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Tuesday, August 2, 2016

SMRT Sequencing Accurately Detects Gene Copy Numbers in Complex Maize Genome

Scientists from Rutgers University and the University of California, Davis, used SMRT Sequencing to study structural variation in maize. They found that this approach delivered more complete information at lower cost than standard methods and generated new findings that could be important for crop breeding. From lead author Jiaqiang Dong, senior author Jo Messing, and collaborators, “Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads” was published in PNAS recently. They chose to evaluate SMRT Sequencing for copy number detection as an alternative to short-read sequencing, which doesn’t span long repeats, and BAC cloning, which…

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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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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, October 13, 2015

ASHG 2015: Highlights from Icahn Institute, UW, Stanford & CSHL Presentations

During the Wednesday afternoon sessions of last week's ASHG conference, several speakers provided helpful insights about their use of SMRT Sequencing for a range of applications. Highlights included the following: Yao Yang, a researcher at the Icahn School of Medicine at Mount Sinai, discussed the development of an assay to genotype the CYP2D6 gene to inform drug dosing in patients. CYP2D6 metabolizes 20-25% of all medications, including antidepressants, anti-psychotics, and opiates. There are more than 100 known variants, which include gene deletions and duplications. Variants can have profound impacts on how patients metabolize drugs, with some individuals being ultra-rapid metabolizers…

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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, July 9, 2015

The Festival of Genomics Review: A Celebration of Long Reads

At the inaugural Festival of Genomics event in Boston, more than 1,500 people turned out to see what was billed as a conference unlike any other. The meeting was indeed unique, featuring a play (starring well-known scientists), a giant chess board, and a Genome Dome, in addition to the more familiar lineup of excellent speakers and workshops. To help kick off the festival, genomic luminaries Craig Venter and James Lupski presented plenary talks on day 1 and set the stage for some exciting science to follow. Lupski’s talk was particularly impactful, as he described how his team at Baylor recently…

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Thursday, April 30, 2015

In Study, Continuous Long Reads Outperform Synthetic Long Reads for Resolving Tandem Repeats

Scientists from Argentina and Brazil published the results of a study comparing long-read approaches to characterize the genome structure of a highly complex region of the Y chromosome in Drosophila melanogaster. They found that Single Molecule, Real-Time (SMRT®) Sequencing outperformed synthetic long reads in accurately representing tandem repeats. The study aimed to resolve the structure of the autosomal gene Mst77F, which had previously been found to have multiple tandem copies; the region, however, was known to be grossly misassembled in the reference. The scientists, from Centro Internacional Franco Argentino de Ciencias de la Información y de Sistemas and Universidade Federal…

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Wednesday, April 15, 2015

In Genome-wide Study, Long Reads Prove Critical for Structural Variant Discovery

In a paper just published in BMC Genomics, a team of scientists led by Baylor’s Human Genome Sequencing Center reports a thorough analysis of structural variation in a personal genome. What makes this study special is the large number of different technologies applied and the sheer volume of data gathered and analyzed for this single genome. The paper also includes the first known analysis of structural variation in a diploid human genome using SMRT® Sequencing, with 10x coverage from PacBio® long reads. Lead authors Adam English and William Salerno and their collaborators at a number of institutions describe the results…

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Monday, November 10, 2014

Nature Paper Offers Novel Sequence, Structural Variant Data for a More Complete Human Genome

A new paper out in Nature extends our view into the human genome and challenges current ideas about genetic variation. “Resolving the complexity of the human genome using single-molecule sequencing” comes from first author Mark Chaisson, senior author Evan Eichler, and their collaborators at the University of Washington, University of Bari Aldo Moro, and University of Pittsburgh. In the paper, the scientists describe an important effort to fill gaps and better characterize structural variation in the human genome by using Single Molecule, Real-Time (SMRT®) Sequencing data. The team sequenced a haploid human genome, using a hydatidiform mole cell line (CHM1),…

