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Saturday, February 20, 2021

Application Brief: Targeted sequencing for amplicons – Best Practices

With Single Molecule, Real-Time (SMRT) Sequencing and the Sequel System, you can easily and cost effectively generate highly accurate long reads (HiFi reads, >99% single-molecule accuracy) from genes or regions of interest ranging in size from several hundred base pairs to 20 kb. Target all types of variation across relevant genomic regions, including low complexity regions like repeat expansions, promoters, and flanking regions of transposable elements.

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Saturday, February 20, 2021

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

With highly accurate long reads (HiFi reads) from the Sequel II System, powered by Single Molecule, Real-Time (SMRT) Sequencing technology, you can comprehensively detect variants in a human genome. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.

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Friday, February 5, 2021

ASHG PacBio Workshop: Towards precision medicine

Euan Ashley from Stanford University started with the premise that while current efforts in the field of genomics medicine address 30% of patient cases, there’s a need for new approaches to make sense of the remaining 70%. Toward that end, he said that accurately calling structural variants is a major need. In one translational research example, Ashley said that SMRT Sequencing with the Sequel System allowed his team to identify six potentially causative genes in an individual with complex and varied symptoms; one gene was associated with Carney syndrome, which was a match for the person’s physiology and was later…

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Friday, February 5, 2021

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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Friday, February 5, 2021

Webinar: Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing

Studying microbial genomics and infectious disease? Learn how the PacBio Sequel II System can help advance your research, with first-hand perspectives from scientists who are investigating SARS-CoV-2 and COVID-19. In this webinar, Melissa Laird-Smith (Mt. Sinai School of Medicine) discusses her work evaluating the impact of host immune restriction in health and disease with high resolution HLA typing. She is joined by Corey Watson (University of Louisville School of Medicine) who talks about overcoming complexity to elucidate the role of IGH haplotype diversity in antibody-mediated immunity. Hosted by Meredith Ashby, Director of Microbial Genomics at PacBio. Access additional PacBio resources…

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Friday, February 5, 2021

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 at at…

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Friday, February 5, 2021

ASHG PacBio Workshop: Applications of third generation sequencing in unsolved disease

In this ASHG 2020 PacBio Workshop Emily Farrow of Children’s Mercy Kansas City, shares how the incorporation of long-read sequencing into the Genomic Answers for Kids research study is increasing diagnostic yields through the identification of novel genetic variation. Emily highlights several cases in which PacBio HiFi sequencing was able to provide insights where short-read sequencing alone was inconclusive, due to limitations stemming from repetitive regions and large structural variants.

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Friday, February 5, 2021

ASHG CoLab: PacBio HiFi reads for comprehensive characterization of genomes and single-cell isoform expression

In this ASHG 2020 CoLab presentation hear Principal Scientists, Aaron Wenger and Elizabeth Tseng share how highly accurate long reads (HiFi reads) provide comprehensive variant detection for both genomes and transcriptomes. Aaron Wenger describes how new improvements in protocols and analysis methods have increased scalability and accuracy of variant calling. As demonstrated in the precisionFDA Truth Challenge V2, HiFi reads (>99% accurate, 15 kb – 20 kb) now outperform short reads for single nucleotide and structural variant calling and match for small indels. This includes calling >30,000 small variants and >10,000 structural variants missed by short reads, many in medically…

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Friday, February 5, 2021

Webinar: Increasing solve rates for rare and Mendelian diseases with long-read sequencing

Dr. Wenger gives attendees an update on PacBio’s long-read sequencing and variant detection capabilities on the Sequel II System and shares recommendations on how to design your own study using HiFi reads. Then, Dr. Sund from Cincinnati Children’s Hospital Medical Center describes how she has used long-read sequencing to solve rare neurological diseases involving complex structural rearrangements that were previously unsolved with standard methods.

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Friday, February 5, 2021

Educational Video: Variant Detection with HiFi Reads – Understanding Results from the precisionFDA Truth Challenge

In this short video, Aaron Wenger, a Principal Scientist at PacBio, explains what highly accurate long reads, or HiFi reads, are and how they help to detect all variant types including single nucleotide, indels, and structural variants. He goes on to recap the precisionFDA Truth Challenge V2 which used Genome in a Bottle (GIAB) benchmarks to evaluate various sequencing technologies. In the 2020 challenge, when ranked for accuracy, PacBio HiFi reads delivered the highest precision and recall in all categories.

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Tuesday, December 22, 2020

FALCON-Phase integrates PacBio and HiC data for de novo assembly, scaffolding and phasing of a diploid Puerto Rican genome (HG00733)

Haplotype-resolved genomes are important for understanding how combinations of variants impact phenotypes. The study of disease, quantitative traits, forensics, and organ donor matching are aided by phased genomes. Phase is commonly resolved using familial data, population-based imputation, or by isolating and sequencing single haplotypes using fosmids, BACs, or haploid tissues. Because these methods can be prohibitively expensive, or samples may not be available, alternative approaches are required. de novo genome assembly with PacBio Single Molecule, Real-Time (SMRT) data produces highly contiguous, accurate assemblies. For non-inbred samples, including humans, the separate resolution of haplotypes results in higher base accuracy and more…

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Tuesday, December 22, 2020

Single molecule high-fidelity (HiFi) Sequencing with >10 kb libraries

Recent improvements in sequencing chemistry and instrument performance combine to create a new PacBio data type, Single Molecule High-Fidelity reads (HiFi reads). Increased read length and improvement in library construction enables average read lengths of 10-20 kb with average sequence identity greater than 99% from raw single molecule reads. The resulting reads have the accuracy comparable to short read NGS but with 50-100 times longer read length. Here we benchmark the performance of this data type by sequencing and genotyping the Genome in a Bottle (GIAB) HG0002 human reference sample from the National Institute of Standards and Technology (NIST). We…

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Tuesday, December 22, 2020

Comprehensive variant detection in a human genome with highly accurate long reads

Introduction: Long-read sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw-read error rates (10-15%), it has remained difficult to call small variants from long reads. Recent improvements in library preparation and sequencing chemistry have increased length, accuracy, and throughput of PacBio circular consensus sequencing (CCS) reads, resulting in 10-20kb reads with average read quality above 99%. Materials and Methods: We sequenced a 12kb library from human reference sample HG002 to 18-fold coverage on the PacBio Sequel II System with three SMRT Cells 8M. The CCS algorithm was used to generate highly-accurate (average…

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