was detected only in FACS-sorted samples. Conclusion Our study demonstrates that MACS is a viable alternative for plasma cell sorting in bone marrow samples of patients with PCN.