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Thursday, June 29, 2017

Study Used Iso-Seq Method to Unravel Activity of Receptors in Prostate Cancer

A new publication in Clinical Cancer Research from scientists at the Mayo Clinic, University of Minnesota, and other institutions presents results from a study to evaluate androgen receptor (AR) isoforms as biomarkers for chemotherapy resistance in prostate cancer patients. The team used the Iso-Seq method with SMRT Sequencing to better characterize the structures of AR variants, discovering that the exon structure of this prostate cancer driver had previously been misreported due to the limitations of short-read sequencing. “Androgen receptor variant AR-V9 is co-expressed with AR-V7 in prostate cancer metastases and predicts abiraterone resistance” comes from lead authors Manish Kohli and…

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Tuesday, June 27, 2017

Iso-Seq Data Supports Annotation Efforts for Key Crops Wheat and Barley

Photo by Craig Nagy Two recent papers underscore the importance of using PacBio full-length RNA sequencing to interrogate transcriptomes for major crops. Together, these publications offer compelling evidence that information considered essential for crop improvement programs is too often missed by short-read sequencers. A team of scientists from the Earlham Institute and other institutions report the assembly and annotation for wheat, an allohexaploid genome. From lead authors Bernardo Clavijo and Luca Venturini, senior author Matthew Clark, and collaborators, “An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal…

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Thursday, June 22, 2017

Stanford Scientists Report First Use of PacBio Whole Genome Sequencing to Identify a Disease-Causing Mutation

An article published today in Genetics in Medicine from Jason Merker, Euan Ashley, and colleagues at Stanford University reports the first successful application of PacBio whole genome sequencing to identify a disease-causing mutation. (Check out Stanford’s news release here.) The authors describe an individual who presented over 20 years with a series of benign tumors in his heart and glands. The individual satisfied the clinical criteria for Carney complex, but after eight years of genetic evaluation, including whole genome short-read sequencing, experts were still unable to pinpoint the underlying genetic mutation and confirm a diagnosis. Ultimately, the authors turned to the…

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Monday, June 19, 2017

At SMRT Leiden, Improvements in Characterizing Genomes, Transcriptomes, and Methylomes

Last month, we co-hosted the 2nd annual SMRT Leiden conference with Leiden University Medical Center. SMRT Leiden featured three days of excellent presentations, including one day focused on bioinformatics. If you missed it, we’ve prepared this quick recap to cover the highlights. In addition, several of the presentations are available to download, and you can check out tweets from day 1 and day 2. The meeting kicked off with a clinical angle: Eric Schadt from the Icahn School of Medicine at Mount Sinai gave a keynote talk about capturing the clinically actionable genome. Noting that we are in an age…

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Tuesday, June 13, 2017

New Maize Reference Genome Will Support Crop Improvement Programs

Photo by Carl Davies, CSIRO A large group of scientists published a new reference genome assembly for maize. It was generated with SMRT Sequencing and other technologies, and represents a major leap forward in accurately portraying and annotating the genome of this important crop. “Improved maize reference genome with single-molecule technologies” comes from lead author Yinping Jiao, senior author Doreen Ware, and collaborators at Cold Spring Harbor Laboratory, the USDA ARS, and many other institutions. They embarked on the project because the existing reference for maize, based on Sanger technology and released in 2009, “is composed of more than 100,000…

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Monday, June 12, 2017

Scientists Use SMRT Sequencing to Reveal Unexpected Adhesin Repertoire in Candida

Candida glabrata In a preprint available from bioRxiv, scientists from the University of Lausanne and Swiss Institute of Bioinformatics present the first SMRT Sequencing results from isolates of the fungal pathogen Candida glabrata. “Comparative Genomics Of Two Sequential Candida glabrata Clinical Isolates” comes from Luis Andre Vale-Silva, Emmanuel Beaudoing, Van Du T. Tran, and Dominique Sanglard. The study involved two C. glabrata samples collected at different times from an HIV-positive patient diagnosed with oropharyngeal candidiasis. Scientists initially turned to short-read sequencing to analyze the genomes, which were of particular interest because C. glabrata is known to rapidly develop resistance to antifungal therapies. However, because sequence data had to…

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Thursday, June 8, 2017

Widespread Methylation in Earliest Fungi Offers Clue to Expression of Essential Genes

The Joint Genome Institute recently announced results from a project that used SMRT Sequencing to generate high-quality genome assemblies and detect epigenetic modifications for fungal species that represent the earliest branches of that kingdom’s phylogeny. The work was done as part of the 1000 Fungal Genomes Project, which aims to better characterize a diverse range of fungal species. Published in Nature Genetics, “Widespread adenine N6-methylation of active genes in fungi” comes from lead author Stephen Mondo, senior author Igor Grigoriev, and collaborators at JGI and other institutions. The major finding is that N6-methyldeoxyadenine (6mA) is seen at the earliest stages…

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Tuesday, June 6, 2017

At CROPS 2017, SMRT Sequencing Powers Reference Plant Genome Assemblies

This week the HudsonAlpha Institute for Biotechnology and the University of Georgia are co-hosting CROPS 2017, a meeting focused on genomic technologies and their use in crop improvement and breeding programs. The three-day event attracts over 200 attendees involved in research and breeding for a range of important crop species. PacBio was proud to be a sponsor of the conference. HudsonAlpha’s Jeremy Schmutz kicked off the meeting with an introductory talk about trends in plant genomics, expanded transcriptome resources, and the improved representation of all plant genomes with many new genome assemblies. Schmutz, who also works with the Joint Genome…

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Friday, June 2, 2017

In Texas, New View of Klebsiella Strain Diversity and Antibiotic Resistance

A sweeping new report on Klebsiella pneumoniae sequence data from scientists at the Houston Methodist Research Institute, Weill Cornell Medical College, and other institutions found more diversity than expected in strains of the pathogen in a Texas population. The publication also indicates the emergence of a virulent, antibiotic-resistant strain of this organism. Published in mBio, “Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307” comes from lead author Wesley Long, senior author James Musser, and collaborators. K. pneumoniae is a dangerous source of infection, often acquired in hospitals and increasingly resistant to antibiotics. Scientists launched…

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