BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.

Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. BISCUIT's performance, flexibility and standards-compliant output allow large, complex experimental designs to be characterized on clinical timescales. BISCUIT is particularly suited for processing data from single-cell DNA methylation assays, with its excellent scalability, efficiency, and ability to greatly enhance mappability, a key challenge for single-cell studies. We also introduce the epiBED format for single-molecule analysis of coupled epigenetic and genetic information, facilitating the study of cellular and tissue heterogeneity from DNA methylation sequencing.

Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing.

SUMMARY: In whole genome sequencing data, polymerase chain reaction amplification results in duplicate DNA fragments coming from the same location in the genome. The process of preparing a whole genome bisulfite sequencing (WGBS) library, on the other hand, can create two DNA fragments from the same location that should not be considered duplicates. Currently, only one WGBS-aware duplicate marking tool exists. However, it only works with the output from a single tool, does not accept streaming input or output, and requires a substantial amount of memory relative to the input size. Dupsifter provides an aligner-agnostic duplicate marking tool that is lightweight, has streaming capabilities, and is memory efficient. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available at https://github.com/huishenlab/dupsifter under the MIT license. Dupsifter is implemented in C and is supported on macOS and Linux.

Interventions to prevent or cease electronic cigarette use in children and adolescents.

BACKGROUND: The prevalence of e-cigarette use has increased globally amongst children and adolescents in recent years. In response to the increasing prevalence and emerging evidence about the potential harms of e-cigarettes in children and adolescents, leading public health organisations have called for approaches to address increasing e-cigarette use. Whilst evaluations of approaches to reduce uptake and use regularly appear in the literature, the collective long-term benefit of these is currently unclear. OBJECTIVES: The co-primary objectives of the review were to: (1) evaluate the effectiveness of interventions to prevent e-cigarette use in children and adolescents (aged 19 years and younger) with no prior use, relative to no intervention, waitlist control, usual practice, or an alternative intervention; and (2) evaluate the effectiveness of interventions to cease e-cigarette use in children and adolescents (aged 19 years and younger) reporting current use, relative to no intervention, waitlist control, usual practice, or an alternative intervention. Secondary objectives were to: (1) examine the effect of such interventions on child and adolescent use of other tobacco products (e.g. cigarettes, cigars types, and chewing tobacco); and (2) describe the unintended adverse effects of the intervention on individuals (e.g. physical or mental health of individuals), or on organisations (e.g. intervention displacement of key curricula or learning opportunities for school students) where such interventions are being implemented. SEARCH METHODS: We searched CENTRAL, Ovid MEDLINE, Ovid Embase, Ovid PsycINFO, EBSCO CINAHL, and Clarivate Web of Science Core Collection from inception to 1 May 2023. Additionally, we searched two trial registry platforms (WHO International Clinical Trials Registry Platform; US National Institutes of Health Ongoing Trials Register ClinicalTrials.gov), Google Scholar, and the reference lists of relevant systematic reviews. We contacted corresponding authors of articles identified as ongoing studies. SELECTION CRITERIA: We included randomised controlled trials (RCTs), including cluster-RCTs, factorial RCTs, and stepped-wedge RCTs. To be eligible, the primary targets of the interventions must have been children and adolescents aged 19 years or younger. Interventions could have been conducted in any setting, including community, school, health services, or the home, and must have sought to influence children or adolescent (or both) e-cigarette use directly. Studies with a comparator of no intervention (i.e. control), waitlist control, usual practice, or an alternative intervention not targeting e-cigarette use were eligible. We included measures to assess the effectiveness of interventions to: prevent child and adolescent e-cigarette use (including measures of e-cigarette use amongst those who were never-users); and cease e-cigarette use (including measures of e-cigarette use amongst children and adolescents who were e-cigarette current-users). Measures of e-cigarette use included current-use (defined as use in the past 30 days) and ever-use (defined as any lifetime use). DATA COLLECTION AND ANALYSIS: Two review authors independently screened the titles and abstracts of references, with any discrepancies resolved through consensus. Pairs of review authors independently assessed the full-text articles for inclusion in the review. We planned for two review authors to independently extract information from the included studies and assess risk of bias using the Cochrane RoB 2 tool. We planned to conduct multiple meta-analyses using a random-effects model to align with the co-primary objectives of the review. First, we planned to pool interventions to prevent child and adolescent e-cigarette use and conduct two analyses using the outcome measures of 'ever-use' and 'current-use'. Second, we planned to pool interventions to cease child and adolescent e-cigarette use and conduct one analysis using the outcome measure of 'current-use'. Where data were unsuitable for pooling in meta-analyses, we planned to conduct a narrative synthesis using vote-counting approaches and to follow the Cochrane Handbook for Systematic Reviews of Interventions and the Synthesis Without Meta-analysis (SWiM) guidelines. MAIN RESULTS: The search of electronic databases identified 7141 citations, with a further 287 records identified from the search of trial registries and Google Scholar. Of the 110 studies (116 records) evaluated in full text, we considered 88 to be ineligible for inclusion for the following reasons: inappropriate outcome (27 studies); intervention (12 studies); study design (31 studies); and participants (18 studies). The remaining 22 studies (28 records) were identified as ongoing studies that may be eligible for inclusion in a future review update. We identified no studies with published data that were eligible for inclusion in the review. AUTHORS' CONCLUSIONS: We identified no RCTs that met the inclusion criteria for the review, and as such, there is no evidence available from RCTs to assess the potential impact of interventions targeting children and adolescent e-cigarette use, tobacco use, or any unintended adverse effects. Evidence from studies employing other trial designs (e.g. non-randomised) may exist; however, such studies were not eligible for inclusion in the review. Evidence from studies using non-randomised designs should be examined to guide actions to prevent or cease e-cigarette use. This is a living systematic review. We search for new evidence every month and update the review when we identify relevant new evidence. Please refer to the Cochrane Database of Systematic Reviews for the current status of this review.

Evaluation of whole-genome DNA methylation sequencing library preparation protocols.

BACKGROUND: With rapidly dropping sequencing cost, the popularity of whole-genome DNA methylation sequencing has been on the rise. Multiple library preparation protocols currently exist. We have performed 22 whole-genome DNA methylation sequencing experiments on snap frozen human samples, and extensively benchmarked common library preparation protocols for whole-genome DNA methylation sequencing, including three traditional bisulfite-based protocols and a new enzyme-based protocol. In addition, different input DNA quantities were compared for two kits compatible with a reduced starting quantity. In addition, we also present bioinformatic analysis pipelines for sequencing data from each of these library types. RESULTS: An assortment of metrics were collected for each kit, including raw read statistics, library quality and uniformity metrics, cytosine retention, and CpG beta value consistency between technical replicates. Overall, the NEBNext Enzymatic Methyl-seq and Swift Accel-NGS Methyl-Seq kits performed quantitatively better than the other two protocols. In addition, the NEB and Swift kits performed well at low-input amounts, validating their utility in applications where DNA is the limiting factor. RESULTS: The NEBNext Enzymatic Methyl-seq kit appeared to be the best option for whole-genome DNA methylation sequencing of high-quality DNA, closely followed by the Swift kit, which potentially works better for degraded samples. Further, a general bioinformatic pipeline is applicable across the four protocols, with the exception of extra trimming needed for the Swift Biosciences's Accel-NGS Methyl-Seq protocol to remove the Adaptase sequence.