Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant ctDNA molecules based on somatic variants, extremely sensitive sequencing methods are required. Here, we describe a new technique, CyclomicsSeq, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule. Consensus calling of the DNA copies increased the base-calling accuracy ~60×, enabling accurate detection of TP53 mutations at frequencies down to 0.02%. We demonstrate that a TP53-specific CyclomicsSeq assay can be successfully used to monitor tumor burden during treatment for head-and-neck cancer patients. CyclomicsSeq can be applied to any genomic locus and offers an accurate diagnostic liquid biopsy approach that can be implemented in clinical workflows

Author Correction: Accurate detection of circulating tumor DNA using nanopore consensus sequencing

The Data Availability statement in the original version of the paper reads: “The sequencing datasets generated during the current study are available upon request at EGA, under accession number EGAS00001003759”. However, as this data upload was not successful, the authors reuploaded the data under a different accession number and have amended the Data Availability statement to read “The sequencing datasets generated during the current study are available upon request at EGA, under accession number EGAS00001007090”. The original article has been corrected.</p

Different routes to liking: How readers arrive at narrative evaluations

Data and analysis script

Different kinds of simulation during literary reading:Insights from a combined fMRI and eye-tracking study

Mental simulation is an important aspect of narrative reading. In a previous study, we found that gaze durations are differentially impacted by different kinds of mental simulation. Motor simulation, perceptual simulation, and mentalizing as elicited by literary short stories influenced eye movements in distinguishable ways (Mak &amp; Willems, 2019). In the current study, we investigated the existence of a common neural locus for these different kinds of simulation. We additionally investigated whether individual differences during reading, as indexed by the eye movements, are reflected in domain-specific activations in the brain. We found a variety of brain areas activated by simulation-eliciting content, both modality-specific brain areas and a general simulation area. Individual variation in percent signal change in activated areas was related to measures of story appreciation as well as personal characteristics (i.e., transportability, perspective taking). Taken together, these findings suggest that mental simulation is supported by both domain-specific processes grounded in previous experiences, and by the neural mechanisms that underlie higher -order language processing (e.g., situation model building, event indexing, integration). (c) 2023 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)

The relation between virtual internships and student teachers' teaching anxiety

Deze studie onderzocht de bruikbaarheid en het effect van virtuele stages op deprofessional anxiety van leraren in opleiding (LIO’s). Twee sessies van een virtuelestage werden uitgevoerd met respectievelijk 27 en 16 LIO’s. Middels vragenlijsten, een focusgroep en interviews werden bevorderende en belemmerende condities van virtuele stages geïnventariseerd. Voor het ontwerp van sessie twee zijn deze condities gerespecteerd. Virtuele stages blijken een significante bijdrage te leveren aan het reduceren van professional anxiety en blijken vooral nuttig voor LIO’s zonder leservaring. Na sessie twee waren LIO’s meer tevreden met het systeem, inhoud, taak en nut van de virtuele stage dan LIO’s uit sessie één. Hoewel er technische belemmeringen waren ervoeren LIO’s de virtuele stages als gebruiksvriendelijk