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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 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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Wednesday, June 6, 2018

New Resource for Microbiologists: Collection of 3,000 Bacteria Genomes Released

[caption id="attachment_26599" align="alignright" width="300"] Haemophilus influenzae, a sample of which was deposited to the NCTC collection by Alexander Fleming, from his own nose.[/caption] The genomes of 3,000 strains of bacteria, including some of the deadliest in the world, are now available to researchers as part of an ambitious project by the UK’s National Collection of Type Cultures (NCTC), in partnership with the Wellcome Sanger Institute and PacBio. Plague, cholera, streptomyces, and 250 strains of E. coli, are among the reference genomes created, as well as all ‘type strains’ of the bacteria in the collection -- the first strains that describe…

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Tuesday, April 24, 2018

Nature Webinar and SMRT Grant Winner Explore Structural Variation for Disease Gene Discovery

Structural variants account for most of the base pairs that differ between human genomes, and are known to cause more than 1,000 genetic disorders, including ALS, schizophrenia, and hereditary cancer. Yet they remain overlooked in human genetic research studies due to inherent challenges of short-read sequencing methods to resolve complex variants, which often involve repetitive DNA.   At a recent webinar co-hosted by Nature Research, Professor Alexander Hoischen joined Principal Scientist Aaron Wenger to discuss how advances in long-read sequencing and structural variant calling algorithms have made it possible to affordably detect the more than 20,000 such variants that are…

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Thursday, April 12, 2018

SMRT Sequencing Enables Characterization of Cavities-Causing Bacteria in Children

We’re told to avoid sugar and refined carbohydrates if we want our teeth to remain strong and cavity-free. But what is the role of microbiota in our oral health? Cavities – or caries – actually occur as the result of bacterial infection that leads to sustained decalcification of tooth enamel and the layer beneath it, the dentin. Left unchecked, it can reach the tooth’s inner layer, with its soft pulp and sensitive nerve fibers, and, in some cases, can cause serious complications such as phylogenetic osteomyelitis and the life-threatening bacterial endocarditis. In addition to diet and host factors, the occurrence…

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Wednesday, April 11, 2018

HudsonAlpha Chooses Sequel System for NIH-Funded Program Focused on Challenging Pediatric Cases

At the HudsonAlpha Institute for Biotechnology, scientists are building on advances in agricultural research to power a clinical pediatric research program. For this work, they’re using the Sequel System to perform whole-genome sequencing on trios of children with developmental disabilities and their parents. HudsonAlpha researchers have been using SMRT Sequencing to resolve challenging plant genomes, deploying a Sequel System and a PacBio RS II for these complex projects. The successfulness of that program led the institute to add a second Sequel System for use in sequencing human genomes. The organization is part of the NIH-funded Clinical Sequencing Exploratory Research Program,…

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Wednesday, November 9, 2016

More than Halfway There: Richard Gibbs Talks Clinical Genetics with Mendelspod

Many scientists who participated in the original Human Genome Project shared a grand vision that individual genomes would one day be part of routine medical care. Genomics veteran Richard Gibbs, founder and Director of the Genome Sequencing Center at Baylor College of Medicine, tells Mendelspod host Theral Timpson in a new podcast interview that “we are more than halfway [there].” In the podcast, Gibbs shares his perspective on the complementary roles that genomics and genetics approaches have in driving our understanding of human biology.  He noted that long before the Human Genome Project gained momentum, the discovery of human single…

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Monday, August 1, 2016

Histogenetics Ramps Up HLA Typing with SMRT Sequencing

PacBio customer HistoGenetics was just awarded a major, multi-year contract to perform HLA typing on as many as thousands of samples per week using SMRT Sequencing. The company is a pioneer and global leader in high-resolution sequence-based HLA typing services. As blog readers know, HLA typing involves analysis of highly polymorphic human leukocyte antigen (HLA) genes comprised within the major histocompatibility complex (MHC) on chromosome 6. Accurate HLA typing is essential for research on donor recipient tissue matching during transplantation, autoimmune disease-association studies, drug hypersensitivity research, and several other applications. But the complexity of the region, which contains thousands of…

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Monday, April 25, 2016

On DNA Day Honoring Discoveries – Y chromosome, Reference Grade De Novo Assemblies & Methylation

Happy DNA Day, everyone! This scientific celebration has us reflecting on the many advancements the community has made in the past year. For a molecule that is sequenced thousands of times a day all over the world, there is still much to learn. Today we’d like to honor some of the remarkable science enabled by SMRT Sequencing since last year’s DNA Day.   Scientists have continued to make progress exploring regions of the genome that have long been considered intractable. Two of our favorite stories this year came from the always-challenging Y chromosome. Researchers studying the mosquitoes that carry malaria…

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Wednesday, December 2, 2015

PMWC 2016: Advancing Genomics for Improved Patient Care

We’re already looking forward to next month’s Personalized Medicine World Conference. Long before “precision medicine” was an industry catchphrase, PMWC was bringing together stakeholders from genomics companies and academic research, regulatory agencies, clinical groups, pharma/biotech, and more. Launched in 2009, the meeting has prompted important discussions as well as insight about how to move the field forward in a thoughtful way. From January 24th to the 27th, some 1,200 PMWC attendees will descend on the Computer History Museum in Mountain View, Calif. The event will kick off with a reception honoring the four awardees of this conference: Merck’s Roger Perlmutter…

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