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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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Tuesday, October 20, 2015

Scientists Reveal Recent Autosome-to-Y Duplication Event in Drosophila

Following on the heels of characterizing 18 Mst77Y genes that were tandemly duplicated within a 96 kb region (Krsticevic FJ, et al., 2015), scientists from institutes in Brazil, Austria, and the United States recently published a study in which they also used the Drosophila melanogaster data release from PacBio to characterize a region of the Y chromosome that had never before been accessible. In a paper published in PNAS, entitled “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” lead author Antonio Bernardo Carvalho, senior author Andrew Clark, and collaborators detail their find of a gene duplicated from…

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Thursday, October 15, 2015

ASHG 2015: Highlights from the Platinum Genome Session and More

During the final days of the ASHG meeting last week in Baltimore, a number of scientists offered great presentations based on data generated with SMRT Sequencing, including an entire session on building platinum genomes. We’ve rounded up the highlights here: Karyn Meltz Steinberg from Washington University’s McDonnell Genome Institute spoke about building a platinum human assembly from single-haplotype genomes. Her team defines “platinum” as covering at least 98% of the sequence with every contig associated with a chromosome. They use long-read PacBio sequencing for de novo sequencing and assembly, followed by scaffolding with BioNano Genomics or Dovetail Genomics technology. When…

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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, October 9, 2015

ASHG Workshop Recap & Recording: Addressing Hidden Heritability with SMRT Sequencing

The PacBio workshop at ASHG 2015 featured talks from two leaders in human genomics, Rick Wilson of Washington University and Richard Gibbs from Baylor University. Mike Hunkapiller, CEO of Pacific Biosciences, opened the workshop with a historical perspective of human genome sequencing, starting with the Human Genome Project.  While advances have been made in technology, throughput and cost reductions, the quality of genomes hasn’t kept pace with decreases in cost, he noted. This is why Hunkapiller was particularly proud to share the news of the company’s launch of the Sequel System – which offers SMRT Sequencing and long reads at…

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Monday, October 5, 2015

Beyond the $1,000 Genome: An Interview with Mark Gerstein

Next-generation sequencing has many people excited about the prospect of the $1,000 genome, however recent discoveries show that short-read sequencing technologies miss important genomic elements, driving scientists to look for an alternative approach. Mark Gerstein, co-director of the computational biology and bioinformatics program at Yale, argues that the true $1,000 human genome has yet to arrive. In a recent conversation with Mendelspod host Theral Timpson, he discussed some of the important, deep technical questions that must first be addressed. This is the second in a series of podcast interviews focused on long-read sequencing, and we have included some highlights from…

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Friday, October 2, 2015

Toward Platinum Genomes: PacBio Releases a New, Higher-Quality CHM1 Assembly to NCBI

As part of our effort to support the National Institutes of Health and the Genome Reference Consortium (GRC) in creating platinum genomes for the research community and improving the reference genome, in 2014 we generated 54X SMRT® Sequencing coverage of the CHM1 cell line, derived from a human haploid hydatidiform mole, using our P5-C3 chemistry, and made it publicly available through the SRA database at NCBI. The CHM1 dataset was quickly taken up by researchers eager to use long, unbiased reads to identify regions of the genome prone to structural variation and to fill in sequence gaps in the GRC-maintained…

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Thursday, October 1, 2015

ASHG 2015: Workshop, Presentations, and First Chance to See the Sequel System

We’re looking forward to the year’s biggest scientific meeting focused on human genetics next week — the American Society of Human Genetics (ASHG) 2015 annual meeting, taking place in Baltimore, Maryland. SMRT® Sequencing will be featured in 36 scientific presentations, as well as our lunchtime workshop. Even if you’re not attending you can attend our workshop virtually to learn more about our newest SMRT Sequencer – the Sequel™ System — and about the latest uses of SMRT Sequencing for human biomedical applications. Our workshop, “Addressing Hidden Heritability through Long-Read Single Molecule, Real-Time (SMRT) Sequencing” will be held on Wednesday, October 7, from…

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