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Monday, February 8, 2016

Discover the Art of SMRT Sequencing:
AGBT Kicks Off This Week

We’re packing our bags for Orlando and the 17th annual Advances in Genome Biology and Technology (AGBT) conference! While we’ll miss the usual Marco Island setting, this year’s talks and posters look as appealing as ever. And as a meeting sponsor, we’ll be right in the thick of it — with a workshop, party, and coffee-lounge-style hospitality suite for AGBT attendees. It’s a thrill to see that more than 40 talks and posters will showcase SMRT Sequencing data, many for human biomedical research applications. Customer presentations include a talk from the National Center for Biotechnology Information on evolving approaches to…

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Wednesday, February 3, 2016

Genome Galaxy Initiative:
Tick Hunter Cory Gall Seeks to Trace the Cause of Acute Febrile Illness

We recently introduced our Genome Galaxy Initiative  in partnership with Experiment, through which we’re helping scientists fund genomic research for the benefit of science and society. One of the first explorers of this initiative is Cory Gall, a graduate student at Washington State University who wants to curb the onset of a disease that may be linked to ticks in Africa. Gall brings our attention to the rising incidence of acute febrile illness occurring in the Mnisi community in South Africa, where close proximity of community animals (including dogs and cattle) and wild animals in a nearby national park may…

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Tuesday, February 2, 2016

Scientists Investigate Minor Influenza Strains in Pandemic, Revealing New Clues in Flu Transmission

On the heels of her remarkable paper tracing influenza evolution in a single host last spring, New York University’s Elodie Ghedin has come out with a new publication in Nature Genetics that offers a higher-resolution view of how the flu spreads through a population. From lead author Leo Poon at the University of Hong Kong and senior author Ghedin, “Quantifying influenza virus diversity and transmission in humans” reports the results of an international collaboration to track the Hong Kong flu pandemic of 2009. The authors began with the premise that much about the genetically diverse influenza A virus is unknown,…

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Wednesday, January 27, 2016

A Genome Galaxy Not So Far Away

Blog readers know that we are committed to supporting open-access research, from working with the informatics developer community to develop improved tools to releasing SMRT Sequencing data so scientists can mine it themselves. We’re proud to launch a new program that takes this commitment to the next level: the Genome Galaxy Initiative. This initiative stems from twin trends in the scientific community: rapidly increasing demand for SMRT Sequencing, even for very small projects, and increasing awareness that alternative funding sources are important to keep pushing genomics forward. We’ve partnered with scientific crowdfunding platform Experiment to connect researchers directly with the…

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Thursday, January 21, 2016

From Genetic Diagnosis to a Career in Genomics Research: An Interview with Jim Lupski

For Jim Lupski, his long-standing interest in the field of genomics is both personal and professional. His personal interest dates from his teenage years, when he was diagnosed with a rare genetic disease called Charcot-Marie-Tooth (CMT) neuropathy. As a clinician and scientist, he made it his mission to find the genetic basis of CMT, and in 1991 published his discovery of the CMT1A duplication, pioneering the field of structural variation and particularly copy number variation. Today he is a practicing pediatrician and a professor of molecular and human genetics at Baylor College of Medicine, where he is the Principal Investigator…

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Tuesday, January 19, 2016

Case Study: Comprehensive View of Maize Genome Offers Regulatory Insight

When Doreen Ware and her team’s latest genome project is complete, the plant science community will have a critical new tool that once seemed virtually impossible: a robust reference assembly for the maize genome. This resource will support breeding of hardier, higher-yielding lines of maize, the number one crop plant in both the U.S. and China. Ware, a computational biologist with the USDA at Cold Spring Harbor Laboratory, says climate change and protecting the environment are major challenges facing agriculture. “We know that we must increase yield in order to meet the expected 9 billion people in less than 25…

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Wednesday, January 6, 2016

Scientists Develop More Accurate Variant-Calling Procedure for Important Drug Metabolism Enzyme Using SMRT Sequencing

In an article entitled “Long-read single-molecule real-time (SMRT) full gene sequencing of cytochrome P450-2D6 (CYP2D6)” in Human Mutation, authors Wangiong Qiao, Yao Yang, Stuart Scott and other colleagues at the Icahn School of Medicine at Mount Sinai demonstrate a new way of analyzing the CYP2D6 gene using PacBio long reads. This gene has been shown to have a central role in drug metabolism and is believed to be directly involved in the metabolism of ~25% of all commonly used drugs. Given its importance, CYP2D6 genotype testing is now being widely used to predict how efficiently patients will metabolize drugs such…

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Tuesday, January 5, 2016

Exploring Large Genomes at the Largest Ag Genomics Meeting in the World: PAG 2016

