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Friday, September 25, 2015

Marc Salit at NIST: Defining Standards for the Human Genome

In the first podcast of a new series on the applications of long-read sequencing, Mendelspod host Theral Timpson interviewed Marc Salit, leader of the Genome Scale Measurements Group at the National Institute of Standards and Technology. Their conversation focused on how and why NIST is involved in establishing baseline measurements for the human genome.Salit, along with Justin Zook and their team at NIST, are managing the Genome in a Bottle (GIAB) Consortium to develop reference materials, data, and methods needed to assess whole human genome sequencing. Their goal is to establish a physical reference genome as a standard against which…

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Thursday, September 24, 2015

At Genome in a Bottle Workshop, Progress on New Reference Materials

Genome in a Bottle consortium The National Institute of Standards and Technology held its latest Genome in a Bottle workshop last month in Gaithersburg, Md., and we were honored to attend. NIST has performed pivotal work to establish reference materials for the genomics community, starting with its RNA spike-in standards (ERCC spike-in controls) and continuing now with the GIAB consortium. These standards are essential for quality control and we’re pleased to be working with NIST to help ensure the highest accuracy in human genome sequencing.Last year, GIAB released its first reference standard, based on the well-studied NA12878 human genome (NIST RM…

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Thursday, September 17, 2015

SMRT Data Analysis: Updates from our Developers Conference

Last month we hosted a SMRT® Informatics Developers Conference, bringing together 150 developers with a passion for improving tools and resources. Our team came back brimming with enthusiasm for tools that will be released in the coming months, and humbled by the commitment we saw from the bioinformatics community to help scientists make SMRT Sequencing data increasingly useful. Thanks to the National Institute of Standards and Technology for hosting our meeting on their campus right before the Genome in a Bottle workshop.The big news we shared with attendees is that the PacBio® System will now output industry-standard BAM files instead…

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Thursday, June 25, 2015

SMRT Data Delivers for Next-Generation HLA Typing at Anthony Nolan Research Institute

A new publication in PLoS One from authors at Anthony Nolan’s Research Institute describes a feasibility study for HLA typing using SMRT® Sequencing. The research institute, where the world’s first bone marrow registry started in 1973, is part of the UK-based charity dedicated to improving the outcomes of bone marrow transplantation. Scientists at Anthony Nolan are leaders in HLA typing, which is an important step in matching a bone marrow or stem cell donor to a patient in need. The Anthony Nolan team adopted the PacBio® system last year, and this publication reflects its efforts to test and establish the…

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Wednesday, October 29, 2014

‘Revolutionizing HLA Typing’: Uppsala’s Ulf Gyllensten on How Long Reads Give Access to New Areas of the Human Genome

In a recent interview with Theral Timpson — part of Mendelspod’s series on long-read sequencing — Ulf Gyllensten, a scientist at Uppsala University, spoke about using PacBio® technology for HLA typing, human genome studies, transcriptomics, and more. Based in the medical genetics and genomics department, Gyllensten focuses on two areas: using systems biology to study biological variation in human physiology and studying the epidemiology of human papilloma virus and its genetic link to cervical cancer. He also works with the National Genomics Infrastructure, a national core facility in Sweden for genotyping and DNA sequencing, where he has access to all…

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Monday, October 6, 2014

‘The Quality of PacBio Data Is Beyond Compare’: Eric Schadt on Applications of SMRT Sequencing to Human Genetics

As part of its continuing series on long-read sequencing, last week Mendelspod aired an engaging interview with Eric Schadt, Professor & Chair of Genetics and Genomic Sciences, and Director of the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai. Having now spent three years in his role at the groundbreaking institute, he reports that they are making great progress in the quest to build better data-driven health profiles around individuals that may better guide healthcare choices. On short-read versus long-read sequencing Short-read sequencing technologies still maintain the advantage in terms of throughput, says Schadt, but there are a…

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Thursday, October 2, 2014

‘We’re Going to Find the Keys’: Dan Geraghty Discusses an Approach to Understanding Causal Genetic Variation

Dan Geraghty, a researcher at Fred Hutchinson Cancer Research Center and CEO of Scisco Genetics, has spent much of his career focused on the genetics of immune response. Recently he talked to Mendelspod host Theral Timpson as part of a continuing series of podcasts on the rise of long-read sequencing. Geraghty explained that while there have been decades’ worth of studies associating the genetics of the major histocompatibility complex (MHC), and the highly polymorphic HLA class 1 and 2 genes, we still haven’t found the key mutations for a variety of different autoimmune diseases such as type 1 diabetes, rheumatoid…

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Monday, September 22, 2014

Maryland Scientists Produce High-Quality, Cost-Effective Genome Assembly of Loa loa Roundworm Using SMRT Sequencing

A paper just released in BMC Genomics details what authors call “the most complete filarial nematode assembly published thus far at a fraction of the cost of previous efforts.” The project was performed using the PacBio® RS II DNA Sequencing System by scientists at the University of Maryland School of Medicine’s Institute for Genome Sciences and the Laboratory of Parasitic Diseases at the National Institute of Allergy and Infectious Diseases. In this genome sequencing effort, scientists generated a de novo assembly of Loa loa, a roundworm that infects humans. L. loa, transmitted to humans by deer flies, causes loiasis. The…

