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PAG Conference: Domestication: through the canines of a dingo

Ballard, Bill
University of New South Wales

2018

Description +

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.

PAG Conference: Long-read sequencing reveals complex genomic architecture in independent carnivorous plant lineages

Renner, Tanya
Pennsylvania State University

2018

Description +

In this PAG 2018 presentation, Tanya Renner of Pennsylvania State University shares research using PacBio SMRT Sequencing to understand the genomes and transcriptomes of carnivorous plants. She describes the humped bladderwort, Utricularia gibba, as having an extreme genome due to its small size (100 Mbp) despite containing numerous tandem gene duplications and having undergone two whole genome duplications. Renner shares ongoing research into two Drosera species, commonly known as sundews, which through whole genome sequencing are illuminating carnivorous plant genome structural evolution including the transition from monocentric to holocentric chromosomes.

PAG Conference: Using cattle subspecies crosses to explore chromosome of origin expression through Iso-seq analysis

Williams, John
University of Adelaide

2018

Description +

In this PAG 2018 presentation, John Williams of University of Adelaide, presents research on using PacBio SMRT Sequencing to explore the genetic origins of cattle subspecies, Angus (Bos taurus taurus) and Brahman (Bos taurus indicus). He shares RNA sequencing data using the PacBio Iso-Seq method to compare transcriptomes and phase allelic expression and describes how the IsoPhase technique enables evaluation of SNPs through transcriptome mapping back to the single genome of a cross-bred individual. Using a genomic and transcriptomic approach, two high-quality genomes from a single individual and gene isoforms specific to each subspecies are being identified.

Video: Structural variant detection with SMRT Sequencing

Wenger, Aaron
PacBio

2017

Description +

In this video, Aaron Wenger, a research scientist at PacBio, describes the use of long-read SMRT Sequencing to detect structural variants in the human genome. He shares that structural variations – such as insertions and deletions – impact human traits, cause disease, and differentiate humans from other species. Wenger highlights the use of SMRT Sequencing and structural variant calling software tools in a collaboration with Stanford University which identified a disease-causing genetic mutation.

Podcast: Huh? 30 Million Americans Have a Rare Disease? Howard Jacob on the State of Clinical Sequencing

Jacob, Howard
HudsonAlpha Institute for Biotechnology

2017

Description +

Howard Jacob, Chief Genomics Officer at the HudsonAlpha Institute for Biotechnology, explored the role of genomics in diagnosing rare diseases. In this podcast he shared his views on the economics of clinical sequencing and how long-read sequencing is advancing the ability to sequence an individual’s genome –de novo– and use structural variant calling to make clinical diagnoses. He concluded with the hurdles limiting adoption of clinical sequencing and his vision for the future of genomic medicine.

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

Hatas, Emily
PacBio

2017

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.

ASHG PacBio Workshop: Expansion sequence variations underlie distinct disease phenotypes in SCA10

McFarland, Karen
University of Florida

2017

Description +

In this ASHG 2017 presentation, Karen McFarland of the University of Florida presented research on spinocerebellar ataxia type 10 (SCA10), a progressive neurodegenerative disease caused by repeat expansions. She outlined efforts to sequence these repeat expansions including using CRISPR-Cas9 system coupled with SMRT Sequencing. McFarland shared findings from a study of a Parkinson’s disease patient and family that showed variations in expansion sequence can underlie distinct disease phenotypes.

ASHG PacBio Workshop: Long-read sequencing for detecting clinically relevant structural variation

Brunner, Han
Radboud University Medical Center

2017

Description +

In this ASHG 2017 presentation, Han Brunner of Radboud University Medical Center presented research using SMRT Sequencing to detect structural variants to uncover the genetic causes of intellectual disability. He shared that long-read sequencing enabled detection of 25,000 structural variants per genome. Brunner presented data from patient trios to identify de novo structural variant candidates and ongoing validation work to determine the causative mutations of intellectual disability.

ASHG PacBio Workshop: Multiplatform Discovery of Haplotype-Resolved Structural Variation in Human Genome

Lee, Charles
The Jackson Laboratory for Genomic Medicine

2017

Description +

In this ASHG 2017 presentation, Charles Lee of The Jackson Laboratory for Genomic Medicine presented work from the Human Genome Structural Variation Consortium. He shared data from efforts to utilize multiple platforms for the comprehensive discovery of structural variations—including insertions, deletions, inversions and mobile element insertions—in individual genomes. By combining various technologies, this research identified 7 times more structural variation per person than was previously known to exist.

ASHG PacBio Workshop: PacBio Applications Updates & Future Roadmap

Korlach, Jonas
PacBio

2017

Description +

In this ASHG 2017 presentation, Jonas Korlach, the CSO of PacBio shared updates on three applications featuring SMRT Sequencing on the Sequel System, highlighting structural variant detection, targeted sequencing and the Iso-Seq method of RNA sequencing. He provided details on structural variant calling using pbsv to call insertions and deletions and compared PacBio variant calling with other technologies. Korlach described how targeted sequencing can be used to interrogate repeat expansions, detect and phase minor variants and can access medically relevant but previously inaccessible gene targets. He presented research featuring the Iso-Seq method that identified isoforms, corrected previous isoform annotations and expanded knowledge of the number of long noncoding RNAs in the human genome. Korlach concluded with a roadmap of the future of SMRT Sequencing including analysis and performance improvements for the Sequel System.

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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 Shendure

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.