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Monday, April 29, 2019

AACR 2019 Highlights: Long Reads, Structural Variants, and Iso-Seq Analysis

PacBio’s booth at AACR 2019 This month’s meeting of the American Association for Cancer Research (AACR) in Atlanta was a great showcase of the latest academic and translational research in this field. Years ago, the idea of analyzing cancer genomes played a niche role at the conference. Now, genomic and transcriptomic assessments are widely accepted as pivotal ways to understand cancer. This may have been best embodied by the organization’s choice for a new president: genome assembly pioneer Elaine Mardis. As usual, the PacBio team was out in force for the AACR conference. We attended talks, presented posters, and greeted…

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Wednesday, April 24, 2019

Now Available: Sequel II System Delivers ~8 Times as Much Data as Previous System

We’re thrilled to announce the launch of the Sequel II System, reducing project costs and timelines with approximately eight times the data output compared to the previous Sequel System. It enables customers to comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. The Sequel II System is based on the proven technology and workflow underlying the previous version of the system, but contains updated hardware to process the new…

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Monday, April 22, 2019

Rapid Response: A Role for SMRT Sequencing in Infectious Disease Control

Researchers rely on PacBio long-reads for richness and resolution when probing genomes, and these same attributes are becoming increasingly relevant in clinical settings. One field where the technology shows particular promise is infectious disease control. When a disease outbreak hits a hospital, it is crucial that the pathogen and its transmission path are rapidly and accurately identified. As PacBio researchers demonstrated in CLP magazine, current microbial detection techniques that rely solely on short-read DNA sequences can misidentify pathogens, resulting in incorrect prognosis and misinformed treatment decisions. SMRT Sequencing, on the other hand, can paint a complete picture of entire genomes,…

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Saturday, April 20, 2019

Smoking out Structural Variants in the Cannabis Genome

With its unique medicinal and psychoactive compounds, the popularity of cannabis is spreading… well, like a weed. Now legal in 10 states for recreational use, and in 33 for medical use (with the FDA approval of the first oral cannabis drug for epilepsy on June 25, 2018), the once-forbidden plant is primed to become one of the most talked-about — and valuable — agriculture crops. But what needs to be done to take this promising crop into the clinic? Sound science, accurate testing protocols, and strident tracking systems — all of which can be achieved through genomics, according to Kevin…

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Wednesday, April 17, 2019

German Shepherd Genome Project Fetches Popular Vote

Maya and her partner, Sgt. Nic Banuelos, of the UWPD K9 unit First there was Shadow, the poodle owned by gene-entrepreneur Craig Venter. Then there was Tasha, a female Boxer. Will the next de-coded dog be Maya, a German Shepherd Dog that helps police the campus at the University of Wisconsin-Madison? Maya has been basking in social media celebrity alongside her human companion Sgt. Nic Banuelos, PhD students Lauren Baker and Emily Binversie, technician Jorden Gruel, veterinary surgeon-scientists Susannah Sample and Peter Muir, and Peter’s woven likeness, after winning the 2019 Plant and Animal SMRT Grant, co-sponsored by Histogenetics. We…

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Tuesday, April 16, 2019

Now Available: Low DNA Input Workflow for SMRT Sequencing

We are pleased to announce the availability of our protocol for template preparation to support low DNA input for sequencing on the Sequel System. The low DNA input workflow features a 3.5-hour library prep using the SMRTbell Express Template Prep Kit 2.0 (PN 100-938-900) from as little as 150 ng of input gDNA. This workflow can be used for de novo genome assembly of up to 300 Mb and can be scaled up for larger genomes with additional gDNA input. How low is low? This publication in the journal Genes shows how a team at the Wellcome Sanger Institute used…

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Thursday, April 11, 2019

Microbial Sequencing Used to Unravel Mysteries of Aquatic Environments

Dr. Cody Sheik While some microbiologists can study their organisms of interest by growing them in cultures in the lab, many don’t have that luxury. Most microbes and algae cannot be cultured, which is why environmental microbiologist Cody Sheik relies so heavily on DNA sequencing and why he is especially excited to use the PacBio platform for metagenomic studies using both targeted and shotgun sequencing approaches. Sheik’s first exposure to PacBio sequencing came shortly after joining the faculty at the University of Minnesota at Duluth, where the sulfate-reducing bacterium Desulfovibrio desulfuricans strain G11 was being used as a model organism.…

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Monday, April 8, 2019

Complete Genomes Within Reach: Multiplexing Enables Efficient Microbial Sequencing

Research interest in the human microbiome and the roles our bacterial, viral, and single-cell eukaryote co-inhabitants play in health, nutrition, immunity, and disease has exploded. Yet accurately measuring the composition of these microbial communities remains complex. Sequence-based approaches allow the genetic material from complete collections of microbes to be analyzed without the need to cultivate the microorganisms. But each step in the process of collecting, extracting, preparing, sequencing and analyzing the DNA and data introduces its own set of errors and biases. At the Innovation Lab of the University of Minnesota Genomics Center, research scientist Ben Auch and his colleagues…

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Thursday, April 4, 2019

Many Studies Show Causal Variant Discovery Potential of SMRT Sequencing

by Jonas Korlach, CSO It’s been really exciting to see a spate of publications coming out that demonstrate the utility of SMRT Sequencing for determining the underlying genetic cause of diseases that have long gone unsolved. Discovery of the pathogenic variants behind these diseases is not just academic progress; it can give answers to people who have been seeking them for years or even generations. Here are several recent examples of the great work happening in this area. Congratulations to these teams and all other scientists who are using SMRT Sequencing to advance our understanding of disease.   Mapping the…

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Tuesday, April 2, 2019

In Study, SMRT Sequencing Provides Higher-Resolution HLA Typing Associated with Improved Patient Survival Rates

In a study just published in the Journal of Biology of Blood and Marrow Transplantation, scientists at the Anthony Nolan Research Institute demonstrated that ultra-high-resolution HLA typing performed with SMRT Sequencing identified stronger matches associated with improved survival rates among patients who received hematopoietic cell transplants. The Anthony Nolan Research Institute, which is funded by Anthony Nolan, a registered UK charity that maintains the world’s oldest stem cell registry, implemented SMRT Sequencing to fully phase and characterize HLA genes with high accuracy. The HLA genes are highly polymorphic and complex, making them very difficult to resolve fully with conventional technologies.…

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