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Friday, August 30, 2019

From Parakeet to Potoo, International Consortium Releases 100 High-Quality Vertebrate Genomes

100 high-quality assemblies released by the Vertebrate Genome Project include the genome of the critically endangered vaquita porpoise UPDATE (October 2020): A preprint of the vaquita reference genome has been published. With her distinctive dark eyeshadow, grey lipstick-like markings and delicate disposition, she was a natural film star. And her life certainly provided enough drama for any Hollywood blockbuster, complete with high-speed boat chases in pursuit of black market “cocaine of the sea” cartels. Unfortunately, her ending was not a happy one. But efforts by an international consortium of conservation geneticists are making sure her legacy isn’t lost. The DNA…

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Wednesday, August 21, 2019

New Initiative to Generate 5,000 High-Quality Microbial Genomes for Chinese Database

An ambitious project to sequence 5,000 microbial genomes was jointly initiated by a consortium of 10 institutions across China, including Nankai University, China CDC, Academy of Military Medical Science, Third Institute of Oceanography-Ministry of Natural Resources, South China Sea Institute of Oceanology-CAS, China National Center for Food Safety Risk Assessment, Shandong University, Tianjin University of Science & Technology, East China University of Science and Technology, and Tianjin Biochip Corporation (TBC).  TBC, a PacBio service provider in China, has led the sequencing phase of the project, which is expected to be completed by the end of 2019. We recently sat down with…

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Monday, August 19, 2019

When Size Matters: Using SMRT Sequencing to Help Patients With Repeat Expansion Disorders 

Patients with myotonic dystrophy type 1 (DM1) want to know their size — the size of the expansion of repeats of the unstable CTG sequences that cause the progressive deterioration of neuromuscular functions that they might face.  Size matters to them, because it has been found to correlate with the severity and onset of symptoms, which can range from severe cardiac and respiratory abnormalities and intellectual impairment in children, to muscle weakness, hypersomnolence or cataracts in adults. The earlier the onset, the more severe the symptoms tend to be. The autosomal disorder, which is the most common form of inherited…

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Thursday, August 15, 2019

At ESHG, SMRT Sequencing Contributed to De Novo Assemblies, Structural Variant Discovery

The annual meeting of the European Society of Human Genetics — held last month in the sleek Swedish Exhibition & Congress Center in Gothenburg, Sweden — was a terrific assembly of thousands of scientists who are together pushing the boundaries of what’s possible in genome research. The PacBio team particularly enjoyed seeing so many impressive ESHG presentations with scientific results from SMRT Sequencing pipelines featuring applications such as de novo whole genome sequencing, structural variant detection, the Iso-Seq method, and targeted sequencing.   Mark Chaisson For example, in a plenary talk, the University of Southern California’s Mark Chaisson (@mjpchaisson) spoke…

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Monday, August 12, 2019

PacBio HiFi Reads: ‘Most Effective Stand-Alone Technology for de Novo Assembly’

UPDATE: The article is now published in the Annals of Human Genetics.   A new preprint evaluates the utility of PacBio HiFi reads for assembly of a human genome.  The study is a follow-up to a recent publication in Nature Biotechnology that introduced a technique to generate sequencing reads with both long read length and high accuracy. Evan Eichler discussed the challenges of segmental duplications during a presentation at SMRT Leiden in May. Illustration by Alex Cagan of the Sanger Institute. “Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads” comes from lead authors…

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Wednesday, August 7, 2019

SMRT Sequencing Helps Crack the Code of Elusive Centromeres

Crucial assembly sites and mitosis mediators, centromeres are central to every cell, but missing from even the most complete genome assemblies.  Until now. In a PLOS Biology paper, Amanda Larracuente and colleagues at the University of Rochester and Barbara G. Mellone of the University of Connecticut, described how they sequenced the repetitive regions of the fruit fly genome, including its centromeres, using SMRT Sequencing.  Embedded in blocks of highly repetitive satellite DNA, centromeres have eluded efforts at assembly. Only recently, long-read single molecule sequencing technologies have made it possible to obtain assemblies of highly repetitive parts of multicellular genomes such…

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Monday, July 29, 2019

HiFi Reads Add Unparalleled Accuracy to the Long-Read Sequencing Arsenal

To enable better understanding of biology, sequencing data must be accurate and complete. This is especially true when seeking out variants and determining their implications. Luckily, technical and software improvements for SMRT Sequencing are making it easier to efficiently generate genome assemblies with unparalleled accuracy. As presented in a webinar by PacBio Staff Scientist Sarah Kingan (@drsarahdoom) and GoogleAI Genomics Project Lead Andrew Carroll (@acarroll_ATG), HiFi reads enabled by circular consensus sequencing (CCS) on the new Sequel II System challenge the notion that sequencing technologies require a tradeoff between length and accuracy. Highly accurate long reads (HiFi reads) offer the…

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Thursday, July 18, 2019

RNA Sequencing SMRT Grant Winner to Help Hone New Therapeutic Strategy in Acute Myeloid Leukemia

