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Tuesday, September 18, 2018

Must-Have PacBio Applications & Services: Getting the Most from SMRT Sequencing

In addition to the most common applications, like whole genome sequencing for de novo assembly, there are several other features you can utilize to advance your science or incorporate to offer your customers a broad range of the best PacBio services. Here’s a sampling of the most recent updates and releases.   Iso-Seq Analysis for Genome Annotation or Targeted Isoform Discovery The isoform sequence (Iso-Seq) application generates full-length cDNA sequences – from the 5’ end of transcripts to the poly-A tail – eliminating the need for transcriptome reconstruction using isoform-inference algorithms. It’s even easier to help your customers annotate their…

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Thursday, September 13, 2018

Building a Digital Genome Ark: Vertebrate Genome Project Releases 15 New Reference Genomes

[caption id="attachment_29874" align="alignright" width="300"] The duck-billed platypus genome is one of 15 high-quality assemblies released by the Vertebrate Genome Project[/caption] When creating a global genomic ark of creatures great and small, scientists are turning to the comprehensive coverage and quality of PacBio sequencing. The Vertebrate Genomes Project (VGP), an international consortium of more than 150 scientists from 50 academic, industry and government institutions in 12 countries, recently released the first 15 of an anticipated 66,000 high-quality reference genomes representing all vertebrate species on Earth. The VGP consortium spent three years selecting technologies and workflows to produce higher quality, “platinum-level” genomes,…

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Wednesday, September 12, 2018

How to Incorporate New Features into Your Sequencing Services Menu

[caption id="attachment_18580" align="alignright" width="206"] Pacific Biosciences HQ[/caption] Many people who run a sequencing core lab would prefer to focus on science instead of business, but all core lab managers know that it’s imperative to keep a steady stream of clients and projects filling the pipeline. In a recent blog post we offered 5 ways to attract more customers to your sequencing services. Now let’s take a look at how you can incorporate new services and upgrades into your facility. Keeping up with the latest and greatest advancements in sequencing technology isn’t just about the sequencing instruments. Companies like PacBio regularly…

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Thursday, September 6, 2018

New Look at Breast Cancer Cell Line Sheds Light on Structural Complexity

In an exciting paper that made the cover of Genome Research, scientists from Cold Spring Harbor Laboratory and collaborating institutions report the genome sequence and transcriptome of a commonly used breast cancer cell line. They determined that the cell line harbors far more structural variants than previously thought with results that call into question cancer genome analysis based solely on short-read sequencing data. In “Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line,” lead author Maria Nattestad, senior author Michael Schatz, and collaborators describe an in-depth investigation of SK-BR-3, an important…

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Tuesday, September 4, 2018

Webinar Summary: Developing Benchmark Sets for Structural Variants

[caption id="attachment_29573" align="alignright" width="200"] Justin Zook[/caption] A map of every individual’s genome will soon be possible, but how will we know if it is correct? Benchmarks are needed in order to check the performance of sequencing, and any genomes used for such a purpose should be comprehensive and well characterized. Enter the Genome in a Bottle Project (GIAB), a consortium of geneticists and bioinformaticians committed to the creation and sharing of high-quality reference genomes. Unlike other initiatives, such as the 1000 Genomes Project, that are seeking to sequence many representatives of different populations, GIAB is interested in sequencing just a…

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Friday, August 31, 2018

International Eagle Conservation Efforts Bolstered By New Genome Release

Genetics is not only key to discovering and tracing new traits in an organism, but also conserving old ones -- and in some cases, the species itself. A deep understanding of genetic variation within and among species can be used to reconstruct their evolutionary history, to examine their contemporary status, and to predict the future effects of management strategies. With this in mind, scientists at the UK’s Wellcome Sanger Institute were keen to incorporate endangered species among 25 genomes to be sequenced as part of a project to mark its 25-year anniversary, and the first assembly to be released is…

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Tuesday, August 7, 2018

PacBio Sequencing Reveals Food Processing & Pathogenic Strains of Yeast are the Same Species

[caption id="attachment_28852" align="alignright" width="300"] Candida krusei, a form of yeast that is known to be drug-resistant and able to cause opportunistic infections in humans[/caption] What’s in a name? Too much, when it comes to the taxology of yeast, it turns out. Scientists from University College of Dublin have found that two distinctly named species of yeast are in fact 99.6% identical at the base pair level, and collinear. In other words, they are the same species. It was a bit of a shock, especially considering one of the yeast species, Pichia kudriavzevii, is commonly used in food production and classified…

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Wednesday, August 1, 2018

Something to Crow About: SMRT Sequencing Aids Conservation of Rare Hawaiian Bird

Brought to the brink of extinction, the future of Hawaii’s only lineage of the crow family (Corvidae) is looking up thanks to intensive conservation genomics efforts using PacBio de novo assemblies. In Hawaiian mythology, the ‘alalā is said to lead souls to their final resting place on the cliffs of Ka Lae, the southernmost tip on the Big Island of Hawaii. As one of the largest native bird populations, it also had a vital role in the ecosystem, helping to disperse and germinate seeds of many indigenous plant species. Disease, predators and shrinking habitats led to a complete loss of…

