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Tuesday, February 14, 2017

AGBT Virtual Poster: Analysis method for amplification-free SMRT sequencing and assessment on repeat expansions in Huntington’s disease

Adam Ameur from the National Genomics Infrastructure at SciLifeLab presented this poster at AGBT 2017. In it, he details a validation study for the use of CRISPR/Cas9 to capture genomic targets without the use of amplification. Results from 12 Huntington’s patients indicate that this approach paired with SMRT Sequencing generates accurate repeat counts in the HTT gene.

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Tuesday, February 14, 2017

AGBT Virtual Poster: Using the PacBio Iso-Seq method to search for novel colorectal cancer biomarkers

Early detection of colorectal cancer (CRC) and its precursor lesions (adenomas) is crucial to reduce mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test that detects the blood-derived protein hemoglobin. However, FIT sensitivity is suboptimal especially in detection of CRC precursor lesions. As adenoma-to-carcinoma progression is accompanied by alternative splicing, tumor-specific proteins derived from alternatively spliced RNA transcripts might serve as candidate biomarkers for CRC detection.

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Tuesday, February 14, 2017

AGBT Virtual Poster: Interspecies interation amoung meat spoilage-related lactic acid bacteria

In this AGBT 2017 poster, the University of Helsinki’s Petri Auevinen reports on efforts to understand bacteria that grow on, and subsequently spoil, food. This analysis monitored DNA modifications and transcriptomic changes in three species of lactic acid bacteria. Scientists discovered that the organisms’ metabolic profiles change substantially when grown together compared to those cultured individually, and are now studying how Cas protein activity changes under these conditions too.

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Monday, February 13, 2017

AGBT Virtual Poster: Generation of local reference genomes using PacBio and BioNano data, and analysis of the “dark matter” of structural variants in 1000 Swedish genomes

In this AGBT 2017 poster, Ulf Gyllensten from Uppsala University presents two local reference genomes generated with PacBio and Bionano Genomics data. These assemblies include structural variation and repetitive regions that have been missed with previous short-read efforts, including some new genes not annotated in the human reference genome.

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Monday, February 13, 2017

AGBT Virtual Poster: Single-molecule sequencing reveals the presence of distinct JC polyomavirus populations in patients with progressive multifocal leukoencephalopathy

At AGBT 2017, Lars Paulin from the University of Helsinki presented this poster on whole genome sequencing of the virus responsible for progressive multifocal leukoencephalopathy, a rare and dangerous brain infection. His team used long amplicon analysis to resolve the whole virus genome from three patient samples, pooled them for SMRT Sequencing, and identified variants and rearrangements. This work represents the first time the viral genome was sequenced from patients.

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Thursday, October 20, 2016

ASHG Virtual Poster: The MHC Diversity in Africa Project (MDAP) pilot – 125 African high resolution HLA types from 5 populations

In this ASHG 2016 poster video, Martin Pollard from the Wellcome Trust Sanger Institute and the University of Cambridge describes an ambitious project to better represent natural variation in the complex MHC region by sequencing the locus in thousands of people from various populations in Africa. A pilot project in five populations has already revealed a lot of diversity in the region, which is important for human disease, vaccine response, and organ transplantation. Pollard says SMRT Sequencing is the only technology that can deliver the full-length haplotypes necessary to identify complete variation in this highly polymorphic complex. Plus: plans to…

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Thursday, October 20, 2016

ASHG Virtual Poster: Alternative splicing in FMR1 premutations carriers

In this ASHG 2016 virtual poster, Flora Tassone from UC Davis describes her study of the molecular mechanisms linked to fragile X syndrome and associated disorders, such as FXTAS. She is using SMRT Sequencing to resolve the FMR1 gene in premutation carriers because it’s the only technology that can generate full-length transcripts with the causative CGG repeat expansion. Plus: direct confirmation of predicted isoform configurations.

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Thursday, October 20, 2016

ASHG Virtual Poster: Effect of coverage depth and haplotype phasing on structural variant detection with PacBio long reads

PacBio bioinformatician Aaron Wenger presents this ASHG 2016 poster demonstrating human structural variation detection at varying coverage levels with SMRT Sequencing on the Sequel System. Results were compared to truth sets for well-characterized genomes. Results indicate that even low coverage of SMRT Sequencing makes it possible to detect hundreds of SVs that are missed in high-coverage short-read sequencing data.

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Wednesday, October 19, 2016

ASHG Virtual Poster: Enrichment of unamplified DNA and long-read SMRT Sequencing to unlock repeat expansion disorders

PacBio’s Jenny Ekholm presents this ASHG 2016 poster on a new method being developed that enriches for unamplified DNA and uses SMRT Sequencing to characterize repeat expansion disorders. Incorporating the CRISPR/Cas9 system to target specific genes allows for amplification-free enrichment to preserve epigenetic information and avoid PCR bias. Internal studies have shown that the approach can successfully be used to target and sequence the CAG repeat responsible for Huntington’s disease, the repeat associated with ALS, and more. The approach allows for pooling many samples and sequencing with a single SMRT Cell.

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