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Explore our SMRT resources

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Video
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Webinar: Chasing alternative splicing in cancer: Simplified full-length isoform sequencing

Ashby, Meredith
PacBio

20170425

Description +

Tremendous flexibility is maintained in the human proteome via alternative splicing, and cancer genomes often subvert this flexibility to promote survival. Identification and annotation of cancer-specific mRNA isoforms is critical to understanding how mutations in the genome affect the biology of cancer cells. While microarrays and other NGS-based methods have become useful for studying transcriptomes, these technologies yield short, fragmented transcripts that remain a challenge for accurate, complete reconstruction of splice variants. The Iso-Seq method developed at PacBio offers the only solution for direct sequencing of full-length, single-molecule cDNA sequences needed to discover biomarkers for early detection and cancer stratification, to fully characterize gene fusion events, and to elucidate drug resistance mechanisms. The Iso-Seq library preparation protocol has recently been optimized for the higher-throughput PacBio Sequel platform, decreasing the need for size fractionation steps, reducing sample input requirements, and increasing the throughput per SMRT cell. We will review the simplified protocol and share results from applying the new method to both a cancer cell line and fresh frozen tumor samples. We will then review several examples of how researchers are using the Iso-Seq method to undercover new cancer biology, including the identification of candidate biomarkers for early detection of colorectal cancer and the discovery of a novel biomarker for drug resistance in prostate cancer. Researchers are encouraged to consider how the Iso-Seq method can provide new insights into their own cancer research and submit a brief application to win a SMRT Grant via our website.

Video
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Webinar: Detecting structural variants in PacBio reads – tools and applications

Wenger, Aaron
PacBio

20170927

Description +

Most of the basepairs that differ between two human genomes are in intermediate-sized structural variants (50 bp to 5 kb), which are too small to detect with array CGH but too large to reliably discover with short-read NGS. PacBio Single Molecule, Real-Time (SMRT) Sequencing fills this technology gap. SMRT Sequencing detects tens of thousands of structural variants in a human genome, approximately five times the sensitivity of short-read NGS. To discover variants using SMRT Sequencing, we have developed pbsv, which is available in version 5 of the PacBio SMRT Link software suite. The pbsv algorithm applies a sequence of stages: 1) identify reads with signatures of structural variation, 2) cluster nearby reads with similar signatures, 3) summarize each cluster into a consensus variant, and 4) filter for variants with sufficient read support. The pbsv algorithm is designed for individuals, trios, and population cohorts. For visualization, we have extended the popular genome browser IGV to better support structural variants and PacBio long reads. The improvements are available in IGV 2.4. To evaluate pbsv, we generated high coverage of a diploid human genome and then titrated to lower coverage levels. The false discovery rate for pbsv is low at all coverage levels. Sensitivity is high even at modest coverage, above 85% at 10-fold and 95% at 20-fold. We also applied pbsv to identify structural variants in an individual with Carney complex for whom short-read whole genome sequencing was non-diagnostic. Filtering for rare, genic structural variants left six candidates, one of which was determined to be likely causative. These applications demonstrate the ability of pbsv to detect structural variants in low-coverage PacBio sequencing and suggest the importance of considering structural variants in any study of human genetic variation.

Video
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Webinar: PacBio targeted sequencing of long amplicons using PCR or hybrid capture

Kujawa, Steve
PacBio

20170511

Description +

Targeted sequencing experiments commonly rely on either PCR or hybrid capture to enrich for targets of interest. When using short read sequencing platforms, these amplicons or fragments are frequently targeted to a few hundred base pairs to accommodate the read lengths of the platform. Given PacBio’s long readlength, it is straightforward to sequence amplicons or captured fragments that are multiple kilobases in length. These long sequences are useful for easily visualizing variants that include SNPs, CNVs and other structural variants, often without assembly. We will review methods for the sequencing of long amplicons and provide examples using amplicons that range from several kilobases up to 17 kilobases. In addition, we will review methods for the capture of fragments longer than 5 kb using hybrid capture technologies and show an example in which a panel of 35 Alzheimer’s Disease genes are captured.

