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Tuesday, December 1, 2020

ASHG PacBio Workshop: Characterization of a large, human-specific tandem repeat array associated with bipolar disorder and schizophrenia

In this ASHG workshop presentation, Janet Song of Stanford School of Medicine shared research on resolving a tandem repeat array implicated in bipolar disorder and schizophrenia. These psychiatric diseases share a number of genomic risk variants, she noted, but scientists continue to search for a specific causal variant in the CACNA1C gene suggested by previous genome-wide association studies. SMRT Sequencing of this region in 16 individuals identified a series of 30-mer repeats, containing a total of about 50 variants. Analysis showed that 10 variants were linked to protective or risk haplotypes. Song aims to study the function of these variants…

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Tuesday, December 1, 2020

ASHG PacBio Workshop: The Iso-Seq method for discovering alternative splicing in human diseases

In this ASHG workshop presentation, Elizabeth Tseng of PacBio showed how the Iso-Seq method can be used to discover disease-associated alternative splicing. Because this approach to isoform sequencing yields accurate, full-length transcripts requiring no assembly, it’s ideal for disease studies that need a more comprehensive picture of alternative splicing activity. Tseng offered several published examples of how the Iso-Seq method has been used for everything from single-gene studies to whole-transcriptome studies, and also detailed how the latest Sequel System chemistry recovers more genes and produces more usable reads.

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Tuesday, December 1, 2020

PAG Conference: The Bat1K project: bat genome, biology and implications

In this presentation, Sonja Vernes of the Max Plank Institute shares her work with the Bat1K project which aims to catalog the genetic diversity of all living bat species. She highlights the unique biology of bats, from their widely varying sizes to their capacity for healthy aging and disease resistance and provides recent findings from ongoing efforts to sequence and annotate the genomes of 21 phylogenetic families of bats.

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Tuesday, December 1, 2020

AGBT Presentation: Single cell isoform sequencing (scIso-Seq) identifies novel full-length mRNAs and cell type-specific expression

In this AGBT presentation from AGBT 2019, Jason Underwood, shares information about single-cell isoform sequencing (scIso-Seq), focusing on a collaborative project with the labs of Evan Eichler and Alex Pollen. For this effort, scientists used Drop-seq sample prep and then loaded cDNA products onto the Sequel System. Results from a barnyard experiment using mouse and human cells as well as from cerebral organoids demonstrated that this approach could deliver cell type-specific gene expression data. Underwood also presents data from the Sequel II System comparing chimp and human organoids, resulting in information about 14,000 unique genes with important insights for post-transcriptional…

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Tuesday, December 1, 2020

User Group Meeting: No Assembly Required – Making the most of Iso-Seq data

In this PacBio User Group Meeting presentation, PacBio scientist Kristin Mars speaks about recent updates, such as the single-day library prep that’s now possible with the Iso-Seq Express workflow. She also notes that one SMRT Cell 8M is sufficient for most Iso-Seq experiments for whole transcriptome sequencing at an affordable price.

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Tuesday, December 1, 2020

Webinar: A HiFi View – Sequencing the gut microbiome with highly accurate long reads

In this webinar, Dr. Ashby gives attendees a brief update on PacBio’s metagenomics solutions on the Sequel II System. Then, Dr. Ma, University of Maryland School of Medicine, discusses her work using long read sequencing to identify high-resolution microbial biomarkers associated with leaky gut syndrome in premature infants. Finally, Dr. Weinstock, The Jackson Laboratory, talks about the potential of highly accurate long reads to enable strain-level resolution of the human gut microbiome by resolving intraspecies variation in multiple copies of the 16S gene.

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Tuesday, December 1, 2020

ASHG PacBio Workshop: Latest product and application updates

In this ASHG 2020 PacBio Workshop Jonas Korlach, CSO, shares how the new PacBio Sequel IIe System makes highly accurate long-read sequencing easy and affordable so?all scientists can gain comprehensive views of human genomes and transcriptomes. He goes on to provide updates on the applications including human WGS for variant detection, de novo genome assembly, single-cell full-length RNA sequencing, and targeted sequencing using PCR and No-Amp methods.

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Tuesday, December 1, 2020

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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Tuesday, December 1, 2020

ASHG PacBio Workshop: Identification and characterization of informative genetic structural variants for neurodegenerative diseases

Michael Lutz, from the Duke University Medical Center, discussed a recently published software tool that can now be used in a pipeline with SMRT Sequencing data to find structural variant biomarkers for neurodegenerative diseases with a focus on Alzheimer’s disease, ALS, and Lewy body dementia. His team is particularly interested in short sequence repeats and short tandem repeats, which have already been implicated in neurodegenerative disease.

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Tuesday, December 1, 2020

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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Tuesday, December 1, 2020

AGBT PacBio Workshop: De novo sequencing of the naked mole rat genome

At AGBT 2017, Margaret Roy from Calico Life Sciences discussed a de novo genome sequencing effort for the naked mole rat. This animal has a remarkably long life span and resistance to cancer, both of which make it interesting for studies of life extension. The team is using SMRT Sequencing for a more complete, contiguous assembly than the two existing short-read-based assemblies. Included: data from the Sequel System.

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Tuesday, December 1, 2020

Webinar: Using Iso-Seq analysis to build a better annotation

Long-read sequencing technologies like Iso-Seq analysis present researchers with a powerful tool for probing the transcriptomes of many species. The ability to sequence transcripts from end-to-end has revealed transcription complexity on a scale that was previously impossible. This sequence rich information has also improved our ability to predict transcript functions and biotypes. Researchers can now use Iso-Seq analysis to discover transcript models in almost any species with an accuracy on par with human and mouse annotations. In this webinar, Richard Kuo discusses the core concepts behind Iso-Seq analysis and how to use it to improve or build a new transcriptome…

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Tuesday, December 1, 2020

Webinar: SMRT Sequencing applications in plant and animal sciences: an overview

In this webinar, Emily Hatas of PacBio shares information about the applications and benefits of SMRT Sequencing in plant and animal biology, agriculture, and industrial research fields. This session contains an overview of several applications: whole-genome sequencing for de novo assembly; transcript isoform sequencing (Iso-Seq) method for genome annotation; targeted sequencing solutions; and metagenomics and microbial interactions. High-level workflows and best practices are discussed for key applications.

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