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Thursday, January 24, 2019

Scientists Produce Valuable New Human Structural Variation Resource Using SMRT Sequencing

In an effort to produce a comprehensive list of structural variants in the human genome, scientists from the University of Washington, the University of Chicago, Washington University, and Ohio State University sequenced 15 human genomes and have now released the results of their in-depth analysis. The Cell publication, “Characterizing the Major Structural Variant Alleles of the Human Genome,” comes from lead authors Peter Audano and Arvis Sulovari, senior author Evan Eichler, and collaborators. The data generated by this work “provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity,” the…

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Wednesday, January 16, 2019

Q&A: Scientists Discovered Somatic Recombination in the Brain. Now What?

Jerold Chun The recent Nature paper describing the first evidence of somatic gene recombination in the human brain has been getting so much attention that we went back to the lab’s PI to learn more. Jerold Chun is Professor in the Degenerative Diseases Program and Senior Vice President of Neuroscience Drug Discovery at Sanford Burnham Prebys Medical Discovery Institute in La Jolla, Calif. He spoke with us about this remarkable discovery in the APP gene in patients with sporadic Alzheimer’s disease, the decades-long hunt for somatic recombination in genes active in the brain, and how SMRT Sequencing made a difference.…

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Tuesday, January 15, 2019

One For All: HiFi Long Reads for de Novo Assembly and Comprehensive Variant Detection

UPDATED August 12, 2019 This paper is now published in Nature Biotechnology. ORIGINAL POST January 15, 2019 CCS read protocol We’re excited to report on new SMRT Sequencing advances that will ultimately help users generate extremely accurate, single-source data for large-scale genome projects. We demonstrate this new approach in a preprint on bioRxiv, and intend to fully support the new data type in upcoming product releases for the broader SMRT Sequencing community. The preprint describes a collaborative effort to comprehensively characterize a human genome — we chose the well-analyzed HG002/NA24385 sample available as a benchmark from the Genome in a…

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Monday, January 14, 2019

Webinar Recap: SMRT Sequencing offers Many Advantages for Microbial Research

According to many, PacBio is the new “gold standard” in microbial sequencing. Chief Scientific Officer Jonas Korlach notes that its ability to simultaneously provide long sequencing reads (genome contiguity), high consensus accuracy (genome accuracy), minimal sequence bias (genome completeness), and methylation detection (bacterial epigenome) has made it the technology of choice for users who need to reliably produce high quality genomes. In a presentation for the virtual Microbiology & Immunology conference, Korlach highlighted PacBio’s strengths in the field, including multiplexed microbial sequencing on the Sequel System and full-length bacterial RNA sequencing.   Microbial de novo genome assembly Multiple bacterial genomes…

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Wednesday, January 9, 2019

Scientists Resolve Epilepsy-Causing Repeat Expansion with Sequel System

Scientists in Japan report using the unique properties of SMRT Sequencing to detect a structural variant (SV) responsible for a hereditary form of epilepsy. The 4.6 kb intronic repeat insertion was found from low-coverage whole genome sequence data, leading the team to suggest that this approach could be useful for determining the genetic mechanisms behind many unexplained diseases. “Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases” comes from lead author Takeshi Mizuguchi, senior author Satoko Miyatake, and collaborators at Yokohama City University and the University of Occupational and Environmental Health School…

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Tuesday, January 8, 2019

SMRT Grant Winner: Uncovering the Metabolic Secrets of Hibernation

What has four legs, lots of fat and fur, and will possibly help uncover novel mechanisms to combat diabetes? Photo courtesy of WSU Bear Center Grizzly bears! If humans were to undergo regular, extended cycles of weight gain and inactivity, they’d likely end up with obesity, muscle atrophy, or type 2 diabetes. But grizzly bears experience no ill effects from their annual fat gain and sedentary hibernation. Somehow they are able to switch their insulin resistance between seasons, and researchers at Washington State University are hoping to figure out how, with possible therapeutic value for humans. We’re proud to support…

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