To cool or not to cool: Targeted temperature management to prevent ventricular tachycardia associated with Brugada syndrome.

Key Clinical Message: A robust inflammatory and febrile response from acute viral illness such as with SARS-CoV-2 in patients with Brugada syndrome may lead to triggering of ventricular arrhythmias. The use of targeted temperature management (TTM) using cooling devices may mitigate the febrile triggering of ventricular arrhythmias in patients with Brugada syndrome. Abstract: Brugada syndrome (BrS) is an autosomonal dominant genetic disorder, with a risk of ventricular tachycardia (VT). Triggers of VT in BrS include fevers. Here, we report a case of BrS secondary to SARSs-CoV-2 infection and the use of targeted temperature management (TTM) to decrease fever and prevent VT triggering.

Peer-to-Peer Social Media as an Effective Prevention Strategy: Quasi-Experimental Evaluation.

BACKGROUND: Substance use by adolescents remains to be at unacceptably high levels, and there is evidence that teens' social norms are becoming more favorable toward recreational use and perceived safety of substances such as marijuana and prescription opioids. Social media offer a low-cost, potentially high-impact approach to disseminate prevention messages. OBJECTIVE: Living the Example (LTE) is a program that trains adolescent youth ambassadors to develop and disseminate prevention messages within their own social media networks and through in-school activities. This study aimed to evaluate the effects of exposure to LTE-based social media on students in the youth ambassadors' networks. METHODS: The George Washington (GW) University designed and implemented a quasi-experimental evaluation of the LTE program in 3 Maryland high schools. Before program launch, a sample of 826 students (wave 1) at the 3 schools, drawn from a census of freshmen enrolled in a class attended by all students at the grade level, completed a survey. A total of 584 students were surveyed at the wave 2 program midpoint and 542 at the wave 3 endpoint. The survey contained questions on drug use-related attitudes, beliefs, intentions, and behaviors, all based on validated measures. We evaluated the effects of LTE on the intended next 30-day drug use, and controlling for LTE self-reported exposure, age, and gender from waves 2 and 3 was appended into a single dataset. We first conducted ordinal logistic regressions for each drug use intention in wave 3 (ie, sell or distribute illegal drugs, smoke cigarettes, drink beer/wine/hard liquor when parents do not know about it, use marijuana, use lysergic acid diethylamide, cocaine, amphetamines or other illegal drugs, use heroin, use synthetic drugs, and use any prescription pills without a prescription) to examine the association between LTE exposure and drug use intentions. We included an interaction term for the study wave to examine intervention effects. RESULTS: We found a significant positive effect of LTE exposure on all 8 measured drug use intentions: sell/distribute illegal drugs; smoke cigarettes; drink beer, wine, or liquor when my parents do not know about it; use marijuana; use cocaine, amphetamines, or other illegal drug; use heroin; use synthetic drugs; use any prescription pills without a prescription (all P<.05; odds ratios ranging from 2.12 to 3.71). We also found that boys were more likely than girls to exhibit reduced drug use intentions. We also found reductions in 30-day intentions between the second and third survey waves for all 8 measured drug use variables. CONCLUSIONS: Overall, the results are consistent with and indicate a stronger LTE effect in this study compared with a previous pilot study. LTE appears to offer a protective effect, with exposure to program messages leading to reduced/improved drug use intentions.

Markedly Improved Glycemic Control in Poorly Controlled Type 2 Diabetes following Direct Acting Antiviral Treatment of Genotype 1 Hepatitis C.

Type 2 diabetes mellitus (T2DM) is often associated with hepatitis C virus (HCV) infection. Successful HCV treatment may improve glycemic control and potentially induce remission of T2DM. We report a case of an obese 52-year-old woman with mixed genotype 1a/1b HCV infection with compensated cirrhosis and a 10-year history of poorly controlled T2DM on insulin therapy. Following successful therapy with sofosbuvir, simeprevir, and ribavirin, her insulin requirements decreased and her glycosylated hemoglobin (HgA1c) normalized despite weight gain. This case suggests an association between HCV and T2DM and the potential for significant improvement in glycemic control with eradication of HCV.

Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation.

The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.

Spaced Seed Data Structures for De Novo Assembly.

De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction.

Sealer: a scalable gap-closing application for finishing draft genomes.

BACKGROUND: While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low sequence coverage, repetitive elements and short read length make de novo genome assembly difficult, often resulting in sequence and/or fragment "gaps" - uncharacterized nucleotide (N) stretches of unknown or estimated lengths. Some of these gaps can be closed by re-processing latent information in the raw reads. Even though there are several tools for closing gaps, they do not easily scale up to processing billion base pair genomes. RESULTS: Here we describe Sealer, a tool designed to close gaps within assembly scaffolds by navigating de Bruijn graphs represented by space-efficient Bloom filter data structures. We demonstrate how it scales to successfully close 50.8% and 13.8% of gaps in human (3 Gbp) and white spruce (20 Gbp) draft assemblies in under 30 and 27 h, respectively - a feat that is not possible with other leading tools with the breadth of data used in our study. CONCLUSION: Sealer is an automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes. We expect Sealer to have broad utility for finishing genomes across the tree of life, from bacterial genomes to large plant genomes and beyond. Sealer is available for download at https://github.com/bcgsc/abyss/tree/sealer-release.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

DIDA: Distributed Indexing Dispatched Alignment.

