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Friday, October 20, 2017

ASHG 2017 Day 4: CRISPR/Cas9 Targeting and Structural Variant Calling CoLabs

It was a packed house as PacBio scientists led the inaugural CoLabs presentation at ASHG17 A new program at ASHG this year came from the CoLaboratories, or educational theaters featuring 30-minute talks on a variety of clinical, laboratory, and data analysis topics. We were honored to present in the inaugural CoLabs today, with PacBio scientists offering tips on CRISPR/Cas9 enrichment as well as long-read whole genome sequencing for structural variant discovery. Tyson Clark, Ph.D Tyson Clark, director of applications development, gave a talk titled “Targeted Enrichment without Amplification and SMRT Sequencing of Repeat-Expansion Disease Causative Genomic Regions.” He demonstrated a…

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Thursday, October 19, 2017

ASHG Day 2: Population and Clinical Genetics, Plus a SMRT Sequencing Roadmap

The PacBio team hosted a luncheon workshop at ASHG yesterday titled “Population and Clinical Genetics Studies Using Long-read SMRT Sequencing.” Thanks to all the conference attendees who took time out of a very busy meeting to join us! If you couldn’t attend, we summarized the highlights below and will share recordings of the presentations soon. Long-read Sequencing – for Detecting Clinically Relevant Structural Variation Han Brunner, M.D Han Brunner, Head of Clinical Genetics at Radboud University Medical Center, kicked off the event with a talk about using SMRT Sequencing to detect clinically relevant structural variation. Introducing himself as a consumer…

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Wednesday, October 18, 2017

ASHG 2017 Day 1: Structural Variation, Reference Genomes, and More Diversity

The annual meeting of the American Society of Human Genetics kicked off with a splash yesterday in Orlando, Fla. The PacBio team was thrilled that the opening talks in the presidential address and plenary session included a significant focus on increasing diversity in genetic studies to better characterize underrepresented populations. Nancy Cox, ASHG president, highlighted a number of excellent efforts to address this but noted, “Compared with what we need, what we’ve done so far is really just a drop in the bucket.” As regular blog readers know, we work closely with groups around the world to build population-specific reference…

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Thursday, October 12, 2017

HGSV Consortium Study Identifies Sevenfold Increase in Structural Variation

UPDATE (April 16, 2019): The paper has now been published in Nature Communications. ORIGINAL POST (October 12, 2017): The Human Genome Structural Variation Consortium, a successor to the 1000 Genomes Project Consortium, recently released a preprint describing an in-depth study of structural variant (SV) detection in human genomes. The scientists found that PacBio long-read sequencing and complementary technologies dramatically improve sensitivity for these important genomic elements when compared to standard short-read sequencing. “Multi-platform discovery of haplotype-resolved structural variation in human genomes” comes from lead authors Mark Chaisson, Ashley Sanders, and Xuefang Zhao; along with corresponding authors Charles Lee, Evan Eichler,…

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Tuesday, October 10, 2017

Automated De Novo Assembly Pipeline Now Available in Bluebee Cloud Platform

Good news for cloud-loving PacBio users: genomics analysis service Bluebee has now implemented HGAP4 for de novo assembly of SMRT Sequencing data. It creates a fully automated, end-to-end assembly pipeline for genomes of all sizes from unmapped BAM files. The pipeline is available now to all Bluebee users. This new analysis service expands the use of SMRT Sequencing data beyond the realm of bioinformatics experts. Bluebee’s platform is designed for ease of use and alleviates the pressure of setting up compute clusters or other on-site tech solutions. Bluebee will also handle updating the pipeline as new versions are released, so…

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Thursday, October 5, 2017

Sequel System Boosts Coverage, Provides 40-fold Cost Reduction for Amplicon Sequencing

UPDATED March 27, 2018 This paper is now available at BMC Genomics. ORIGINAL POST October 5, 2017 A new preprint from scientists at the University of Guelph in Canada and the University of Pennsylvania reports the evaluation of SMRT Sequencing with the Sequel System as a replacement for Sanger platforms for amplicon sequencing. They found that long-read PacBio sequencing was highly accurate, exceeded Sanger coverage metrics, and reduced costs by 40-fold. “A Sequel to Sanger: Amplicon Sequencing That Scales” comes from lead author Paul Hebert, senior author Evgeny Zakharov, and collaborators. The team embarked on this project in the hopes of…

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