During June 2017-April 2018, active tuberculosis with Beijing SIT1 isolates was diagnosed in 14 persons living in 4 distant cities in France. Whole-genome sequencing indicated that these patients belonged to a single transmission chain. Whole-genome sequencing-based laboratory investigations enabled prompt tracing of linked cases to improve tuberculosis control.
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http://dx.doi.org/10.3201/eid2503.181124 | DOI Listing |
Lab Invest
January 2025
Université de Caen Normandie, INSERM U1086 ANTICIPE, Caen, France; UNICANCER, Comprehensive Cancer Center François Baclesse, Caen, France; Université de Caen Normandie, US PLATON- ORGAPRED core facility, Caen, France; Université de Caen Normandie, US PLATON, UNICANCER, Comprehensive Cancer Center François Baclesse- Biological Resource Center 'OvaRessources', Caen, France. Electronic address:
PARP inhibitors (PARPi) have been shown to improve progression-free survival, particularly in homologous recombination deficient (HRD) ovarian cancers. Identifying patients eligible to PARPi is currently based on next-generation sequencing (NGS), but the persistence of genomic scars in tumors after restoration of HR or epigenetic changes can be a limitation. Functional assays could thus be used to improve this profiling and faithfully identify HRD tumors.
View Article and Find Full Text PDFAm J Hum Genet
January 2025
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA. Electronic address:
More than 50% of families with suspected rare monogenic diseases remain unsolved after whole-genome analysis by short-read sequencing (SRS). Long-read sequencing (LRS) could help bridge this diagnostic gap by capturing variants inaccessible to SRS, facilitating long-range mapping and phasing and providing haplotype-resolved methylation profiling. To evaluate LRS's additional diagnostic yield, we sequenced a rare-disease cohort of 98 samples from 41 families, using nanopore sequencing, achieving per sample ∼36× average coverage and 32-kb read N50 from a single flow cell.
View Article and Find Full Text PDFJ Infect Public Health
January 2025
Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan. Electronic address:
Background: We aimed to evaluate the efficacy of integrating the Varia5 multiplex assay (qPCR) and whole genome sequencing (WGS) for monitoring SARS-CoV-2, focusing on their overall performance in identifying various virus variants.
Methods: This study included 140 naso-pharyngeal swab samples from individuals with suspected COVID-19. We utilized our self-developed Varia5 multiplex assay, which targets five viral genes linked to COVID-19 mutations, in conjunction with comprehensive genomic analysis performed through whole genome sequencing (WGS) using the Oxford Nanopore system.
Diagn Microbiol Infect Dis
January 2025
National Reference Laboratory of Control and Monitoring of Antibiotic Resistance (NRL-CMAR), Department Microbiology, National Center of Infectious and Parasitic Diseases (NCIPD), 26 Yanko Sakazov Blvd., Sofia, Bulgaria.
Increased incidence of Clostridioides difficile infections were documented in Bulgarian hospitals during COVID-19. WGS was performed on 39 isolates from seven hospitals during 2015-2022. Antimicrobial resistance and toxin genes were inferred from genomes.
View Article and Find Full Text PDFSci China Life Sci
January 2025
Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
Genomic sources from China are underrepresented in the population-specific reference database. We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups (1,081 Sinitic, 56 Mongolic, 40 Turkic, and 30 Tibeto-Burman people) living in North China included in the 10K Chinese People Genomic Diversity Project (10K_CPGDP) to characterize the genetic architecture and adaptative history of ethnic groups in the Silk Road Region of China. We observed a population split between Northwest Chinese minorities (NWCMs) and Han Chinese since the Upper Paleolithic and later Neolithic genetic differentiation within NWCMs.
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