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Thursday, January 7, 2021

Application Brief: Targeted sequencing for amplicons – Best Practices

With Single Molecule, Real-Time (SMRT) Sequencing and the Sequel System, you can easily and cost effectively generate highly accurate long reads (HiFi reads, >99% single-molecule accuracy) from genes or regions of interest ranging in size from several hundred base pairs to 20 kb. Target all types of variation across relevant genomic regions, including low complexity regions like repeat expansions, promoters, and flanking regions of transposable elements.

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Wednesday, January 6, 2021

Labroots Webinar: More comprehensive views of human genetic variation

In this BioConference Live webinar, PacBio CSO Jonas Korlach highlights how multi-kilobase reads from SMRT Sequencing can resolve many of the previously considered ‘difficult-to-sequence’ genomic regions. The long reads also allow phasing of the sequence information along the maternal and paternal alleles, demonstrated by full-length, fully phased HLA class I & II gene sequencing. In addition, characterizing the complex landscape of alternative gene products is currently very difficult with short-read sequencing technologies, and he describes how long-read, full-length mRNA sequencing can be used to describe the diversity of transcript isoforms, with no assembly required. Lastly, in the exciting area of…

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Wednesday, January 6, 2021

AGBT 2015 Highlights: Customer interviews day 1

PacBio customers discuss their applications of PacBio SMRT Sequencing and long reads, including Lemuel Racacho (Children’s Hospital of Eastern Ontario Research Institute), Matthew Blow (JGI), Yuta Suzuki (U. of Tokyo), Daniel Geraghty (Fred Hutchinson Cancer Center), and Mike Schatz (CSHL)

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Wednesday, January 6, 2021

Xtalks Webinar: Long genomic DNA fragment capture and SMRT Sequencing enables accurate phasing of cancer and HLA loci

In this webinar, the presenters describe a targeted sequencing workflow that combines Roche NimbleGen’s SeqCap EZ enrichment technology with PacBio’ SMRT Sequencing to provide a more comprehensive view of variants and haplotype information over multi-kilobase, contiguous regions. They demonstrate that 6 kb fragments can also be utilized to enrich for long fragments that extend beyond the targeted capture site and well into (and often across) the adjacent intronic regions. When combined with SMRT Sequencing, multi-kilobase genomic regions can be phased and variants, including complex structural variants, can be detected in exons, introns and intergenic regions.

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Wednesday, January 6, 2021

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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Wednesday, January 6, 2021

AGBT Virtual Poster: Targeted SMRT Sequencing of difficult regions of the genome using a Cas9, non-amplification based method

Targeted sequencing has proven to be an economical means of obtaining sequence information for one or more defined regions of a larger genome. However, most target enrichment methods are reliant upon some form of amplification. Amplification removes the epigenetic marks present in native DNA, and some genomic regions, such as those with extreme GC content and repetitive sequences, are recalcitrant to faithful amplification. Yet, a large number of genetic disorders are caused by expansions of repeat sequences. Furthermore, for some disorders, methylation status has been shown to be a key factor in the mechanism of disease. We have developed a…

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Wednesday, January 6, 2021

Webinar: Understanding, curating, and analyzing your diploid genome assembly

The goal of this session is to help users complete their PacBio genome assembly and generate the best resource for their research. Kingan begins with a brief review of the diploid assembly process used by FALCON and FALCON-Unzip, highlighting the enhanced phasing of the Unzip module, and concluding with recommendations for genome polishing. Next, she explores how heterozygosity can influence the assembly process and how read coverage depth along the assembly can reveal important characteristics of assembly structure. Kingan then recommends approaches, including specific tools, that can be used to quality filter and curate the assembly, including annotation-, coverage-, and…

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Wednesday, January 6, 2021

PAG Conference: Domestication: through the canines of a dingo

In this PAG 2018 presentation, Bill Ballard of University of New South Wales, presents research into the origins and potential domestication of the Australian dingo, winner of the 2017 SMRT Grant Program. Ballard used PacBio long-read whole genome sequencing to sequence and assemble the dingo genome. Ongoing work focuses on identifying common and unique genomic regions with a domestic dog genome to better understand shared ancestry and ultimately to aid in dingo conservation efforts.

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Wednesday, January 6, 2021

PAG Conference: How SMRT Sequencing is accelerating plant and animal genomics

In this presentation, Justin Blethrow provides an overview of recent and upcoming developments across PacBio’s SMRT Sequencing product portfolio, and their implications for PacBio’s major applications. In presenting the product roadmap, he illustrates how key new products coming in 2019 will make SMRT Sequencing dramatically more affordable and easy to use, and how they will enable customers to routinely produce highly accurate, single-molecule long reads.

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Wednesday, January 6, 2021

PAG Conference: Reference-quality drosophila genome assemblies for evolutionary analysis of previously inaccessible genomic regions

In this presentation, Andrew Clark from Cornell University describes work from a collaboration with Manyuan Long of the University of Chicago and Rod Wing of the University of Arizona to look at heterochromatic regions with long simple satellite repeats in drosophila genomes. The group used PacBio sequencing to create new genome assemblies of 10 drosophila species, including de novo assemblies of two individual flies using as little as 26 ng of gDNA.

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Wednesday, January 6, 2021

User Group Meeting: Sequencing chemistry & application updates

To start Day 1 of the PacBio User Group Meeting, Jonas Korlach, PacBio CSO, provides an update on the latest releases and performance metrics for the Sequel II System. The longest reads generated on this system with the SMRT Cell 8M now go beyond 175,000 bases, while maintaining extremely high accuracy. HiFi mode, for example, uses circular consensus sequencing to achieve accuracy of Q40 or even Q50.

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Wednesday, January 6, 2021

Webinar: Beyond Gene Editing: How CRISPR/Cas9 enables sequencing of difficult regions of the genome

In this webinar, Jenny Ekholm and Paul Kotturi provide an overview of the PacBio No-Amp targeted sequencing application and its uses for targeting hard-to-amplify genes. This approach couples CRISPR-Cas9 with Single Molecule, Real Time (SMRT) Sequencing to enrich targets, without the need for PCR amplification, and generate complete sequence information with base-level resolution.

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