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Webinar: A New Paradigm in DNA Sequencing – Highly Accurate Single-Molecule Long Reads

Korlach, Jonas and Corney, Dave
PacBio

2018

Description +

In this webinar, Jonas Korlach, PacBio Chief Scientific Officer, and Dave Corney, Associate Principal Scientist, Next Generation Sequencing from GENEWIZ, describe the recent release of Sequel System 6.0, which has revolutionized long-read sequencing by providing users the ability to generate highly accurate single-molecule reads. Users no longer need to compromise read length for accuracy, because it is now possible to have both including Sanger-quality reads as long as 15 kb. They share the benefits in applications such as whole genome sequencing, structural variant detection, targeted sequencing and RNA sequencing of full-length transcripts using the Iso-Seq method. From those new to SMRT Sequencing to experienced users, this webinar provides an update on recent performance improvements, scientific discoveries powered by PacBio and future applications to enable your research.

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Tutorial: Iso-Seq analysis application [SMRT Link v6.0.0]


PacBio

2018

Description +

This tutorial provides an overview of the Isoform Sequence (Iso-Seq) analysis application. The Iso-Seq application provides reads that span entire transcript isoforms, from the 5′ end to the 3′ poly A-tail. Generation of accurate, full-length transcript sequences greatly simplifies analysis by eliminating the need for transcript reconstruction to infer isoforms using error-prone assembly of short RNA-seq reads. This tutorial covers features of SMRT Link v6.0.0.

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Tutorial: Structural variant calling [SMRT Link v6.0.0]


PacBio

2018

Description +

This tutorial provides an overview of the Structural Variant Calling application in SMRT Link and a live demo of how to launch an analysis in SMRT Link and interpret the results. This application identifies large (default: = 20 bp) insertions, deletions, inversions and translocations in a sample relative to a reference from.This tutorial covers features of SMRT Link v6.0.0.

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Webinar: Assembling high-quality genomes to solve nature’s mysteries

Block, Barbara and Peluso, Paul
Nature

2018

Description +

In this webinar, Barbara Block of Stanford University and Paul Peluso of PacBio describe how plant and animal whole genome sequencing remains a challenging endeavor, particularly due to genome size, high density of repetitive elements, and heterozygosity. Because of this, often only a single, fragmented reference genome is available for a species, genus, or even family, limiting the ability to answer important biological questions. Looking at the trends in genome assembly and annotation over the past year, such as pan-genomes and phasing, this webinar explores how Single Molecule, Real-Time (SMRT) Sequencing is utilized to develop long-lasting genomic resources, supporting research that fuels breeding programs, informs industrial product development, and shapes our understanding of life on Earth. They then dive into the world of bluefin tuna biology to explore how sequencing the genomes of different populations of bluefin tuna may help protect this sushi delicacy from overfishing.

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ASHG PacBio Workshop: Amplicon SMRT Sequencing applications in human genetics

Scott, Stuart
Icahn School of Medicine at Mount Sinai

2018

Description +

In this ASHG workshop presentation, Stuart Scott of the Icahn School of Medicine at Mount Sinai, presented on using the PacBio system for amplicon sequencing in pharmacogenomics and clinical genomics workflows. Accurate, phased amplicon sequence for the CYP2D6 gene, for example, has allowed his team to reclassify up to 20% of samples, providing data that’s critical for drug metabolism and dosing. In clinical genomics, Scott presented several case studies illustrating the utility of highly accurate, long-read sequencing for assessing copy number variants and for confirming a suspected medical diagnosis in rare disease patients. He noted that the latest Sequel System chemistry improved throughput and read length, as well as reducing error profile and increasing the capacity for multiplexing.

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

Song, Janet
Stanford University

2018

Description +

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 in mouse models or human brain organoid models in the future.

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ASHG PacBio Workshop: PacBio product updates and roadmap – announcing the release of new chemistry and software

Korlach, Jonas
PacBio

2018

Description +

In this ASHG workshop presentation , Jonas Korlach, CSO of PacBio, walked attendees through recent product updates and the coming technology roadmap. The Sequel System 6.0 release offered major improvements to accuracy, throughput, structural variant calling, and large-insert libraries, he said, showing examples of 35 kb libraries. Looking ahead, Korlach said that the V2 express library preparation product should be available early in 2019, with the new 8M SMRT Cell being introduced sometime later.

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

Tseng, Elizabeth
PacBio

2018

Description +

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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User Group Meeting: Application of genome assembly in Bovinae species

Smith, Tim
PacBio

2018

Description +

In this PacBio User Group Meeting presentation, Tim Smith of the USDA’s Agricultural Research Service describes efforts to generate reference-grade genome assemblies for various bovine species and analyze them to understand factors such as how selective breeding has affected certain breeds. Genome assemblies he presents span cattle, water buffalo, and gaur. Smith shows data for each assembly, noting that as data production shifted to the Sequel System, long-read PacBio data became even better at producing highly contiguous assemblies.

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User Group Meeting: Development, validation, and applications of a high-fidelity, species-specific, eubacterial pan-domain microbiome assay on the PacBio System

Ehrlich, Garth
PacBio

2018

Description +

In this PacBio User Group Meeting presentation, Garth Ehrlich of Drexel University College of Medicine shares his work on developing a microbiome assay that uses SMRT Sequencing to provide high-quality coverage of the 16S bacterial rRNA for species identification. The microbiome analysis pipeline, MCSMRT, takes advantage of PacBio circular consensus sequencing (CCS) technology and second-generation pathway analysis system for generating extremely high-fidelity sequences that provide the user with ultra-high-confidence species-level microbiome data.

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User Group Meeting: Future developments of SMRT Sequencing

Korlach, Jonas
PacBio

2018

Description +

Jonas Korlach closes the 2018 User Group Meeting with an outlook and perspectives on SMRT Sequencing, highlighting what possibilities the Sequel System 6.0 release. Learn more about this release at: https://www.pacb.com/products-and-services/sequel-system/latest-system-release/

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User Group Meeting: Introduction to the PacBio 2018 user group meeting

Korlach, Jonas
PacBio

2018

Description +

PacBio CSO, Jonas Korlach, kicks off the North America 2018 User Group Meeting with a recap of how SMRT Sequencing has evolved and a preview of the Sequel System 6.0 release. Learn more about this release at: https://www.pacb.com/products-and-services/sequel-system/latest-system-release/

Event

PAG XXVII

January 12, 2019-January 16, 2019

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