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Purpose: Although deep targeted DNA sequencing of liquid biopsies has shown prognostic utility in large B-cell lymphoma (LBCL), the routine clinical adoption of these assays remains limited because of their high costs.
Materials And Methods: Here, leveraging a well-annotated cohort encompassing both frontline and relapsed/refractory (R/R) LBCL, we profiled patient plasma samples with two complementary modalities-ultra-low-pass whole-genome sequencing (ULP-WGS) and deep targeted DNA sequencing, the former being a cost-effective method to profile large scale chromosomal abnormalities and estimate tumor burden.
Results: Our findings revealed a strong association of high cell-free tumor burden by both genomic profiling modalities with established measures of tumor burden and patient survival. Notably, the associations with survival remained statistically significant after accounting for international prognostic index scoring. Furthermore, we showed that del(17p) in circulating tumor DNA as detected by ULP-WGS was strongly associated with mutation status and predicted for significantly inferior outcome in frontline LBCL patients but not in patients with R/R LBCL.
Conclusion: Our study demonstrates that ULP-WGS can provide robust prognostic biomarkers for both frontline and R/R LBCL, highlighting its broad applicability for risk stratification.
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http://dx.doi.org/10.1200/PO-25-00200 | DOI Listing |
J Appl Microbiol
September 2025
Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed-to-be-University), Pillaiyarkuppam, Pondicherry - 607 402, India.
Aim: To investigate the phenotypic and genomic features of three multidrug-resistant (MDR) clinical mucoid and non-mucoid uropathogenic Escherichia coli (UPEC) strains to understand their antimicrobial resistance, biofilm formation, and virulence in urinary tract infections (UTIs).
Methods And Results: The UPEC strains A5, A10, and A15 were isolated from two UTI patients. Phenotypic assays included colony morphology, antibiotic susceptibility, motility, and biofilm formation.
Brief Bioinform
August 2025
Department of Respiratory Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, No. 157, Xiwu Road, Xincheng District, Xi'an 710004, China.
Accurate tumor mutation burden (TMB) quantification is critical for immunotherapy stratification, yet remains challenging due to variability across sequencing platforms, tumor heterogeneity, and variant calling pipelines. Here, we introduce TMBquant, an explainable AI-powered caller designed to optimize TMB estimation through dynamic feature selection, ensemble learning, and automated strategy adaptation. Built upon the H2O AutoML framework, TMBquant integrates variant features, minimizes classification errors, and enhances both accuracy and stability across diverse datasets.
View Article and Find Full Text PDFMicrobiol Resour Announc
September 2025
Department of Bioscience and Bioengineering, Indian Institute of Technology-Roorkee, Roorkee, Uttarakhand, India.
CHRFS5, HL_CHRU_S18, S48B, HL_CHRU_S16, S19, HL_CHRU_S79, and HL_CHRU_S111 were isolated from the biofilm of catheter tip of renal failure patients. Whole genome sequencing predicted the presence of multiple antibiotic-resistant gene cassettes.
View Article and Find Full Text PDFFront Microbiol
August 2025
Animal Health Laboratory, EU/WOAH and National Reference Laboratory for Brucellosis, Anses/Paris-Est University, Maisons-Alfort, France.
Many species from the genus are causative agents of the bacterial zoonosis brucellosis. Until recently, it was generally believed that these bacteria exhibit strict host specificity; however, recent findings suggest otherwise. is an atypical species, no threat to humans, with a broad host spectrum, primarily found in wildlife and rodents, and is the only species isolated from soil, aquatic environments, and frogs, suggesting its environmental persistence and adaptability to diverse ecological niches.
View Article and Find Full Text PDFFront Oncol
August 2025
Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing University, Jiaxing, Zhejiang, China.
Objective: The diagnosis of precancerous lesions of colorectal cancer (CRC) presents significant challenges in clinical practice. In this study, we conducted a clinical investigation using the UCAD technique after analyzing chromosomal copy number variations (CNVs) in formalin-fixed, paraffin-embedded (FFPE) samples from various pathological stages, aiming to evaluate the value of detecting chromosomal instability (CIN) in CRC diagnosis.
Methods: Based on colonoscopic pathological findings, we selected 39 FFPE specimens of tubular adenomas, 8 FFPE specimens of villous adenomas, 16 cases diagnosed as tubular-villous adenomas, and 14 cases without defined pathological subtype classification.