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Wednesday, April 27, 2016

Upcoming Webinars on Biomedical Research, Data Analysis, and Structural Variation

We’ve got several educational webinars coming up, and we hope you can join us! Our first event will be hosted by Front Line Genomics on April 28 (4:00 p.m. BST / 11:00 a.m. EST / 8:00 a.m. PST). “Applying PacBio Long-Read Sequencing for Human Biomedical Research” will include Adam Ameur of the National Genomics Infrastructure in Sweden; Giancarlo Russo from the Functional Genomics Center Zurich; and our CSO Jonas Korlach. Each participant will offer a brief presentation, with audience Q&A at the end. We’ve also teamed up with DNAnexus to offer two webinars on best practices for SMRT Sequencing data…

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Monday, April 25, 2016

On DNA Day Honoring Discoveries – Y chromosome, Reference Grade De Novo Assemblies & Methylation

Happy DNA Day, everyone! This scientific celebration has us reflecting on the many advancements the community has made in the past year. For a molecule that is sequenced thousands of times a day all over the world, there is still much to learn. Today we’d like to honor some of the remarkable science enabled by SMRT Sequencing since last year’s DNA Day.   Scientists have continued to make progress exploring regions of the genome that have long been considered intractable. Two of our favorite stories this year came from the always-challenging Y chromosome. Researchers studying the mosquitoes that carry malaria…

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Wednesday, April 20, 2016

Benchmarking Study:
Full-Length 16S Sequencing Offers Better Phylogenetic Resolution

Scientists from the Joint Genome Institute and other institutions recently reported a new SMRT Sequencing approach to microbial profiling using full-length sequencing of the 16S rRNA gene. In a benchmarking study, they demonstrate that this method allows for more accurate taxonomic classification than is possible with typical short-read sequencing methods. Lead author Esther Singer, senior author Tanja Woyke, and collaborators at USDA-ARS, the University of British Columbia, and other research groups published “High-resolution phylogenetic microbial community profiling” in The ISME Journal earlier this year. The scientists note that while 16S phylogenetic analysis has traditionally been performed with gold-quality Sanger sequencing,…

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Monday, April 18, 2016

First Comprehensive Analysis of Mosquito Y Chromosome Offers Clues for Vector Control

A new PNAS paper offers the first detailed analysis of the Anopheles gambiae Y chromosome, which could prove critical for biological and infectious disease research. The report uncovered extensive remodeling of the Y chromosome, which consists almost entirely of highly repetitive sequence. The authors say this study “provides a long-awaited foundation for studying male mosquito biology, and will inform novel mosquito control strategies based on the manipulation of Y chromosomes.” “Radical remodeling of the Y chromosome in a recent radiation of malaria mosquitoes” comes from lead authors Andrew Brantley Hall, Philippos-Aris Papathanos, Atashi Sharma, and Changde Cheng, along with senior…

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Friday, April 15, 2016

Japanese Scientists Find Gene Fusion Driving B Cell Leukemia

In a new Nature Genetics paper, scientists from the University of Tokyo and several other Japanese institutes and hospitals present results of a sweeping study of gene fusions driving a form of leukemia in teenagers and young adults. They used SMRT Sequencing to validate the gene fusion. “Recurrent DUX4 fusions in B cell acute lymphoblastic leukemia of adolescents and young adults” comes from lead author Takahiko Yasuda and senior author Hiroyuki Mano, along with many collaborators. The team embarked on the search for new oncogenes responsible for acute lymphoblastic leukemia (ALL) in subjects from 15 to 39 years of age…

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Thursday, April 14, 2016

Accelerating Cancer Research Discovery with SMRT Sequencing at AACR 2016

The PacBio team is gearing up for the annual meeting of the American Association for Cancer Research (AACR), which will be held April 16-20 in New Orleans. We’re looking forward to introducing the AACR community to the Sequel System, our new SMRT Sequencing platform that’s half the price and a third of the size of our PacBio RS II System. With 5-10 Gb of throughput per SMRT Cell, we think the Sequel System will be a great fit for the cancer research world.   Presentations Sunday, April 17, 4:15 – 6:15 p.m., Room 243, Morial Convention Center MS.BSB01.01. Minisymposium: Novel…

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Wednesday, April 13, 2016

Genome and Transcriptome Analysis Help Scientists Deconstruct Cancer Complexity

At Cold Spring Harbor Laboratory, scientists used SMRT® Sequencing to decode one of the most challenging cancer genomes ever encountered. Along the way, they built a portfolio of open-access analysis tools that will help researchers everywhere make structural variation discoveries with long-read sequencing data. When Mike Schatz realized a few years ago that his PacBio® System had reached the throughput needed to process human genomes, he decided to give it a real challenge: the incredibly complicated, massively rearranged SK-BR-3 breast cancer cell line. The genome consists of 80 chromosomes, and that’s just the tip of the complexity iceberg. “We were…

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Monday, April 11, 2016

From Earthworms to Alpacas: Vote Now to Choose the Next SMRT Grant Program Winner!

