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Sunday, October 25, 2020

AGBT PacBio Workshop: SMRT Sequencing roadmap: better throughput, lower costs

In this AGBT 2017 talk, PacBio CSO Jonas Korlach provided a technology roadmap for the Sequel System, including plans the continue performance and throughput increases through early 2019. Per SMRT Cell throughput of the Sequel System is expected to double this year and again next year. Together with a new higher-capacity SMRT Cell expected to be released by the end of 2018, these improvements result in a ~30-fold increase or ~150 Gb / SMRT Cell allowing a real $1000 real de novo human genome assembly. Also discussed: Additional application protocol improvements, new chemistry and software updates, and a look at…

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Sunday, October 25, 2020

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

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.

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Sunday, October 25, 2020

AGBT PacBio Workshop: High-throughput HLA class I whole gene and HLA class II long range typing on PacBio RSII and Sequel Platforms

In a talk at AGBT 2017, Histogenetics CEO Nezih Cereb reported on how SMRT Sequencing is allowing his team to produce full-length, phased sequences for HLA alleles, which are important for matching organ transplants to recipients. The company is typing thousands of samples per day on their PacBio RS II systems and their new Sequel System. Cereb noted that SMRT Sequencing is unique in its ability to reliably phase mutations in the HLA alleles without imputation. Cereb concluded with his plans to use this approach for other complex regions, such as KIR, and announced their continued increasing HLA typing capacity…

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Sunday, October 25, 2020

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

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…

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Sunday, October 25, 2020

Video: Structural variant detection with SMRT Sequencing

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.

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Sunday, October 25, 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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Sunday, October 25, 2020

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

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.

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Sunday, October 25, 2020

User Group Meeting: No Assembly Required – Making the most of Iso-Seq data

In this PacBio User Group Meeting presentation, PacBio scientist Kristin Mars speaks about recent updates, such as the single-day library prep that’s now possible with the Iso-Seq Express workflow. She also notes that one SMRT Cell 8M is sufficient for most Iso-Seq experiments for whole transcriptome sequencing at an affordable price.

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Sunday, October 25, 2020

User Group Meeting: New genotype to phenotype associations in viral metagenomes enabled by SMRT Sequencing

In this PacBio User Group Meeting lightning talk, Shawn Polson of the University of Delaware speaks about viral metagenomes, which are more challenging to distinguish than their bacterial counterparts because viruses have no 16S equivalent. By using SMRT Sequencing, his team generated higher-resolution data about viral genomes and aims to use this information as a guide to how these genomes function.

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Sunday, October 25, 2020

Webinar: Opportunities for using PacBio Long-read sequencing for COVID-19 research

In this Labroots webinar, Meredith Ashby, Director of Microbial Genomics at PacBio, describes the utility of highly accurate long-read sequencing, known as HiFi sequencing, to understand the SARs-CoV-2 viral genome. HiFi sequencing enables mutation phasing and rare variant detection to understand viral stability and mutation rates, as well as providing insights into viral population structure for monitoring viral evolution. Ashby also shares how HiFi sequencing can be used to explore the host immune response to COVID-19, specifically by providing full-length sequencing of the B cell repertoire, IGH locus and HLA genes. Access additional COVID-19 Sequencing Tools and Resources.

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Sunday, October 25, 2020

Webinar: Discover full-length RNA sequencing – No assembly required

In this webinar we present Single Molecule, Real-Time (SMRT) Sequencing and the Iso-Seq method, which allow you to generate full-length cDNA sequences — no assembly required — to characterize transcript isoforms within targeted genes or across an entire transcriptome. The presenters share how the Iso-Seq method: (1) Provides high quality, full-length transcript sequences of up to 15 kb; (2) Allows for one-day library prep on a single SMRT Cell 8M to comprehensively characterize a whole transcriptome; (3) Facilitates discovery of alternative splicing events, fusion gene detection, and allelic specific isoform detection; and (4) Enables discovery of potential cancer-specific isoforms in…

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Sunday, October 25, 2020

Webinar: SMRT Sequencing applications for human genomics and medicine

In this webinar, Adam Ameur of SciLifeLab at Uppsala University shares how he uses Single Molecule, Real-Time (SMRT) Sequencing applications for medical diagnostics and human genetics research, including sequencing of single genes and de novo assembly of human genomes as well as a new method for detection of CRISPR-Cas9 off-targets.

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Tuesday, April 21, 2020

Long-read sequencing for rare human genetic diseases.

During the past decade, the search for pathogenic mutations in rare human genetic diseases has involved huge efforts to sequence coding regions, or the entire genome, using massively parallel short-read sequencers. However, the approximate current diagnostic rate is

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Tuesday, April 21, 2020

The bracteatus pineapple genome and domestication of clonally propagated crops.

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513?Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated…

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