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Thursday, October 22, 2020

PacBio and Invitae Team Up to Develop Whole Genome Sequencing-Based Assays for Pediatric Epilepsy Diagnostics

We’re excited to announce a research collaboration with Invitae focused on the investigation of clinically relevant molecular targets for use in the development of advanced diagnostic testing for epilepsy. To support this collaboration, Invitae is expanding its PacBio sequencing capacity to meet the growing demand for clinical applications dependent on highly accurate genomic information. More than half of epilepsies can be traced to a genetic cause. When a child presents with seizures, genetic testing can help identify more than 100 underlying, often rare conditions. Early genetic testing may be the most cost-effective, direct, and accurate diagnostic tool for children, shortening…

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Wednesday, October 21, 2020

The HiFi Sequencing Advantage for Metagenome Assembly

Assembly and binning of metagenome data are the first steps in many metagenomics analysis pipelines, and with good reason. Metagenome assembled genomes (MAGs) and circularized MAGs (CMAGs) allow recovery of complete genes and operons, thereby improving predictions of metabolic capacities. MAGs also provide information about gene synteny and enable better taxonomic profiling. However, as discussed in a recent review by Chen et. al. draft MAGs with poor completeness or high contamination can lead to incorrect conclusions.  One way to improve assembly completeness and contiguity is to use long-read sequencing. However, not all long reads are the same. Did you know…

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Thursday, October 15, 2020

Pediatric Partnership Powered by PacBio Aims to Solve Difficult Rare Disease Cases

Kids have lots of questions. But even the world’s top scientists don’t have all the answers — especially when it comes to rare genetic disorders afflicting children.  Our HiFi reads, highly accurate long reads, generated by our Sequel II and new Sequel IIe Systems, are helping researchers uncover disease-causing genetic variants that had previously gone undetected by other technology, contributing to increased solve rates for rare diseases. We’re particularly excited to see this technology applied to translational research in children. We will be collaborating with Children’s Mercy Kansas City as part of its Genomic Answers for Kids (GA4K) program, which…

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Thursday, October 8, 2020

A Living Legacy of Microbiology Celebrates 100 Years

As the world faces an unprecedented pandemic caused by a novel coronavirus, the scientific spotlight has shone brightly on infectious disease research. And although interest in Public Health England’s (PHE) Culture Collections is often focused on its historical cultures, its relevance in our modern world has never seemed sharper.  The National Collection of Pathogenic Viruses (NCPV) has been helping scientists from around the world address the current history-making infectious disease event. It is also anticipating future outbreaks, and building collections of pathogenic viruses to aid research into potential threats to human health. “The question of which virus will be next…

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Monday, October 5, 2020

Meet the New Sequel IIe System: Delivering Fast & Affordable HiFi Sequencing

The new Sequel IIe System provides direct access to HiFi sequencing Still soaring from the success of last year’s launch of the award-winning Sequel II System, we’re excited to announce the next evolution of the instrument: the Sequel IIe System. This evolution includes increased computing power and advanced on-instrument data processing. This means the instrument can directly produce the widely coveted, highly accurate long reads, known as HiFi reads, that have made the original Sequel II System indispensable for many labs — and save users time and money in the process.  Just how much of an improvement does the new…

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Thursday, October 1, 2020

Webinar: Crops and Corvids get the Pangenome Treatment with HiFi Sequencing

Nearly gapless, reference-quality chromosome-level assemblies — in less than a day? Yes, it’s possible, thanks to the high accuracy and low computational needs of PacBio HiFi reads.  Kevin Fengler, computational genomics lead at Corteva Agriscience, welcomed watchers to the brave new world of the pangenome during the recent webinar, “Beyond a Single Reference Genome – The Advantages of Sequencing Multiple Individuals.” We are now living in an era where you can generate a reference genome assembly that’s specific for each application or trait of interest, Fengler said.  Graphic alignment of dozens of genomes in a pangenome collection allows researchers to…

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Monday, September 21, 2020

Checkmate, Chromosome 8: The First End-to-End Sequence of a Human Autosome

Even in the field of genomics where new breakthroughs occur every few months, completion of the first-ever fully sequenced human autosome is a momentous achievement. Highly accurate, no gaps, no mis-joins — just chromosome 8 in all its glory. It’s a remarkable feat and we are honored that PacBio HiFi reads played a pivotal role in helping to achieve it. The complete centromere sequence of chromosome 8 shows a diversity of satellite repeats and other abundant genomic repeats, now with near perfect base-level resolution from end to end. Logsdon, G et al. (2020) This work is described in a preprint…

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Wednesday, September 16, 2020

Easy and Affordable: Full-Length 16S HiFi Sequencing with PacBio Service Providers

