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Thursday, March 30, 2017

At AACR, Revealing Structural Variants and a New SMRT Grant Program

We’re excited to be heading to Washington, DC, for the annual meeting of the American Association for Cancer Research. The PacBio team always enjoys hearing about the latest in cancer translational research at AACR, along with thousands of leading scientists in the field. Many of those scientists have already learned that SMRT Sequencing provides a unique view into cancer, revealing structural variation, phasing distant variants, and delivering full-length isoform sequences. With uniform coverage, industry-leading consensus accuracy, and reads extending to tens of kilobases, PacBio long-read sequencing gives researchers the ability to monitor and make sense of even the most complex…

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Wednesday, March 29, 2017

IGV 3 Improves Support for PacBio Long Reads

The recent beta release of version 3 of the popular genome browser IGV greatly improves support for PacBio data [1].  The long reads (up to 50 kb) and random error profile of PacBio SMRT® sequencing facilitate new applications in genome assembly, structural variant discovery, and haplotype phasing.  These unique properties and applications benefit from customized data visualization. IGV 3 extends support for PacBio long reads with: performance improvements to enable viewing variants at multi-kilobase scales; a “quick consensus” mode that suppresses single read random errors; labels for large insertion and deletion structural variants; and “group by base” to explore haplotype…

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Monday, March 27, 2017

Scientists Confirm Transplant-Associated Infection with SMRT Sequencing

Image of vancomycin-resistant Enterococcus courtesy of CDC/ Janice Haney Carr A new PLoS One publication cites the use of SMRT Sequencing to clarify the transmission path of infection in a transplant recipient. This work is an excellent example of the clinical utility offered by long-read PacBio sequencing. The project was spurred by the frustrating inability to distinguish between hospital-acquired infections and donor-to-recipient infections through solid organ transplants. Scientists and clinicians from the Icahn School of Medicine at Mount Sinai and the University of Texas Medical School teamed up to apply advanced sequencing technologies in the case of a liver transplant…

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Thursday, March 23, 2017

Metal-Devouring Plant Genomes Get SMRT Treatment with Sequel System: 2016 SMRT Grant Program Winner Results

Blog readers may recall that last year’s SMRT Grant winner was Renying Zhuo from the Chinese Academy of Forestry. We’re pleased to report that the project is now complete! Zhuo proposed sequencing the genomes of two strains of the Sedum alfredii plant from the same ecosystem — one that accumulates cadmium ions from polluted soil and one that doesn’t. The goal was to use high-quality assemblies for comparative genomic analysis to determine the genetic mechanisms responsible for this remediation effect. Plant DNA was sequenced on the Sequel System by RTL Genomics, and genome assembly was performed by Computomics. (We’re also grateful…

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Tuesday, March 21, 2017

New Goat Genome Assembly Breaks Continuity Record, Expands Breeding Tools

Photo of San Clemente Island goat kids by Cliff, courtesy of Wikimedia Commons Efforts to produce a reference-grade goat genome assembly for improved breeding programs have paid off. A new Nature Genetics publication reports a high-quality, highly contiguous assembly that can be used to develop genotyping tools for quick, reliable analysis of traits such as milk and meat quality or adaptation to harsh environments. The program also offers a look at how different scaffolding approaches perform with SMRT Sequencing data. “Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome” comes from lead authors Derek Bickhart, Benjamin…

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Thursday, March 16, 2017

Vote for the World’s Most Interesting Genome! Snakes, Slugs, Pigeons, Beetles & Dingoes Compete for SMRT Sequencing Treatment

Our team of scientist reviewers has considered hundreds of submissions for the latest SMRT Grant award and narrowed the selection to five finalists. Now it’s your turn! We welcome the community to vote for their favorite project now through April 5th. The winner will receive SMRT Sequencing and genome assembly or Iso-Seq analysis sponsored by PacBio and our partners, the Arizona Genomics Institute and Computomics. Here’s a look at the entries from our five finalists:   Project: Temple Pitviper Principal investigators: Mrinalini Mrinalini, National University of Singapore; Ryan McCleary, Utah State University; Manjunatha Kini, National University of Singapore #SeqtheViper The highly venomous snake…

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Tuesday, March 7, 2017

High-Quality, Chromosome-Scale Quinoa Genome Valuable for Breeding Better Crops

A new genome assembly has remarkable promise to boost the global food supply. Scientists from King Abdullah University of Science and Technology and other institutions sequenced quinoa, a nutritious grain that can grow in marginal lands and other suboptimal environments. Their assembly offers new clues that could help improve breeding efforts to make the plant more accessible worldwide. “The genome of Chenopodium quinoa” was published recently in Nature by lead author David Jarvis, senior author Mark Tester, and a large group of collaborators. They focused on this plant, which is believed to have been domesticated more than 7,000 years ago in…

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Friday, March 3, 2017

‘Mobilome’ Study of Antibiotic Resistance Implicates Transposon Activity

Klebsiella pneumoniae A recent effort to understand the genetic mechanisms behind swappable elements of drug-resistance among bacteria built on previous studies of Enterobacteriaceae isolates collected at the National Institutes of Health Clinical Center. The work was made possible by high-quality genome assemblies of these organisms generated earlier with SMRT Sequencing technology. In this project, scientists from the U.S., France, and Brazil teamed up to learn precisely how drug-resistance plasmids are spread from one species to another. They report the results of that investigation in mBio with the publication “Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids” from lead author Susu He,…

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Wednesday, March 1, 2017

Scientists Explore Extremophile Genome with SMRT Sequencing

Photo by Liam Quinn A recent Nature publication from a large team of scientists in Europe, Canada, and the US reports the use of SMRT Sequencing to elucidate the genome of Fragilariopsis cylindrus, a single-celled eukaryotic diatom adapted to living in polar waters of the Antarctic Ocean. The work has implications for the biotechnology industry, which looks to extremophiles as a potential source of important enzymes. “Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus” comes from lead author Thomas Mock, senior author Igor Grigoriev, and many collaborators at the University of East Anglia, Earlham Institute, Joint Genome Institute, University of…

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