Forensic lab-on-a-chip DNA analysis
Metatranscriptome of a marine pelagic crustacean community using nanopore sequencing
Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis
...Published in Annals of Clinical Microbiology and Antimicrobials
BackgroundPathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore...
Rapid virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing
...Published in Virology Journal
BackgroundNewcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND. However, these diagnostics are hindered by the genetic diversity and rapid evolution of NDVs.MethodsAn am...
Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass.
Published in Bioresource technology
In this work, liquid and solid fractions of grass biomass were used as co-substrates for anaerobic co-digestion of sewage sludge. The input of grass biomass was increased gradually, and the underlying methanogenic microbiome was assessed by means of microscopy-based cell counting and full-length 16S rRNA gene high-throughput sequencing, proving for...
Evaluation of MinION nanopore sequencing for rapid enterovirus genotyping.
Published in Virus research
Enteroviruses (EV) are associated with a range of serious infections, including aseptic meningitis, hand foot and mouth disease, myocarditis, acute flaccid paralysis and encephalitis. Improved methods for assessing EV genotypic diversity could assist molecular epidemiology studies, clinical diagnosis and environmental surveillance. We report new me...
Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing
Published in Molecular Biology Reports
The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirable, but their adoption for molecular assays is hurdled by the high degree of fragmentation and by the chemical-induced mutations stemming from the fixat...
Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events
Published in Breast Cancer Research
BackgroundLaboratory assays evaluating the effect of DNA sequence variants on BRCA1 mRNA splicing may contribute to classification by providing molecular evidence. However, our knowledge of normal and aberrant BRCA1 splicing events to date has been limited to data derived from assays targeting partial transcript sequences. This study explored the u...
Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing
...Published in Acta Neuropathologica
Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically. For central nervous system tumors, the current World Health Organization classification explicitly demands molecular testing, e.g., ...
MinION as part of a biomedical rapidly deployable laboratory.
Published in Journal of biotechnology
Fast turnaround times are of utmost importance for biomedical reconnaissance, particularly regarding dangerous pathogens. Recent advances in sequencing technology and its devices allow sequencing within a short time frame outside stationary laboratories close to the epicenter of the outbreak. In our study, we evaluated the portable sequencing devic...