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Tuesday, July 22, 2014

At ISMB, Gene Myers’ Keynote Offers History, Future of Genome Assembly

At ISMB 2014 in Boston earlier this month, Gene Myers of the Max-Planck Institute for Molecular Cell Biology and Genetics, presented a keynote address entitled “DNA Assembly: Past, Present, and Future.”  Myers received the prestigious Senior Scientist Accomplishment Award from the International Society for Computational Biology (ISCB) at the event. The ISCB Senior Scientist Accomplishment Award honors respected leaders in computational biology and bioinformatics for their significant contributions to these fields through research, education, and service. Myers is being honored as the 2014 winner for his outstanding contributions to the bioinformatics community, particularly for his work on sequence comparison algorithms,…

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Tuesday, May 13, 2014

A New Approach for HLA Typing: SMRT Sequencing

Two recent news announcements demonstrate the utility of our Single Molecule, Real-Time (SMRT®) Sequencing technology in the challenging realm of HLA typing.  HLA typing — or analysis of genes in the human leukocyte antigen region of the human genome — is of critical importance for research in tissue transplantation matching, autoimmune disease-association studies, drug hypersensitivity research, and other applications. But analyzing those genes, which are highly polymorphic and contain thousands of alleles that code for proteins important in recognizing foreign antigens, has proven difficult with most technologies. Use of Sanger or short-read sequencing technologies has required other methods for confirmation…

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Tuesday, January 21, 2014

Genome Research Paper: Resolve Complex Genomic Regions for a ‘Fraction of the Cost’ With SMRT Sequencing

A new Genome Research paper describes the application of Single Molecule, Real-Time (SMRT®) Sequencing to resolve repeat-heavy genomic regions in important reference genomes such as human and chimpanzee. In the process, the authors drew some important conclusions about cost, pooling, and coverage requirements for this type of work. “Reconstructing complex regions of genomes using long-read sequencing technology” comes from lead author John Huddleston and senior author Evan Eichler at the University of Washington, along with collaborators at Washington University, the University of Bari, Bilkent University, and Pacific Biosciences. In the paper, Eichler and his collaborators note the steep cost of…

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Monday, September 16, 2013

Genome Biology Paper Highlights Affordability and Scale of PacBio-Based Finished Microbial Genomes

A new paper released in Genome Biology on September 13 from lead author Sergey Koren at the National Biodefense Analysis and Countermeasures Center offers a thorough overview of SMRT® Sequencing for microbes, from per-genome cost to potential for assembling complete genomes. In “Reducing assembly complexity of microbial genomes with single-molecule sequencing,” Koren and co-authors consider microbial genome assembly, which evolved over time from the Sanger days of manually finished genomes to short-read sequencers that offered lots of sequence data but virtually no finished genomes. Today, that evolution has continued with SMRT® Sequencing, which allows for rapid and complete genome assembly.…

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Monday, August 19, 2013

Scientists Assess Error Modes in Sequencing Platforms and Find SMRT Sequencing ‘Least Biased’

A paper from scientists at the Broad Institute reports a rigorous study of bias across all major sequencing platforms. In “Characterizing and measuring bias in sequence data,” published in Genome Biology, lead author Michael Ross and his colleagues report that SMRT® Sequencing on the PacBio® sequencer is the “least biased” in coverage of all the technologies studied. The authors assessed sequences for coverage bias, or uniformity of read distribution, and error bias, or incorrect call at a given position. For coverage bias, they report that PacBio performed best in extreme GC content (both GC-rich and GC-poor) and suggest this may…

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Tuesday, July 30, 2013

Single-Molecule Sequencing Technology Q&A with Nobel Laureate Rich Roberts

BioMed Central has published an interesting Q&A session on its Biome blog with Nobel Laureate Richard Roberts about why he believes in SMRT Sequencing and thinks non-users should take another look at it, too. He also discusses the critical need for funding to support the functional annotation of the genomes being sequenced, including for new bioinformatics tools. “We should be greatly increasing our efforts to gain functional insights into the millions of genes we are discovering by sequencing and for which we either have no idea of what they do, or many of our predictions are simply wrong,” he says.…

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Wednesday, July 3, 2013

Genome Biology Commentary Discusses the Advantages of SMRT Sequencing

A new commentary in Genome Biology from highly respected scientific authors, including a Nobel Prize winner, highlights the benefits of Single Molecule, Real-Time (SMRT®) Sequencing.  The commentary, entitled “The advantages of SMRT sequencing,” comes from Richard Roberts at New England BioLabs, Mauricio Carneiro at the Broad Institute, and Michael Schatz at Cold Spring Harbor Laboratory. The authors begin with the premise that the PacBio® RS is sometimes overlooked as a next-generation sequencing option, even though it serves as “ideal approach to the complete sequencing of small genomes.” The commentary focuses on three advantages of SMRT Sequencing: extraordinarily long reads, methylation…

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