We’re looking forward to the International Plant and Animal Genome conference, taking place January 9-13 in San Diego. PAG features leading plant and animal scientists from around the world, and we’re continually impressed by their new discoveries and creative approaches to understanding large and complex genomes. This year PAG attendees will have a number of opportunities to learn more about how SMRT Sequencing reveals new information about even well-characterized plant and animal genomes. We’ll be exhibiting in booth #421 — and showing off our new Sequel System — so please stop by and tell us about your work. We’ll also…

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Wednesday, December 2, 2015

PMWC 2016: Advancing Genomics for Improved Patient Care

We’re already looking forward to next month’s Personalized Medicine World Conference. Long before “precision medicine” was an industry catchphrase, PMWC was bringing together stakeholders from genomics companies and academic research, regulatory agencies, clinical groups, pharma/biotech, and more. Launched in 2009, the meeting has prompted important discussions as well as insight about how to move the field forward in a thoughtful way. From January 24th to the 27th, some 1,200 PMWC attendees will descend on the Computer History Museum in Mountain View, Calif. The event will kick off with a reception honoring the four awardees of this conference: Merck’s Roger Perlmutter…

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Monday, November 16, 2015

Scientists Use the Iso-Seq Method to Study Genes Linked to Prostate Cancer

A team of scientists from Australia, Canada, and the US published fascinating new work that may help explain gene expression patterns seen in prostate cancer. In the course of the project, they used SMRT Sequencing and found a novel fusion transcript linking two genes with high sequence identity. “Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer” was published in Molecular and Cellular Endocrinology by lead author Gregor Tevz, senior author Colleen Nelson, and a number of collaborators. In it, the scientists attempted to untangle expression signals from two relaxin genes, which…

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Wednesday, November 11, 2015

Scientists Publish High-Quality, Near-Complete Genome of Resurrection Grass Oropetium

We’re excited about a new Nature paper from the winners of our 2014 “Most Interesting Genome in the World” SMRT Grant program. “Single-molecule sequencing of the desiccation tolerant grass Oropetium thomaeum” comes from lead authors Robert VanBuren and Doug Bryant along with senior author Todd Mockler at the Donald Danforth Plant Science Center, as well as a number of collaborators at other institutions. In it, the authors report a virtually complete genome of Oropetium thomaeum, a grass with an estimated genome size of 245 Mb and the handy ability to regrow even after extreme drought once water becomes available. The…

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Monday, November 9, 2015

Steven Marsh from Anthony Nolan Discusses the Past and Future of Donor Matching

Mendelspod host Theral Timpson recently interviewed Professor Steven Marsh, Director of Bioinformatics at the Anthony Nolan Research Institute, a UK-based organization dedicated to improving the outcomes of bone marrow transplantation and host to the world’s first bone marrow registry. Prof. Marsh and his team have dramatically improved the resolution of HLA typing — one of the methods used for matching compatible donors with transplant recipients — using long, accurate reads from PacBio sequencing. Their fascinating conversation covers the past, present, and future of HLA typing — highlights are below. Short History of HLA Typing — There’s a Lot More Diversity…

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Monday, November 2, 2015

Welcome to Silicon Valley, Festival of Genomics!

This week the Festival of Genomics comes to the West Coast, and we’re excited to be a founding sponsor of the Front Line Genomics organization. Not only is it our first chance to show off the new Sequel System in our home state, but there will also be a number of great talks reporting SMRT Sequencing results.  Here are the some of the presentations to consider if you’re attending the event: Wednesday, November 4 11:30 a.m. Ali Bashir, Icahn School of Medicine at Mount Sinai Uncovering Neglected Regions of the Human Genome: Assembly and Architecture via Single Molecule Technologies 12:00…

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Thursday, October 22, 2015

Scientists Sequence Klebsiella Strain Resistant to All Known Antibiotics

A new publication reports the discovery and analysis of a nightmare bacterium that’s genetically resistant to all commercially available classes of antibiotics. The paper, “Stepwise evolution of pandrug-resistance in Klebsiella pneumonia,” came out this month in Scientific Reports from Nature. Lead authors Hosam Zowawi and Brian Forde, along with senior author David Paterson and several collaborators, studied an isolate recovered from the urine of an 87-year-old patient who was hospitalized in the United Arab Emirates last year. They used SMRT Sequencing to characterize the strain and its genetic mechanisms for drug resistance. That strain, MS6671, “was found to be non-susceptible to…

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Wednesday, October 21, 2015

Guest Blog: Rich Roberts Urges Scientists to ‘Think Methylation’ in Microbial Sequencing

Richard Roberts, Nobel Laureate and Chief Scientific Officer of New England Biolabs, offers his thoughts on the utility of methylation data for understanding prokaryotes. In his words: “Please run SMRT Analysis to detect methylation in your prokaryotic PacBio data. Most bacteria and archaea encode DNA methylases, many of which are known components of restriction-modification systems. Usually, these are quite specific in terms of the sequences they recognize; the restriction component becomes a key defense mechanism preventing phages, plasmids, and other DNA elements from infecting the cell. Until recently, it was quite difficult to determine the recognition sequences of these methylases.…

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