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Thursday, November 21, 2019

Users Report on SMRT Sequencing: Sequel II System, HiFi Reads, Iso-Seq Analysis, Microbiomes, and More

We’d like to extend a sincere thanks to everyone who attended our two-day North America User Group Meeting, held this year at our Certified Service Provider, the University of Delaware Sequencing and Genotyping Center (@UD_DNAcore). With representation from 80+ organizations and over 160 attendees, the event was a great environment for sharing best practices and networking with the SMRT Sequencing community. Also, a big thanks to our host, Bruce Kingham (@bkingham) and team, as well as our partners: Agilent, Biosoft Integrators, Circulomics, Covaris, Diagenode, Perkin Elmer, Sage Science and Shoreline Biome. If you weren’t able to attend the meeting, we’ve…

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Wednesday, November 20, 2019

SMRT Sequencing to Help Reveal Secrets of the Soil in Understudied South-East Asian Rainforests

The tropical rainforests of Danum Valley, Borneo, is full of dipterocarp trees, which have a particular symbiotic relationship with fungi that is rare in rainforests elsewhere in the world. Photo by Joe Taylor The most important creatures in a tropical rainforest aren’t necessarily the ones you can see. They work their magic underground, recycling organic matter and processing and transporting vital nutrients for their leafy neighbors above ground.  Microbiologist Joe Taylor wants to learn all about what they are and what they do. And now a grant from PacBio and Maryland Genomics will enable him to reveal some of the…

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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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