For the first time ever, the winner of this year’s “Explore Your Most Interesting Genome” SMRT Grant program will be decided by the community. We’ll be using our new Genome Galaxy Initiative and Experiment’s dedicated-to-science crowdfunding platform for this worldwide event. Here’s how it works: our top five finalists will be engaging with you directly through their project pages on the Genome Galaxy Initiative via Experiment where you will have the opportunity to learn more and ask scientists about their projects.  We will be conducting daily polls so you can cast your vote for the project you feel should be…

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Thursday, March 31, 2016

With Greater Contiguity, New Gorilla Genome Assembly Offers Insights into Gene Content, SVs, and More

In a Science paper published today, scientists from the University of Washington, the McDonnell Genome Institute, and other organizations present a new gorilla genome assembly generated with PacBio long-read sequencing, representing an over 150-fold improvement over previous assemblies. From lead authors David Gordon, John Huddleston, Mark Chaisson, and Christopher Hill, and senior author Evan Eichler, the paper reports that the new assembly recovers nearly all reference exons missing from the previous assembly, and provides an unprecedented look at structural variation, genetic diversity, ancestral evolution, repeat structures, and more. The project was launched to address shortcomings with the existing gorilla assembly,…

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Wednesday, March 30, 2016

New Study Uses SMRT-ChIP Method to Find Novel Methylation in Mouse Embryonic Stem Cells

In a new Nature publication, scientists from Yale and other institutions report the discovery of N6-methyladenine (N6-mA) in mouse embryonic stem cells (ESCs), contrary to the conventional wisdom that the only form of methylation in mammals is 5-methylcytosine. Through the project, the team also developed a new method for pairing chromatin immunoprecipitation (ChIP) with SMRT Sequencing. Both of these developments have significant implications for the genomics community. “DNA methylation on N6-adenine in mammalian embryonic stem cells” comes from lead author Tao Wu and senior author Andrew Xiao, both at Yale School of Medicine. The team also included collaborators from the…

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Thursday, March 24, 2016

CSHL Scientists Discuss Long-Read Sequencing for More Contiguous Assemblies and Complex Genomes

Much like the “sharpen” tool in Photoshop brings a picture into tighter focus and enhances the fine detail, long-read sequencing offers enhanced resolution of genomic information, according to Cold Spring Harbor Laboratory colleagues Mike Schatz and Maria Nattestad. The scientists spoke with Mendelspod’s Theral Timpson about how long-read sequencing is advancing their research in unique and powerful ways; a brief recap of their conversation follows. Schatz uses PacBio sequencing to establish incredibly accurate assemblies of microbial, crop, animal, and human genomes. Indeed, SMRT technology has significantly improved his work on the flatworm Macrostomum lignano, an organism with regenerative powers. With…

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Tuesday, March 15, 2016

Genome Galaxy Initiative:
On a Mission to Sequence the Beautiful and Mysterious Kākāpō

Photo courtesy of Andrew Digby, DOC New Zealand New Zealand is more than an amazing vacation destination or the setting of the Lord of the Rings movies; it’s also home to a wealth of fascinating species that evolved in isolation for millions of years. The critically endangered kākāpō bird is one such species, and it needs your help now. David Iorns, a native New Zealander and founder of the Genetic Rescue Foundation, has launched a crowdfunding campaign to raise money and pursue a grand vision: saving kākāpōs from extinction.  With a high-quality genome already underway using SMRT Sequencing, Iorns wants…

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Thursday, March 3, 2016

Prevalent Methylation in Prokaryotic Genomes Suggests Regulatory Functions

A new publication from scientists at Lawrence Berkeley National Laboratory, the Joint Genome Institute, and other organizations reports a landmark study of genome-wide methylation in prokaryotes. The analyses of 230 bacteria and archaea species revealed both more methylation than expected and novel epigenetic mechanisms. “­­­The Epigenomic­­­ Landscape of Prokaryotes” from lead author Matthew Blow, senior author Richard Roberts, and collaborators was recently published in PLoS Genetics. The team used SMRT Sequencing to detect 6-methyladenosine (m6A), 4-methylcytosine (m4C), and 5-methylcytosine (5mC) across the 230 genomes. “Bisulfite sequencing has enabled genome-wide surveys of 5mC methylation, but a historic absence of tools for…

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Monday, February 29, 2016

On Rare Disease Day, Celebrating the Contributions of Genomics

Today we are celebrating Rare Disease Day with like-minded folks all over the world. The tribute kicked off in 2008 and has gathered so much momentum that people in more than 80 countries are expected to participate in 2016. Each disease is rare — affecting fewer than 1 in 1,500 people — but because there are so many of these diseases, together they affect millions of people globally. Here at PacBio, many of our team members have their own stories about dealing with rare disease, and we imagine the same is true of our blog readers. We’re so proud that…

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Thursday, February 25, 2016

New Views of Microbial Communities Call for Updates to Infectious Disease Tenets

Robert Koch In a perspective recently published in Science magazine, scientists Allyson Byrd and Julie Segre from the National Human Genome Research Institute used recent advances in microbial analysis to look at Koch’s postulates through a new lens. Published by Robert Koch in 1890, these principles have become widely accepted in microbiology as the definitive means to prove that a specific pathogen is the cause of an infectious disease. As summarized by Byrd and Segre, the postulates dictate that: “First, the microorganism occurs in every case of the disease; second, it is not found in healthy organisms; and third, after…

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