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Thursday, October 31, 2019

ASHG 2019: CoLab Session Highlights Structural Variation and Transcriptome Sequencing

At ASHG 2019, PacBio scientists Aaron Wenger and Liz Tseng offered a CoLab presentation. At the annual meeting of the American Society of Human Genetics in Houston, PacBio scientists presented how our Sequel II System performs for structural variant (SV) detection and for whole transcriptome sequencing. The educational workshop focused on experiments that can be done using a single SMRT Cell 8M on the Sequel II System. The event kicked off with Aaron Wenger walking through SV analysis, which he said has mirrored the development path of single nucleotide variants, from proof-of-concept to individual rare disease studies and now to…

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Friday, October 18, 2019

Adaptive Selection of CNVs: UW Team Applies SMRT Sequencing to the Melanesian Genome

PingHsun Hsieh presents his findings at ASHG. In a new Science publication, researchers from the University of Washington and other institutions report detailed analyses revealing the adaptive importance of copy number variants (CNVs) acquired from Denisovan and Neanderthal ancestors, the closest relatives of modern humans, in the modern-day Melanesian population. The team used PacBio long-read sequencing to study these complex stretches of DNA and the Iso-Seq method to generate full-length transcript data. “Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes” comes from lead author PingHsun Hsieh (@phhBenson), senior author Evan Eichler, and collaborators.…

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Monday, October 14, 2019

In New Tibetan Genome Assembly, Variants for Living at Altitude and the Imprint of Archaic DNA

The high-altitude Tibetan Plateau. Photo by McKay Savage via Wikimedia Commons A recent bioRxiv preprint reports efforts to sequence the genome of a Tibetan individual and detect the genetic underpinning of adaptive traits associated with tolerating high altitude. The authors used SMRT Sequencing to achieve extremely high contiguity and accuracy, and incorporated scaffolding and other complementary technologies to build a robust assembly. The results are reported in the preprint, “De novo assembly of a Tibetan genome and identification of novel structural variants associated with high altitude adaptation.” Lead author Ouzhuluobu, senior author Bing Su, and collaborators discuss their evaluation of the…

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Thursday, October 10, 2019

Review: Long-Read Sequencing Helps Uncover Genetic Basis for Rare Disease

A new review article nicely sums up the utility of long-read sequencing for solving rare diseases that cannot be explained by other methods. The paper, published in the Journal of Human Genetics, comes from authors Satomi Mitsuhashi and Naomichi Matsumoto at Yokohama City University in Japan. The scientists note that long-read sequencing serves as a good complementary approach for cases that are not solved with short-read sequencing alone. “The approximate current diagnostic rate is <50% using [short-read whole exome and genome sequencing], and there remain many rare genetic diseases with unknown cause,” Mitsuhashi and Matsumoto write. “There may be many…

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Monday, October 7, 2019

Keeping a Close Eye on MRSA: Lessons Learned from PacBio Sequencing Surveillance 

Harm van Bakel When MRSA hits your hospital, what do you do?  If you’re located in Europe or other places where infection rates are still relatively low, you can take a seek-and-destroy approach, isolating an affected patient and working out in concentric circles to identify contacts and potential transmissions.  If you’re in New York City, however, the strategy is not so simple. Hospital-associated infections with methicillin-resistant Staphylococcus aureus are endemic in the Big Apple, and this has required a fresh approach to treat and prevent the costly bacterial menace.  At Mount Sinai Hospital, the strategy now involves SMRT Sequencing. Established…

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Friday, October 4, 2019

In Memoriam: Jo Messing, Developer of Shotgun Sequencing

The DNA sequencing community lost one of its founding fathers last month with the death of Jo Messing, director of the Waksman Institute at Rutgers University. Dr. Messing, who died at the age of 73, developed shotgun sequencing and the M13 sequencing vector used for cloning in the 1980s. Because he declined to patent this work, it was freely available and quickly became the foundation for a burgeoning molecular genetics field. Dr. Messing’s scientific acumen and commitment to innovation in DNA sequencing remained a guiding force for the community throughout his life. In a PNAS paper published just a few…

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Wednesday, October 2, 2019

When Complete Isn’t Complete: C. Elegans Genome Gets a Makeover

Cover artwork by Daisy S. Lim It was the first multicellular eukaryotic genome sequenced to apparent completion, but it turns out the Caenorhabditis elegans reference that’s been used as a resource for the past 20 years does not exactly correspond with any N2 strain that exists today.  Assembled using sequence data from N2 and CB1392 populations of uncertain lineage grown in at least two different laboratories during the 1980s and 1990s, accuracy of the C. elegans reference genome is limited both by genetic variants and by the limitations of the technology of the time (clone-based Sanger technology). It is believed…

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