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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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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, 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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Thursday, August 6, 2020

“Murder Hornet” Genome Rapidly Assembled by USDA as Part of Real-Time Invasive Species Response Initiative

With a nickname like “murder hornet,” it’s no wonder the two-inch long Asian giant hornet (Vespa mandarinia) has caused a stir amongst those terrified of insect invasions.  Various species of paper wasp (left) compared to the Asian giant hornet (right) Photo by Hanna Royals, USDA. The wasps — which are actually more dangerous to bees than humans — have made another recent appearance in Washington state, and Agricultural Research Service (ARS) scientists are hoping a new rapidly-generated genome sequence of one of the insects will help in their quest to quash an invasion. Released August 6, the first high-quality genome…

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Tuesday, July 7, 2020

Sequencing 101: From DNA to Discovery – The Steps of SMRT Sequencing

Starting a sequencing project can be daunting. First of all, there are several types of sequencing technologies, each based on unique processes. At PacBio, we use a technology called Single Molecule, Real-Time (SMRT) Sequencing.   Learn how SMRT Sequencing works in this short video:   Although each sequencing project is unique, there are five main steps to go from DNA to discovery with SMRT Sequencing:   Step 1: Sample Prep Similar to cooking, for the best results, start with the best ingredients. The ideal sequencing starter is high molecular weight DNA. There are plenty of kits on the market that…

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Wednesday, June 17, 2020

Webinar: Increasing Solve Rates for Rare and Mendelian Diseases with Long-Read Sequencing

It’s well known that finding the genetic cause of rare diseases can be complex — that’s why so many remain unsolved. But researchers are beginning to get a grasp on just how complex these conditions can be, thanks to the heightened power of PacBio. PacBio principal scientist Aaron Wenger kicked off a recent webinar with a quote from University of Washington scientist Evan Eichler, who said “there are three key aspects to genetic disease associations: comprehensive variant discovery, accurate allele-frequency determination, and an understanding of the pattern of normal variation and its effect on expression.”  Wenger explained how HiFi reads…

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Monday, June 1, 2020

Webinar: Using SMRT Sequencing to Understand SARS-CoV-2 and the Host Immune Response

As the flurry of research around the SARS-CoV-2 virus continues at an unprecedented pace, scientists are beginning to tackle some of the more complex immunological responses with the help of Single Molecule, Real-Time (SMRT) sequencing. Hundreds of people tuned in live to a special May 7 webinar, “Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing.” Meredith Ashby, Director of Microbial Genomics at PacBio, described some of the resources being generated by both PacBio and our users in order to help labs who are using SMRT Sequencing technology to investigate SARS-CoV-2 and COVID-19. These include two microbial sequencing…

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Thursday, May 21, 2020

Sequencing 101: Understanding Accuracy in DNA Sequencing

For scientists who utilize DNA sequencing in their research but are not experts in the underlying technology, it can be difficult to determine the accuracy of sequencing results — and even harder to compare accuracy across sequencing platforms. Furthermore, accuracy differs not only between technologies but also across genomic regions as some stretches of the genome are inherently more difficult to read. It is critically important to understand accuracy in DNA sequencing to distinguish important biological information from sequencing errors.   What are the Types of Sequencing Accuracy? HiFi reads are generated by combining multiple consecutive observations of a DNA…

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Wednesday, April 22, 2020

Sequencing 101: Why Are Long Reads Important for Studying Viral Genomes?

The COVID-19 pandemic has brought a sudden urgency to virus research and led many of us to dig more deeply into all the tools available for characterizing viral genomes, from RT-PCR to DNA sequencing. For all their outsized impact on human health, viruses have remarkably small and simple genomes, some just a few thousand bases in length, and most lacking any repetitive structures. With such tidy genomes, you may wonder, why would scientists want to sequence them with a long-read technology like PacBio HiFi reads? Quasispecies develop as variants are introduced to the viral genome through mutations. While it is…

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Tuesday, April 7, 2020

Sequencing 101: Video Introduction to PacBio Sequencing and the Sequel II System

We’re pleased to release a short video describing PacBio Sequencing and our latest platform, the Sequel II System. If you’ve ever wondered how Single Molecule, Real-Time (SMRT) Sequencing works, what the Sequel II System is, and what applications are available, this video is a great place to start. We are excited to share the capabilities of our Sequel II System as it makes SMRT Sequencing affordable for scientists in any lab and provides comprehensive views of genomes, transcriptomes, or epigenomes. The Sequel II System also produces highly accurate long reads, known as HiFi reads, to deliver the highest quality sequencing…

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Wednesday, March 25, 2020

Sequencing 101: The Evolution of DNA Sequencing Tools

Welcome to the Sequencing 101 blog series – where we will provide introductions to sequencing technology, genomics, and much more! If you’re not immersed in the field of DNA sequencing, it can be challenging to keep up with the rapid evolution among all the platforms and technologies on the market. Let’s start with a quick overview of how these different technologies came about — and how each is used today. The evolution of sequencing technology.   First Generation Sequencing – Starting the Era of Genomics The process of Sanger sequencing. DNA sequencing as we know it originated in the late…

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Monday, March 16, 2020

A Menagerie of New Genomes Released by International Ensembl Project

The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP)   Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project.  The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data.    Thirteen of the new assemblies have…

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Friday, February 28, 2020

A Rare Opportunity to Help Tackle Daughter’s Rare Disease

The rarest day on the calendar is February 29th — which makes it the perfect time to celebrate Rare Disease Day. On this day, we join millions of people around the world making time to honor the patients, caregivers, healthcare professionals and scientists who deal with rare diseases every day.  Zoe Harting was diagnosed with Type 1 SMA and was not expected to live past the age of 2, but is now reaching unprecedented milestones as an energetic 7-year-old, thanks to an experimental treatment. And we didn’t have to look far to find someone affected.  Bioinformation John Harting, of our…

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Wednesday, February 12, 2020

NARMS Scientists Track Antibiotic Resistance in Foodborne Bacteria Using SMRT Sequencing

Launched in 1996, NARMS is a U. S. public health surveillance system that tracks antimicrobial susceptibility of select foodborne enteric bacteria. We hear a lot about the growing crisis of antibiotic resistance in human health, but it turns out this is just the most visible place it appears as it moves through our complex modern environment. For example, when intensive farming is used to feed large urban populations, antibiotic resistance can first emerge on farms and gain access to human communities through the food system.   One of the key groups on the front lines of monitoring antibiotic resistance from farm…

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