One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA), and is free for academic use.

Therapeutic Role of Innovative Anti-Inflammatory Medications in the Prevention of Acute Coronary Syndrome.

An improved understanding of the pathogenesis of acute coronary syndromes and its relationship to atherosclerotic plaque rupture and thrombosis has contributed to the investigation of novel therapies for prevention and treatment. New data ascribe an increasingly important role of active inflammation in contributing to thinning of the atherosclerotic fibrous cap and plaque instability. Despite this understanding, there are currently no therapeutic approaches to specifically target the unstable plaque. Multiple randomized trials investigating treatment strategies have recently been completed or are currently being conducted, using anti-inflammatory medications, such as methotrexate, colchicine, darapladib, varespladib, losmapimod, and canakinumab, to reduce the incidence of cardiovascular events including acute coronary syndromes. These anti-inflammatory medications differ in their mechanism of action from having widespread targets (as is the case for methotrexate and colchicine) to having specific targets (as is the case for darapladib, varespladib, losmapimod, and canakinumab). The trials investigating the efficacy of darapladib in reducing cardiovascular events revealed no significant benefit when compared with the current standard of care. The varespladib studies were terminated early because of adverse outcomes. However, the outcomes of the remaining drug studies may still contribute to novel therapeutic approaches in the treatment of patients with unstable coronary artery disease.

Kleat: cleavage site analysis of transcriptomes.

In eukaryotic cells, alternative cleavage of 3' untranslated regions (UTRs) can affect transcript stability, transport and translation. For polyadenylated (poly(A)) transcripts, cleavage sites can be characterized with short-read sequencing using specialized library construction methods. However, for large-scale cohort studies as well as for clinical sequencing applications, it is desirable to characterize such events using RNA-seq data, as the latter are already widely applied to identify other relevant information, such as mutations, alternative splicing and chimeric transcripts. Here we describe KLEAT, an analysis tool that uses de novo assembly of RNA-seq data to characterize cleavage sites on 3' UTRs. We demonstrate the performance of KLEAT on three cell line RNA-seq libraries constructed and sequenced by the ENCODE project, and assembled using Trans-ABySS. Validating the KLEAT predictions with matched ENCODE RNA-seq and RNA-PET libraries, we show that the tool has over 90% positive predictive value when there are at least three RNA-seq reads supporting a poly(A) tail and requiring at least three RNA-PET reads mapping within 100 nucleotides as validation. We also compare the performance of KLEAT with other popular RNA-seq analysis pipelines that reconstruct 3' UTR ends, and show that it performs favourably, based on an ROC-like curve.

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters.

Large datasets can be screened for sequences from a specific organism, quickly and with low memory requirements, by a data structure that supports time- and memory-efficient set membership queries. Bloom filters offer such queries but require that false positives be controlled. We present BioBloom Tools, a Bloom filter-based sequence-screening tool that is faster than BWA, Bowtie 2 (popular alignment algorithms) and FACS (a membership query algorithm). It delivers accuracies comparable with these tools, controls false positives and has low memory requirements. Availability and implementaion: www.bcgsc.ca/platform/bioinfo/software/biobloomtools.

Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.

BACKGROUND: Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) and gene fusions, are important in the detection, prognosis, and treatment of human cancers. RESULTS: We describe Barnacle, a production-grade analysis tool that detects such chimeras in de novo assemblies of RNA-seq data, and supports prioritizing them for review and validation by reporting the relative coverage of co-occurring chimeric and wild-type transcripts. We demonstrate applications in large-scale disease studies, by identifying PTDs in MLL, ITDs in FLT3, and reciprocal fusions between PML and RARA, in two deeply sequenced acute myeloid leukemia (AML) RNA-seq datasets. CONCLUSIONS: Our analyses of real and simulated data sets show that, with appropriate filter settings, Barnacle makes highly specific predictions for three types of chimeric transcripts that are important in a range of cancers: PTDs, ITDs, and fusions. High specificity makes manual review and validation efficient, which is necessary in large-scale disease studies. Characterizing an extended range of chimera types will help generate insights into progression, treatment, and outcomes for complex diseases.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

UNLABELLED: White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20,356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies. AVAILABILITY: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435.

Synthesis of novel tetrahydro-1H-pyrazolo[4,3-c]pyridines via intramolecular nitrilimine cycloaddition.

The preparation of novel tetrahydro-1H-pyrazolo[4,3-c]pyridines is reported. Pivotal to the synthesis of these compounds was the development of mild reaction conditions to generate a highly functionalized nitrilimine capable of undergoing an intramolecular cycloaddition with a tethered alkyne. The desired cycloadduct was formed as an equal mixture of diastereomers.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-ß signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.

De novo assembly and analysis of RNA-seq data.

We describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads from an adult mouse liver poly(A) RNA library, we identified known, new and alternative structures in expressed transcripts, and achieved high sensitivity and specificity relative to reference-based assembly methods.