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Friday, March 14, 2014

AGBT 2014 Presentation Videos: SMRT Sequencing at CSHL, Uppsala U., and Baylor College of Medicine

There were several excellent talks showcasing SMRT® Sequencing data at the annual Advances in Genome Biology and Technology conference. If you didn’t have the opportunity to see them in person, you can watch the recordings: From Cold Spring Harbor Laboratory, Dick McCombie described the need for de novo sequencing, which preserves structural information that can be missed with resequencing. Organisms presented include yeast, Arabidopsis, and rice. McCombie notes that in many cases, full chromosomes are assembled into single contigs with long-read sequencing. He also presented the longest read seen at AGBT: more than 54 Kb. Watch video: A near perfect…

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Saturday, February 15, 2014

AGBT Day 1 & 2 Highlights: Hello GRCh38 & SMRT Sequencing for Pathogen Screening

AGBT 2014 is off to a roaring start - the opening reception was hastily moved indoors when an impressive thunderstorm joined the party. Wednesday’s kickoff plenary session offered an insightful view of the recently released human genome reference, known as GRCh38, which is available with GenBank accession GCA_000001405.15. Valerie Schneider from the National Center for Biotechnology Information gave a presentation on the latest build, highlighting improvements that range from alternate loci to modeled centromeres to error correction of individual bases. The Genome Reference Consortium resolved more than 1,000 reported issues from build 37 with the release of this new build…

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Tuesday, February 11, 2014

AGBT 2014 Preview: Long reads, long flight, long days!

We are flying cross-country to Marco Island, Florida, to attend the fifteenth annual Advances in Genome Biology and Technology conference and, as we have done for years now, we are proud to be sponsoring the event. This year we look forward to connecting with the many researchers who already work with SMRT® Sequencing data, and to meeting others whose scientific efforts could benefit from our technology’s uniquely long reads and base modification information. Here are some of the presentations we’ll be attending: Evan Eichler, University of Washington, “Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism” …

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Thursday, January 16, 2014

Looking Ahead: The 2014 PacBio Technology Roadmap

By Jonas Korlach, Chief Scientific Officer 2013 was an eventful and exciting year for PacBio. As I described in the 2013 roadmap post a year ago, we have applied numerous improvements to SMRT® Sequencing, resulting in longer read lengths, greater sequencing throughput, new and improved data-analysis methods, and more efficient workflows. We are very pleased that these advances resulted in so many publications, conference presentations, and social media contributions, with the number of peer-reviewed scientific publications from the scientific community now exceeding 100. On behalf of all of us at Pacific Biosciences, I would like to express my heartfelt gratitude…

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Friday, December 27, 2013

Breakpoint Detection in Cancer Structural Variants with PacBio May Yield Patient-Specific Data

A new publication from scientists at the University of California, San Diego, demonstrates the use of Single Molecule, Real-Time (SMRT®) Sequencing to identify structural variation (SV) breakpoints in cancer. “Amplification and thrifty single molecule sequencing of recurrent somatic structural variations” was published in Genome Research and comes from authors Anand Patel, Richard Schwab, Yu-Tsueng Liu, and Vineet Bafna. In the paper, the scientists report development of a new method — Amplification of Breakpoints, or AmBre — to detect important structural variant breakpoints. AmBre relies on a PCR-based approach for amplification of the structural variant, followed by sequencing on the PacBio®…

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Thursday, November 14, 2013

ASHG Workshop Recordings: Resolving Structural Variation in Human Genomes

We hosted a structural varation workshop at the annual meeting of the American Society of Human Genetics, and were pleased to see that the speakers' presentations really resonated with attendees – the event was standing-room-only! Jonas Korlach, PacBio CSO, opened the session by sharing a brief update on SMRT® technology, noting that the new P5-C3 chemistry delivers 50% of bases in 10 kb or longer reads. View presentation recording Evan Eichler, Howard Hughes Medical Investigator from the University of Washington discussed his use of the PacBio® system to study difficult-to-sequence regions of the human and chimp genomes. Eichler has identified a…

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