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Monday, July 30, 2018

Diversity of Unexpected CRISPR Edits Revealed by SMRT Sequencing

Image by Ernesto del Aguila III, National Human Genome Research Institute, NIH 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 of on-target edits (rather…

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Friday, July 27, 2018

Deep Dives into DNA of Marine Biology

What lies beneath? Photo by Ruben Gutierrez. “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 habitats relies on more…

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Tuesday, July 24, 2018

SMRT Science, Tips & Tricks Presented at Leiden Meeting

SMRT Art: Jewelry created from upcycled SMRT cells by Olga Pettersson. 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 speakers. Inge Kjaerbolling of…

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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

Computational biologist Doreen Ware harvests maize tissue for RNA isolation. Photo by Miriam Chua c/o USDA 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, but an important study…

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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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