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Friday, April 9, 2021

Creating Core Demand with HiFi Sequencing

In this video, Dave Miller from PacBio and Alvaro Hernandez PhD from the University of Illinois Urbana- Champaign discuss how to create Core Lab demand using PacBio highly accurate long-read, or HiFi, sequencing.

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Friday, April 9, 2021

The Long and Short of Sequencing – Why HiFi Reads are the Future 

PacBio Sequencing and software enable the generation of highly accurate (>99.9%) long reads. HiFi reads are accurate, essential, affordable, and can be used across a range of applications, including detection of all variant types, from single nucleotides to structural variants. PacBio’s end-to-end solutions feature library preparation paired with push-button analysis to support numerous workflows so you can run projects quickly and easily.

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Wednesday, March 24, 2021

AGBT Presentation: Increasing the Solve Rate of Rare and Undiagnosed Genetic Diseases with HiFi Sequencing

In this talk, Jonas Korlach, PhD, Chief Scientific Officer at PacBio describes how using PacBio HiFi reads, which are greater than 99.9% accurate and up to 25 kb long, led to the detection of structural variants in examples of previously unexplained rare genetic diseases. Genetic diseases affect as much as 10% of the population and over 50% of cases currently remain unexplained. Similarly, Mendelian diseases include over 8,500 described disorders, however at present ~40% have an unknown genetic cause. In addition, he highlights the strength of complete, phased, high-accuracy human WGS for simultaneously yielding high-quality information about any other locus…

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Friday, February 26, 2021

Structural variant detection with low-coverage Pacbio sequencing

Despite amazing progress over the past quarter century in the technology to detect genetic variants, intermediate-sized structural variants (50 bp to 50 kb) have remained difficult to identify. Such variants are too small to detect with array comparative genomic hybridization, but too large to reliably discover with short-read DNA sequencing. Recent de novo assemblies of human genomes have demonstrated the power of PacBio Single Molecule, Real-Time (SMRT) Sequencing to fill this technology gap and sensitively identify structural variants in the human genome. While de novo assembly is the ideal method to identify variants in a genome, it requires high depth…

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Friday, February 26, 2021

Detecting pathogenic structural variants with low-coverage PacBio sequencing.

Though a role for structural variants in human disease has long been recognized, it has remained difficult to identify intermediate-sized variants (50 bp to 5 kb), which are too small to detect with array comparative genomic hybridization, but too large to reliably discover with short-read DNA sequencing. Recent studies have demonstrated that PacBio Single Molecule, Real-Time (SMRT) sequencing fills this technology gap. SMRT sequencing detects tens of thousands of structural variants in the human genome, approximately five times the sensitivity of short-read DNA sequencing.

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Friday, February 26, 2021

Improving the reference with a diversity panel of sequence-resolved structural variation

Although the accuracy of the human reference genome is critical for basic and clinical research, structural variants (SVs) have been difficult to assess because data capable of resolving them have been limited. To address potential bias, we sequenced a diversity panel of nine human genomes to high depth using long-read, single-molecule, real-time sequencing data. Systematically identifying and merging SVs =50 bp in length for these nine and one public genome yielded 83,909 sequence-resolved insertions, deletions, and inversions. Among these, 2,839 (2.0 Mbp) are shared among all discovery genomes with an additional 13,349 (6.9 Mbp) present in the majority of humans,…

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Friday, February 26, 2021

TLA & long-read sequencing: Efficient targeted sequencing and phasing of the CFTR gene

Background: The sequencing and haplotype phasing of entire gene sequences improves the understanding of the genetic basis of disease and drug response. One example is cystic fibrosis (CF). Cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies have revolutionized CF treatment, but only in a minority of CF subjects. Observed heterogeneity in CFTR modulator efficacy is related to the range of CFTR mutations; revertant mutations can modify the response to CFTR modulators, and other intronic variations in the ~200 kb CFTR gene have been linked to disease severity. Heterogeneity in the CFTR gene may also be linked to differential responses to…

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Friday, February 26, 2021

A complete solution for full-length transcript sequencing using the PacBio Sequel II System

Long read mRNA sequencing methods such as PacBio’s Iso-Seq method offers high-throughput transcriptome profiling in prokaryotic and eukaryotic cells. By avoiding the transcript assembly problem and instead sequencing full-length cDNA, Iso-Seq has emerged as the most reliable technology for annotating isoforms and, in turn, improving proteome predictions in a wide variety of organisms. Improvements in library preparation, sequencing throughput, and bioinformatics has enabled the Iso-Seq method to be complete solution for transcript characterization. The Iso-Seq Express kit is a one-day library prep requiring 60-300 ng of total RNA. The PacBio Sequel II system produces 4-5 million full-length reads, sufficient to…

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Friday, February 26, 2021

Amplification-free protocol for targeted enrichment of repeat expansion genomic regions and SMRT Sequencing

Many genetic disorders are associated with repeat sequence expansions. Obtaining accurate DNA sequence information from these regions will facilitate researchers to further establish the relationship between these genetic disorders and underlying disease mechanisms. Moreover, repeat interruptions have also been shown to act as phenotypic modifiers in some disorders. Targeted sequencing is an economical way to obtain sequence information from one or more defined regions in a genome. However, most targeted enrichment and sequencing methods require some form of DNA amplification. Amplifying large regions with extreme GC content as seen in repeat expansion disorders is challenging and prone to introducing sequence…

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Friday, February 26, 2021

Copy-number variant detection with PacBio long reads

Long-read sequencing of diverse humans has revealed more than 20,000 insertion, deletion, and inversion structural variants spanning more than 12 Mb in a healthy human genome. Most of these variants are too large to detect with short reads and too small for array comparative genome hybridization (aCGH). While the standard approaches to calling structural variants with long reads thrive in the 50 bp to 10 kb size range, they tend to miss exactly the large (>50 kb) copy-number variants that are called more readily with aCGH. Standard algorithms rely on reference-based mapping of reads that fully span a variant or…

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Friday, February 26, 2021

New advances in SMRT Sequencing facilitate multiplexing for de novo and structural variant studies

The latest advancements in Sequel II SMRT Sequencing have increased average read lengths up to 50% compared to Sequel II chemistry 1.0 which allows multiplexing of 2-3 small organisms (98% of conserved genes) for both individuals. For microbial multiplexing, we multiplexed 48 microbes with varying complexities and sizes ranging 1.6-8.0 Mb in single SMRT Cell 8M. Using a new end-to-end analysis (Microbial Assembly Analysis, SMRT Link 8.0), assemblies resulted in complete circularized genomes (>200-fold coverage) and efficient detection of >3-200 kb plasmids. Finally, the long read lengths (>90 kb) allows detection of barcodes in large insert SMRTbell templates (>15 kb)…

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