Video

Webinar: Sequencing structural variants for disease gene discovery and population genetics

Hoischen, A. and Wenger, A
Nature, PacBio

20180308

Description +

Structural variants (SVs, differences >50 base pairs) account for most of the base pairs that differ between two human genomes, and are known to cause over 1,000 genetic disorders including ALS, schizophrenia, and hereditary cancer. Yet, SVs remain overlooked in human genetic research studies due to the limited power of short-read sequencing methods (exome and whole genome sequencing) to resolve large variants, which often involve repetitive DNA. Recent advances in long-read sequencing have made it possible to detect the over 20,000 SVs that are now known to exist in a human genome. Corresponding advances in long-read SV calling algorithms have reduced coverage requirements, making long-read genome sequencing a cost-effective approach for both disease research and population genetics studies. Learn how human geneticists are adding low-coverage, long-read whole genome sequencing to their study designs to fully power genetic variant discovery and ultimately identify disease-causing variants and genes.

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

Hatas, Emily
PacBio

20171024

Description +

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.

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

Kingan, Sarah
PacBio

20170627

Description +

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 sequence-alignment-based methods for identifying homologous genomic regions in the assembly. The presentation is concluded with a review of the process of submitting diploid genome assemblies to NCBI.

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

Kuo, Richard
The University of Edinburgh

20180228

Description +

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 annotation.

Video

AGBT Virtual Poster: Clinical sequencing using Pacific Biosciences RS II for HLA typing and monitoring of drug resistance in chronic myeloid leukemia (CML)

Gyllensten, Ulf
Uppsala University

20150225

Description +

Ulf Gyllensten from Uppsala University describes his AGBT poster showing the use of SMRT Sequencing for HLA allele typing. He says long reads are essential for sequencing the HLA genes because they link exons in a single read and do not introduce bias, as short-read sequencers can. Looking at fusion transcripts from CML patients generated information that couldn’t be achieved with any other technology, he adds.

Video
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Webinar: A new paradigm in DNA sequencing – Highly accurate single-molecule long reads

Korlach, Jonas and Corney, Dave
PacBio

20181211

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.

Video
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Webinar: Amplicon sequencing with confidence – High-fidelity, long-read PacBio sequencing solutions

Aro, Lori and Heiner, Cheryl
PacBio

20190130

Description +

In this webinar, Lori Aro and Cheryl Heiner of PacBio describe how high-throughput amplicon sequencing using Single Molecule, Real-Time (SMRT) Sequencing and the Sequel System allows for the easy and cost-effective generation of high-fidelity, long reads from amplicons ranging in size from several hundred base pairs to 20 kb. Topics covered include the latest advances in SMRT Sequencing performance for detection of all variant types even in difficult to sequence regions of the genome, multiplexing options to increase throughput and improve efficiency, and examples of amplicon sequencing of clinically relevant targets.

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

Block, Barbara and Peluso, Paul
Nature

20181101

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.

Video
NONE

Webinar: New PacBio solutions for high-resolution microbiology & immunology analysis

Korlach, Jonas
Labroots

20180913

Description +

PacBio sequencing has been recognized as the gold-standard in microbial sequencing due to simultaneously providing long sequence reads (genome contiguity), high consensus accuracy (genome accuracy), minimal sequence bias (genome completeness), and methylation detection (bacterial epigenome). In his talk Jonas Korlach, highlights new advances and updates on applying PacBio sequencing in microbiology, including multiplexed microbial sequencing on the Sequel System and full-length bacterial RNA sequencing. In the second part of his talk, he covers how the generation of high-accuracy, single-molecule consensus reads, through a process called circular consensus sequencing – a capability unique to PacBio sequencing technology – can be leveraged for high-resolution insights into immune repertoires and other immunology relevant studies.

Video
NONE

Webinar: Survey of transcriptome diversity using Iso-Seq analysis

Pillai, Nisha
PacBio

20180705

Description +

The Iso-Seq method enables the sequencing of transcript isoforms from the 5’ end to their poly-A tails, eliminating the need for transcript reconstruction and inference. This webinar provides a comprehensive guide to Iso-Seq method data analysis, bioinformatics, and review key applications.

Video

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

Paxinos, Ellen
PacBio

20160212

Description +

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.

Video

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

Pandya, Chetanya
Icahn School of Medicine at Mount Sinai

20160212

Description +

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.

Video

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

Geraghty, Dan
Fred Hutchinson Cancer Research Center

20150225

Description +

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.

Video

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

Seetin, Matthew
PacBio

20160212

Description +

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.

Event

Advances in Genome Biology and Technology (AGBT) 2019

February 27, 2019-March 2, 2019

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