Analysis of 16S ribosomal RNA has been used for phylogenetics and identifying prokaryotes for decades. But just as scientists have had to refine the Linnaean taxonomy system based on genomic discoveries, improvements in sequencing technology are changing 16S analysis best practices. Several dominant microbial genera in Sakinaw Lake could only be resolved via Full Length 16S or were missed by V4 sequencing (gray boxes). Singer, E. et al. (2016) Researchers at the Joint Genome Institute, for instance, conducted a detailed benchmarking study and found that traditional methods of 16S analysis — which look at just a piece of the gene…

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Tuesday, September 15, 2020

Now Available: Ultra-Low DNA Input Workflow for SMRT Sequencing

The SMRTbell gDNA Sample Amplification Kit enables whole genome amplification starting from as little as 5 ng of genomic DNA. It’s one of the questions we hear most often from scientists working with small organisms: Is it possible to generate truly high-quality, long-read data from minuscule amounts of DNA? With our new kit for ultra-low DNA input projects, the answer is: Absolutely!  The new workflow dramatically reduces the requirements for DNA quantity. Now, scientists need only 5 ng of genomic DNA to kick off a SMRT Sequencing project — that’s less than 2% of the starting volume needed for our…

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Wednesday, September 9, 2020

High Quality HiFi Assemblers Open Up a Wide New World of Genomics Possibilities

With PacBio HiFi sequencing data now readily available for organisms of any size, many exciting results have been published featuring new de novo assembly methods optimized for highly accurate long reads. These methods have produced assemblies for a variety of organisms at quality levels never before thought possible — as measured by completeness, contiguity and correctness. We feel privileged to collaborate with the scientific community on the development of these tools. From Small to Tall When the USDA wanted to rapidly assemble the Asian Giant Hornet as part of its real-time invasive species response initiative, they turned to a tool…

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Monday, August 31, 2020

Colombian SMRT Grant Winners Hope HiFi Sequencing Will Help Save Critically Endangered Toads

The ‘happy toad’ (Atelopus laetissimus) comes in a variety of colors. Meet the ‘happy toad’ Atelopus laetissimus, a harlequin toad found on the slopes of the Sierra Nevada de Santa Marta mountains of Colombia. This toad is brightly colored, with an almost comical slow walk and lots of other unique attributes. But the reason it is delighting scientists and conservationists is its ability to adapt and survive while its relatives are on the brink of extinction. The 2020 Plant and Animal Sciences SMRT Grant Program co-sponsored by PacBio and the DNA Sequencing Center at Brigham Young University will enable a…

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Wednesday, August 26, 2020

Pangenome of Soybean Generated to Capture Genomic Diversity

A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…

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Wednesday, August 19, 2020

A TAL Tale: PacBio Sequencing Helps Unravel Mechanisms of Plant Infection

How do bacteria manipulate plant biology to cause blight and rot? Why are some pathogen strains more virulent than others? How can we engineer resistant staple food crops? These are pressing questions facing researchers looking to sustain and increase crop production against the backdrop of a changing environment.  For one major clade of pathogens, Xanthomonas spp, the answers lay locked within TAL effector genes (TALEs), but assembling these highly variable, repetitive regions was a long-standing obstacle. The key to finally unraveling the tangled assemblies was PacBio long-read sequencing.  Code-breaker Adam J. Bogdanove from Cornell University. Photo by Jesse Winter Plant…

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Monday, August 17, 2020

In Alabama, Scientists Use HiFi Data to Solve Rare Neurodevelopmental Disorders

In an exciting new preprint, scientists from the HudsonAlpha Institute for Biotechnology and the University of Alabama at Birmingham describe the use of PacBio highly accurate long-read sequencing to identify pathogenic variants responsible for previously undiagnosable, rare neurodevelopmental disorders. Lead author Susan Hiatt (@suzieqhiatt), senior author Gregory Cooper, and collaborators conducted genomic analyses of several family trios in an attempt to find causal genetic variants that had been missed with earlier studies. “Large fractions of [neurodevelopmental disorders] cannot be attributed to currently detectable genetic variation,” they report. “This is likely, at least in part, a result of the fact that…

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Tuesday, August 11, 2020

In precisionFDA Challenge, PacBio HiFi Reads Outperform Both Short Reads and Noisy Long Reads

In the recent precisionFDA Truth Challenge V2, which evaluated methods for variant calling in human genomes, approaches that use PacBio HiFi reads delivered the highest precision and recall in all categories: genome-wide, specifically in difficult-to-map regions, and in the major histocompatibility complex (Figure 1).  The challenge had 64 total entries: 17 using PacBio HiFi reads, 24 using Illumina reads, 3 using Oxford Nanopore reads, and 20 using multiple technologies. Twenty-five of the 26 overall most accurate callsets used PacBio HiFi reads (12 PacBio-only, 13 multi-technology), including all of the top 12 (3 PacBio-only, 9 multi-technology). A submission from Google DeepVariant…

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