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Thursday, May 24, 2018

Full-Length HIV Sequences Reveal Distinction Between Viruses in Brain, Other Tissue

Photo by C. Goldsmith Scientists have made important inroads in understanding why patients with HIV develop neurological disorders despite treatments that otherwise hold the virus at bay. The project was made possible with SMRT Sequencing, which generates reads long enough to span the full HIV envelope. “Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues” was recently published in the Journal of NeuroVirology by lead author Robin Brese, senior author Susanna Lamers, and collaborators at the University of Massachusetts Medical School and Bioinfoexperts.…

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Wednesday, May 16, 2018

Disease-Causing LINE-1 Insertions: Rare or Just Hard to Spot?

Patient’s muscle biopsy – Hematoxylin and eosin stain shows severe fibrosis and fat substitution. Arrow indicates a necrotic fiber. LINE-1 (long interspersed nuclear element) insertions cover almost 17% of the human genome, but they are notoriously difficult to resolve accurately with short-read sequencing technology, according to scientists in Portugal. That matters because intronic LINE-1 elements can cause disease. In a recent study, SMRT Sequencing made it possible to analyze the multi-kilobase region and find a mutation causing muscular dystrophy. In “Exonization of an Intronic LINE-1 Element Causing Becker Muscular Dystrophy as a Novel Mutational Mechanism in Dystrophin Gene,” scientists from…

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Monday, May 14, 2018

Codfish Study Employs Target Capture and SMRT Sequencing to Explore Evolution

Many investigators rely on targeted sequencing approaches for deep dives into genomic regions of interest. By designing specific probes — often using short-read sequences directed towards the exome and supported by existing reference genomes or transcriptome assemblies — scientists can home in on exactly the area they want to explore. But what about sequences in intergenic regions not covered by short reads, which could contain crucial regulatory elements varying between populations that might be of functional and evolutionary importance? Or, what about species lacking high-quality reference genomes to guide probe design? A team of Norwegian researchers are tackling these challenges…

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Thursday, May 3, 2018

Introduction of the Iso-Seq Method: State of the Art for Full-Length Transcriptome Sequencing

Photo by John Cobb on Unsplash In eukaryotic organisms, the majority of genes are alternatively spliced to produce multiple transcript isoforms. Gene regulation through alternative splicing can dramatically increase the protein-coding potential of a genome. Therefore, understanding the functional biology of a genome requires knowing the full complement of isoforms. Microarrays and high-throughput cDNA sequencing are useful tools for studying transcriptomes, yet these technologies provide only small snippets of transcripts.  Accurately reconstructing complete transcripts to study gene isoforms has been challenging [1, 2]. The Iso-Seq method produces full-length transcripts using Single Molecule, Real-Time (SMRT) Sequencing [3]. Long read lengths enable…

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