Variety is the spice of life, and one of the drivers of genetic variation is gene splicing.  After a gene is transcribed, there are alternatively spliced transcripts that add even more variety to that gene’s expression and its menu of phenotypes.  It appears that there are types of disorders that take advantage of these varieties. Top amongst them are myeloid disorders, where somatic mutations in splicing factors lead to cell proliferation in myelodysplastic syndromes (MDS) and blood cancers.  Christopher R. Cogle, a physician-scientist at the University of Florida, would like to understand why, in hopes that such knowledge could be…

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Thursday, July 11, 2019

Sanger Scientists Test Sequel II System for Tree-of-Life Projects

Today we offer the final post in our blog miniseries about early access users’ experiences with the new Sequel II System. Shane McCarthy, a scientist at the University of Cambridge who was able to use the new sequencing system at the Wellcome Sanger Institute, gave a presentation on his experience generating data for tree-of-life sequencing projects. McCarthy participates in several of these large-scale projects, such as the Vertebrate Genomes Project, the Sanger 25 Genomes Project, and the Darwin Tree of Life Project. For all of them, the goal is to produce high-quality, phased, chromosome-level assemblies with minimal gaps. Through Sanger’s…

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Monday, July 8, 2019

No-Amp Targeted Sequencing Used to Interrogate Disease-Associated Repeat Expansion

A new publication released in PLOS One from scientists at the Mayo Clinic offers a great look at our CRISPR/Cas9-based, amplification-free targeted sequencing method and its utility for accurately sizing a clinically important repeat expansion. “Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy” comes from lead author Eric Wieben, senior author Michael Fautsch, and collaborators. This is the second group to use the amplification-free technique for this disease; the first performed their work on a PacBio RS II System, while this team used the newer Sequel System. What makes the disease such an interesting target…

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Monday, July 1, 2019

Setting a New Gold Standard in Strain Sequencing: Webinar Describes Cannabis Pan-Genome Project

What makes one strain of cannabis have potent psychoactive properties, and another more suitable for medicinal purposes? Scientists are several steps closer to figuring it all out, thanks to PacBio long-read sequencing and transcriptome analysis of the Cannabis sativa plant. In a recent webinar, Kevin McKernan (@Kevin_McKernan) of Medicinal Genomics (MGC), described how his company’s efforts to create a Cannabis Pan-Genome have already netted interesting results. Using MGC’s assembly of the female Jamaican Lion cultivar as a baseline, genomic DNA from a sibling male plant and multiple offspring were isolated and sequenced with the Sequel II System to identify structural…

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Thursday, June 20, 2019

At Maryland Genomics, Scientists Deploy Sequel II System for a Wide Range of Applications

Maryland Genomics leaders with the Sequel II System In this blog miniseries, we’re recapping presentations from early access users of the Sequel II System. Today, we summarize Luke Tallon’s report from Maryland Genomics, a PacBio Certified Service Provider. Like the other early access users, Maryland received 32 SMRT Cells for use in evaluating the new sequencing system. They tested them across a range of applications: continuous long-read (CLR) sequencing for humans, plants, insects, and bacteria; and HiFi mode, powered by circular consensus sequencing, for human, microbiome, and other samples. Tallon reports that each SMRT Cell 8M averaged about 92 Gb…

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Monday, June 17, 2019

Broad Institute Scientists Use Sequel II System for Trios, Structural Variant Detection

Kiran Garimella As we geared up for the launch of our new Sequel II System, we had the good fortune of working closely with several expert customers in an early access program. Recently, three of those customers reported on their experience with the new sequencing system in a webinar. In this blog series, we’ll be summarizing each speaker’s presentation, and the full recording is available to view. First up was Kiran Garimella (@KiranGarimella), a senior computational scientist at the Broad Institute who focused on the use of HiFi reads, which are long (>10 kb) and accurate (>99%) sequences produced by…

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Thursday, June 13, 2019

The SMRT Special: Journal Focuses on Advances in SMRT Sequencing

Single Molecule, Real-Time (SMRT) Sequencing continues to get smarter and more powerful, with the recent launch of the Sequel II system increasing capabilities and efficiencies of the long-read DNA and RNA PacBio sequencing technology even further. In a special issue devoted entirely to the technology in the MDPI open access journal Genes, guest editors Adam Ameur of Uppsala University and Matthew S. Hestand of the Cincinnati Children’s Hospital Medical Center present eight articles highlighting research conducted using SMRT Sequencing. As this special issue demonstrates, the benefits of SMRT Sequencing to many different areas of research are becoming evident, not only…

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Tuesday, June 11, 2019

Genome in a Bottle Consortium Describes Human Genome Structural Variation Benchmark

UPDATE: The paper has been published in Nature Biotechnology A preprint released this week from the Genome in a Bottle (GIAB) Consortium describes a benchmark set of structural variants (SVs), differences ≥50 bp, in the genome of a human male named HG002. The GIAB benchmark is the first to allow measuring precision (false positives) and recall (false negatives) of different approaches to detecting structural variants. The GIAB Consortium also developed a tool, Truvari, to support evaluation of variant call sets against the benchmark. Earlier GIAB benchmarks, first released in 2014 and last updated in 2017, have led to enormous improvements…

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