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Thursday, November 14, 2019

Webinar Summary: Need accurate isoform-level characterization? Iso-Seq is the answer

Traditional RNA-Seq is done by fragmenting cDNA, and then sequencing the fragmented reads with paired-end sequencing. The problem comes when trying to identify the full-length isoform during assembly. This is computationally challenging, and sometimes intractable.  Iso-Seq is a method of full-length transcript sequencing that eliminates the need for assembly The solution? Long-read isoform sequencing, according to PacBio Principal Scientist Elizabeth Tseng and PacBio user Gloria Sheynkman, a research fellow at Dana-Farber Cancer Institute. The two recently participated in a webinar, sharing their experiences using PacBio’s Iso-Seq method. Tseng started by explaining the method and some of its applications.  “In contrast…

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Tuesday, November 12, 2019

At ASHG Workshop, Customers Describe Long-Read Sequencing of Human Genomes for Disease Gene Discovery and Population Studies

We were delighted to host an educational workshop at last month’s annual meeting of the American Society of Human Genetics (ASHG), where we had the opportunity to feature talks from two customers as well as an overview of SMRT Sequencing. If you couldn’t attend, check out the videos or read the highlights below. Emily Hatas, our director of business development, kicked things off with a look at how SMRT Sequencing has evolved over the years. Compared to the first instrument we offered, the Sequel II System represents a 100-fold improvement in read length and a 10,000-fold improvement in throughput. As…

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Monday, November 11, 2019

Mapping the NLRome: Research Teams Turn to SMRT Sequencing to Trace Plant Immunity

There’s the genome, the transcriptome, the microbiome… and now the NLRome?  Breeders and pathologists have long been interested in uncovering the secrets of plant immunity, and much of their attention has been focused on receptors that can activate immune signalling: cell-surface proteins that recognize microbe-associated molecular patterns (MAMPs), and intracellular proteins that detect pathogen effectors, including nucleotide-binding leucine-rich repeat receptors (NLRs).  Hundreds of NLR genes can be found in the genomes of flowering plants. They are believed to form inflammasome-like structures, or resistosomes, that control cell death following pathogen recognition, and are being investigated as candidates for engineering new pathogen…

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Friday, November 8, 2019

Double Mutations in Oncogene May Improve Patient Response to Targeted Therapy

The PIK3CA oncogene has been the target of intense research scrutiny for decades. Remarkably, though, a new paper in Science today reports completely novel findings about compound mutations that are associated with patients who respond extremely well to targeted therapies. While more studies are needed, this work has important implications for delivering treatment to patients with breast cancer and other common cancers. Neil Vasan “Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors” comes from lead author Neil Vasan, senior authors Maurizio Scaltriti and José Baselga, and collaborators at Memorial Sloan Kettering Cancer Center, the Icahn School…

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Tuesday, November 5, 2019

Finding the Females: New Reference Genome Leads to Better Sex Determination Technique in Tuna

A team of Japanese researchers has used a new Pacific bluefin tuna reference genome to identify male-specific DNA markers in the fish The cultivation and conservation of one of the most important commercial fishes in the world may come down to sex determination — how can you successfully breed a species without knowing the sex of your stock? A Japanese research team has come up with a solution, thanks to a new Pacific bluefin tuna reference genome and the male-specific DNA markers they were able to identify as a result. In a study published recently in the Nature journal Scientific…

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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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Thursday, September 26, 2019

New NHGRI Human Pangenome Reference Initiative Will Use Highly Accurate PacBio Sequencing

University of Washington genome science technicians Melanie Sorensen, Katherine Munson, and Alexandra Lewis at the PacBio Sequencing Services. (Photo by Amy B. Wifert.) The National Human Genome Research Institute has awarded nearly $30 million for new sequencing and bioinformatics initiatives that aim to better represent the full range of human genetic diversity. An entirely new human reference genome — the “pangenome” — will be built from high-quality sequencing of 350 individuals from across the human population. Here at PacBio, we’re excited that highly accurate long-read WGS data from our Sequel II Systems will be an important component of this new…

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Thursday, September 5, 2019

SOLVE-RD Team Adopts PacBio Sequel II System to Solve Rare Diseases

Great news from the rare disease community: the European research program SOLVE-RD has chosen SMRT Sequencing technology to help reveal the genetic mechanisms responsible for these tough-to-diagnose genetic diseases. As part of this work, scientists will sequence more than 500 whole human genomes with the PacBio Sequel II System to pinpoint disease-causing variants. The SOLVE-RD research program, a consortium of more than 20 institutions funded with a five-year, €15 million award from the European Union’s Horizon 2020 initiative, aims to improve the diagnosis and treatment of rare diseases by applying novel tools to cases that were not solved with short-read…

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Wednesday, September 4, 2019

Webinar: No-Amp Targeted Sequencing Yields Base-Level Resolution of Hard-to-Amplify Regions

Until recently, enriching for certain regions of the genome has been virtually impossible. Repeat expansions, extreme GC regions, and other genomic elements are very difficult to target using traditional enrichment methods. That’s why our new “No-Amp” targeted sequencing application  — a streamlined, amplification-free approach based on the CRISPR/Cas9 system — is a valuable addition to the SMRT Sequencing toolbox. No-Amp targeted sequencing combines the CRISPR/Cas9 enrichment method with SMRT Sequencing. Pacific Biosciences does not sell a kit for carrying out the overall No-Amp Targeted Sequencing method. Use of these methods may require rights to third-party owned intellectual property. The method…

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