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Monday, July 30, 2018

Diversity of Unexpected CRISPR Edits Revealed by SMRT Sequencing

[caption id="attachment_28653" align="alignright" width="300"] Image by Ernesto del Aguila III, National Human Genome Research Institute, NIH[/caption] A new Nature Biotechnology publication is sending reverberations through the CRISPR and gene therapy communities. The discovery that the widely used CRISPR/Cas9 method results in far more genomic changes than previously thought — including big deletions and rearrangements — was made possible by the use of long-read SMRT Sequencing. “Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements” comes from Michael Kosicki, Kärt Tomberg, and Allan Bradley at the Wellcome Sanger Institute. The scientists aimed to better understand the possible universe…

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Friday, July 27, 2018

Deep Dives into DNA of Marine Biology

[caption id="attachment_28640" align="alignright" width="225"] What lies beneath? Photo by Ruben Gutierrez.[/caption] "Live every week like it's Shark Week," 30 Rock character Tracy Jordan once quipped to Kenneth the Page, referencing the week-long, dorsal-finned programming phenomenon that has become the Discovery Channel summer ratings mainstay. If it involves diving deeply into the science of the maligned species, we’re all in favor. But why stop there? On our companion long-form Medium blog, we hosted our own Marine Week to highlight recent scientific discoveries across the seas. In “Healthy Marine Ecosystems Rely on Their Tiniest Inhabitants,” we explore how the health of ocean…

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Tuesday, July 24, 2018

SMRT Science, Tips & Tricks Presented at Leiden Meeting

[caption id="attachment_28544" align="alignright" width="300"] SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson.[/caption] When was the last time you sent your DNA off to a day at the spa? Olga Pettersson of the SciLifeLab at Uppsala University lets her molecules relax for up to a week at room temperature to enable them to untangle, achieve better chemical purity, and better sequencing output. It was one of many practical pointers shared by presenters at the popular three-day gathering of PacBio users in Leiden, Netherlands last month. SMRT Leiden featured the scientific discoveries and analytical achievements of more than 30…

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Tuesday, July 17, 2018

Long Look Into Ant Brains Provides Epigenetic Insights

To understand the epigenetic regulation of brain function and behavior, scientists are turning to ants. To understand the ants, they are applying the accurate, long reads of SMRT Sequencing. While the genetic code of many types of ant have been combed through thanks to several genomes assembled through whole-genome shotgun sequencing, there have only been brief glimpses and guesses regarding gene regulation. Existing assemblies are highly fragmented drafts, making epigenetic studies nearly impossible. Eager to determine the epigenetic changes responsible for phenotypic and behavioral plasticity in Camponotus floridanus and Harpegnathos saltator ant species, a team of researchers from the Epigenetics…

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Friday, July 13, 2018

Egyptian Rousette Bat Genome Provides Clues to Antiviral Mystery

When humans are infected with the Marburg virus, the result is often lethal, with hemorrhagic fever and other symptoms similar to Ebola. When bats are infected, the result is…. nothing. The tiny mammals remain asymptomatic. In order to crack this antiviral mystery, a multi-institutional team of scientists sequenced, assembled and analyzed the genome of the bat species Rousettus aegyptiacus, a natural reservoir of Marburg virus and the only known reservoir for any filovirus. Their findings contradicted previous hypotheses about bat antiviral immunity, which assumed  that bats had enhanced antiviral defenses, controlling viral replication early in infection, and developing effective adaptive immune…

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Wednesday, July 11, 2018

Maize Collaborators Embark on Ambitious 26-line Pangenome Project

[caption id="attachment_27906" align="alignright" width="201"] Computational biologist Doreen Ware harvests maize tissue for RNA isolation. Photo by Miriam Chua c/o USDA[/caption] The first reference genome for maize variety B73, completed in 2009, was a major milestone, and an improved version released by Cold Spring Harbor Laboratory scientists in 2017 provided a deeper dive into the genetics of the complex crop. Yet even this new robust reference is not enough for Kelly Dawe, Doreen Ware and Matt Hufford, who have taken up another ambitious project: creating a 26-line pangenome reference collection in just two years. “Maize is not only an important crop,…

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Tuesday, July 10, 2018

One Million Genomes Meeting Discusses Progress and Promise of Population-Scale Genomics

  The PacBio team was honored to attend an excellent Keystone Symposium in Hannover, Germany recently. The event, “One Million Genomes: From Discovery to Health,” offered a rare look at large-scale human genome projects, with many top-notch speakers. The meeting featured speakers from many national genomics efforts, including China, Estonia, Israel, the UK, and the US.  Each of these individual national efforts is essential to overcome the representation bias seen in human genome databases today. Underrepresented groups are currently less likely to get actionable results from clinical genetic tests, a situation that threatens to confer the benefits of precision medicine…

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