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Monday, March 30, 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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Monday, March 30, 2020

ASHG PacBio Workshop: Amplicon SMRT Sequencing applications in human genetics

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…

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Monday, March 30, 2020

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

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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Monday, March 30, 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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Monday, March 30, 2020

ASHG PacBio Workshop: Long-read sequencing for disease genome analysis: Our experiences

In this presentation, Naomichi Matsumoto from Yokohama City University speaks about the use of SMRT Sequencing to solve Mendelian diseases, including the story of how his lab discovered a 12.4 kb structural variant that’s responsible for progressive myoclonic epilepsy in two siblings. He also reports progress in understanding repeat expansion disorders by pairing SMRT Sequencing with new analysis tools designed to highlight repetitive areas.

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Monday, March 30, 2020

ASHG PacBio Workshop: Long-read sequencing in oncology and population research: Perspectives and opportunities

In this presentation, Shawn Levy from the HudsonAlpha Institute for Biotechnology and HudsonAlpha Discovery offers a look at his team’s early access experience with the Sequel II System. Recent work includes a project designed to improve sequencing results from FFPE samples with long-read data. The protocol is still being optimized, but preliminary results indicate that SMRT Sequencing improves the quality of data that can be produced from these highly degraded samples. Looking ahead, Levy’s team will be using SMRT Sequencing to generate about 7,000 long-read genome assemblies for the All of Us program.

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Monday, March 30, 2020

ASHG PacBio Workshop: Addressing hidden heritability through long-read Single Molecule Real-Time (SMRT) Sequencing – Introduction to ASHG Workshop

Mike Hunkapiller, CEO of Pacific Biosciences, opened the PacBio 2015 ASHG Workshop with a historical perspective of human genome sequencing, starting with the Human Genome Project. While advances have been made in technology, throughput and cost reductions, the quality of genomes hasn’t kept pace with decreases in cost. Hunkapiller shared the news of the company’s launch of the Sequel System – which offers SMRT Sequencing and long reads at seven times greater throughput over the PacBio RS II and roughly half the cost, making it feasible to use the system for de novo assembly of high-quality human genomes. He also…

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Monday, March 30, 2020

ASHG PacBio Workshop: Of reference genomes and precious metals

Rick Wilson, Director of the McDonnell Genome Institute at Washington University in St. Louis titled his talk “Of reference genomes and precious metals” and walked the audience through definitions and standards for the various quality levels for de novo assembled human genomes, e.g., platinum, gold, and silver. He noted that this was a good topic for this session because of the important role PacBio has played in the community’s work to create reference-grade genomes. For example, PacBio technology has enabled them to sequence additional genomes (CHM1, CHM13) to a very high quality level. Although these sequences were essential for further…

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Monday, March 30, 2020

ASHG PacBio Workshop: Medical diagnostic challenges and structural variation detection using the PacBio Platform

Richard Gibbs, Director of Baylor College of Medicine’s Human Genome Sequencing Center, talked about the transition to genomic medicine. This hasn’t been as simple as people would like due to such issues as the incomplete reference genome, the difficulty in characterizing some variation, and the lack of knowledge about the function of some genes. At Baylor, most of the human genome sequencing is done for children with Mendelian disorders. He said that among 7,000 samples processed using short-read exome sequencing, only about 25% of these cases are solved. The relatively low diagnosis rate is likely due to structural variation and…

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Monday, March 30, 2020

ASHG PacBio Workshop: Going beyond the $1,000 genome? – the future of high quality de novo human genomes, epigenomes and transcriptomes?

Jonas Korlach, Chief Scientific Officer at PacBio, discussed the technology waves that have followed the initial human genome sequencing project, where we are today, and where we are going. Today, we are in what Korlach calls the 4th wave, where more comprehensive whole-genome re-sequencing is occurring, and we are nearing the 5th, when we will actually be able to free ourselves from reference genomes and sequence everything de novo.

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Monday, March 30, 2020

ASHG Conference: Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing

During this presentation from ASHG 2015, Maria Nattestad of Cold Spring Harbor Laboratory described the study of a Her2-amplified breast cancer cell line using long-read sequencing from PacBio. With reads as long as 71 kb, she was able to characterize extensive and complex rearrangements and found more than 11,000 structural variants. She also used the Iso-Seq method to find gene fusions, including some novel ones.

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Monday, March 30, 2020

ASHG Virtual Poster: De novo assembly of a diploid Asian genome

Yunfei Guo, from the University of Southern California, presents his ASHG 2015 poster on a de novo assembly of a diploid Asian genome. The uniform coverage of long-read sequencing helped access regions previously unresolvable due to high GC bias or long repeats. The assembly allowed scientists to fill some 400 gaps in the latest human reference genome, including some as long as 50 kb.

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Monday, March 30, 2020

ASHG Virtual Poster: Long range phasing of cardiac disease genes using new long read sequencing technologies

Alex Dainis, a graduate student in Euan Ashley’s lab at Stanford University, presents her ASHG 2015 poster on haplotyping for genes linked to hypertrophic cardiomyopathy. Using the Iso-Seq method with SMRT Sequencing, she sequenced full transcripts of two genes of interest, generating data on 150 different isoforms. Rare variants, which could not be found with other technologies, were associated with haplotypes.

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