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Monday, February 4, 2019

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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Monday, February 4, 2019

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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Monday, February 4, 2019

AGBT Virtual Poster: An improved circular consensus algorithm with an application to detect HIV-1 Drug Resistance Associated Mutations (DRAMs)

In this poster presentation, PacBio scientist Ellen Paxinos describes an improved algorithm for circular consensus reads. Using this new algorithm, dubbed CCS2, it is possible to reach arbitrarily high quality across longer insert lengths at a lower cost and higher throughput than Sanger Sequencing. She shows results from the application of CCS2 to the characterization of the HIV-1 K103N drug-resistance associated mutation, which is both important clinically, and represents a challenge due to regional sequence context.

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Monday, February 4, 2019

AGBT Virtual Poster: Unzipping diploid genomes – revealing all kinds of heterozygous variants from comprehensive haplotig assemblies

In this AGBT virtual poster video, Jason Chin, a bioinformatician at PacBio, describes a polyploidy-aware de novo assembly approach called FALCON and a new algorithm, dubbed FALCON-unzip, that involves “unzipping” diploid genomes for de novo haplotype reconstructions from SMRT Sequencing data. These methods are illustrated in a studies of fungal, Arabidopsis and human datasets for the resolution of structural variation and characterization of haplotypes.

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Monday, February 4, 2019

AGBT Virtual Poster: Comparative analysis of somatic fusion gene detection using short read and long read sequencing

Bioinformatics scientist Chetanya Pandya from the Icahn School of Medicine at Mount Sinai presents a poster comparing short-read and long-read sequencing to detect somatic fusion events in cancer samples. SMRT Sequencing identified significantly more fusions, while many of the short-read calls may have been artifacts from challenging regions of the genome.

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Monday, February 4, 2019

AGBT Virtual Poster: Long-read assembly of the Aedes aegypti Aag2 cell line genome resolves ancient endogenous viral elements

In this AGBT poster, PacBio bioinformatician Matthew Seetin presents a new assembly for Aedes aegypti cell line, the mosquito responsible for spreading viruses like Dengue and Zika. SMRT Sequencing generated a gapless assembly with a contig N50 of 1.4 Mb, compared to 82 kb in the previous assembly. The genome features a number of transposable elements and long tandem repeats.

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Monday, February 4, 2019

AGBT Virtual Poster: Insight into MHC and KIR genomic regions associated with autoimmune disease

Dan Geraghty from the Fred Hutchinson Cancer Research Center presents his AGBT poster on a new PacBio-based solution to sequence extended genomic regions — in this case, KIR and MHC, two of the most variable regions of the human genome. He reports data revealing for the first time regions that may be associated with autoimmune diseases such as diabetes, rheumatoid arthritis, and multiple sclerosis, and also shows that sequences were phased, complete, and highly accurate.

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