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Webinar: Detecting Structural Variants in PacBio Reads – Tools and Applications

Wenger, Aaron
PacBio

2017

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.

Podcast: Exploring the Exome and the Future of Genomics with Jay Exploring the Exome and the Future of Genomics with Jay ShendureShendure

Shendure, Jay
University of Washington

2017

Description +

Jay Shendure, a Professor in the Department of Genome Sciences at the University of Washington School of Medicine explores the role of exome sequencing in clinical genomics. In this Podcast he discusses his views on the current and future roles of sequencing in diagnosing Mendelian disorders and investigation of complex regions of the genome.

Tutorial: Minor Variant Analysis


PacBio

2017

Description +

This tutorial provides an overview of the Minor Variants Analysis application in SMRT Link and a live demo of how to launch an analysis in SMRT Link and interpret the results. This application identifies and phases minor single nucleotide variants in complex populations.

Tutorial: Structural Variant Calling


PacBio

2017

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: =50 bp) insertions and deletions in a sample relative to a reference from whole genome sequence data.

Webinar: A Paradigm Shift in HLA Sequencing: From Exons to High-Resolution Allele-Level HLA Typing

Ranade, Swati
PacBio

2017

Description +

Human MHC class I genes HLA-A, -B, -C, and class II genes HLA -DR, -DQ, and -DP play a critical role in the immune system as primary factors responsible for organ transplant rejection. Additionally, the HLA genes are important targets for clinical and drug sensitivity research because of their direct or linkage-based association with several diseases, including cancer, and autoimmune diseases. HLA genes are highly polymorphic, and their diversity originates from exonic combinations as well as recombination events. With full-length gene sequencing, a significant increase of new alleles in the HLA database is expected, stressing the need for high-resolution sequencing. PacBio has developed Single Molecule, Real-Time (SMRT) Sequencing technology that delivers long reads (average read length >10 kb) capable of spanning the lengths of the majority of HLA class I and long amplicons of class II genes. In this webinar, we will demonstrate how SMRT Sequencing is a highly flexible and efficient tool for four field allele-level HLA genotyping without imputation. We will also review multiplexing approaches that enable high-throughput HLA amplicon sequencing on the PacBio platforms.

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

Kingan, Sarah
PacBio

2017

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 presenation is concluded with a review of the process of submitting diploid genome assemblies to NCBI.

Tutorial: SMRT Link v5.0 Overview

Lleras, Roberto
PacBio

2017

Description +

In this video Roberto Lleras shares new module-based features included in SMRT Link v5.0. He summarizes updates to data management, new applications for minor variant analysis and structural variant analysis and new tools for sending analysis files to PacBio tech support.

Webinar: Structural Variant Detection in SMRT Link 5 with PBSV

Wenger, Aaron
PacBio

2017

Description +

In this video Aaron Wenger describes the new structural variant detection application, known as pbsv, available in SMRT Link v5.0. This application identifies large (default: =50 bp) insertions and deletions in a sample relative to a reference from whole genome sequence data. Aaron details pbsv commands and use of the application in SMRT Link.

Webinar: Addressing “NGS Dead Zones” with third generation PacBio sequencing

Korlach, Jonas
PacBio

2017

Description +

SMRT Sequencing is a DNA sequencing technology characterized by long read lengths and high consensus accuracy, regardless of the sequence complexity or GC content of the DNA sample. These characteristics can be harnessed to address medically relevant genes, mRNA transcripts, and other genomic features that are otherwise difficult or impossible to resolve. I will describe examples for such new clinical research in diverse areas, including full-length gene sequencing with allelic haplotype phasing, gene/pseudogene discrimination, sequencing extreme DNA contexts, high-resolution pharmacogenomics, biomarker discovery, structural variant resolution, full-length mRNA isoform cataloging, and direct methylation detection.

Webinar: PacBio Targeted Sequencing of Long Amplicons Using PCR or Hybrid Capture

Kujawa, Steve
PacBio

2017

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.

Webinar: Chasing Alternative Splicing in Cancer: Simplified Full-length Isoform Sequencing

Ashby, Meredith
PacBio

2017

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.

Webinar: Beginner’s Guide to PacBio SMRT Sequencing Data Analysis

Singh, Siddharth
PacBio

2017

Description +

PacBio SMRT Sequencing is fast changing the genomics space with its long reads and high consensus sequence accuracy, providing the most comprehensive view of the genome and transcriptome. In this webinar, I will talk about the various data analysis tools available in PacBio’s data analysis suite – SMRT Link – as well as 3rd party tools available. Key applications addressed in this talk are: Genome Assemblies, Structural Variant Analysis, Long Amplicon and Targeted Sequencing, Barcoding Strategies, Iso-Seq Analysis for Full-length Transcript Sequencing

Webinar: An Introduction to PacBio’s Long-Read Sequencing & How It Has Been Used to Make Important Scientific Discoveries

Turner, Stephen
PacBio

2017

Description +

In this Webinar, we will give an introduction to Pacific Biosciences’ single molecule, real-time (SMRT) sequencing. After showing how the system works, we will discuss the main features of the technology with an emphasis on the difference between systematic error and random error and how SMRT sequencing produces better consensus accuracy than other systems. Following this, we will discuss several ground-breaking discoveries in medical science that were made possible by the longs reads and high accuracy of SMRT sequencing.

AGBT Conference: A community effort using multiple technologies to produce a dramatically improved genome assembly of the Zika virus mosquito vector

Neafsey, Daniel
Broad Institute

2017

Description +

At AGBT 2017, the Broad Institute’s Daniel Neafsey reported a large collaborative effort to sequence the mosquito that carries Zika virus. The team is using long-read PacBio sequencing to produce a high-quality genome assembly, which Neafsey expects will replace the 10-year-old Sanger assembly for Aedes aegypti. The new assembly reduces the number of contigs by at least 10-fold, boosts the contig N50 to nearly 2 Mb, and features more complete gene content.

Event

TropAg2017

November 20, 2017-November 22, 2017

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