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Monday, January 27, 2020

When Snakes Strike: SMRT Sequencing Reveals Hidden “Venom-ome”

A team of scientists from SciGenom Research Foundation in India has assembled the genome and transcriptome of the lethal Indian Cobra (Naja naja) using PacBio long-read sequencing Snake milking, horse blood harvesting and brewing — antivenom production is still more medieval art than modern science. But a new high-quality snake genome may finally pull it into the 21st century. As recently reported in Nature Genetics, a team of scientists led by Somasekar Seshagiri, a former staff scientist at Genentech and now president of the nonprofit SciGenom Research Foundation (@SGRF_Science) in India, assembled the genome and transcriptome of the lethal Indian…

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Thursday, January 23, 2020

Project to Rapidly Sequence Maize Pangenome Delivers Publicly Available Resource

Matt Hufford, associate professor at Iowa State University, helped produce a 26-line maize pangenome assembly collection Maize researchers have been rejoicing over a New Year’s gift delivered by a group of 33 scientists: A 26-line “pangenome” reference collection.  The multi-institutional consortium of researchers used the Sequel System and BioNano Genomics optical mapping to create the assemblies and high-confidence annotations. They released the results on January 9, and in several presentations at the Plant and Animal Genome XXVIII Conference, less than two years after the ambitious project was funded by a $2.8 million National Science Foundation grant.  The collection includes comprehensive,…

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Monday, January 13, 2020

Direct Phased Genome Assembly Using Nighthawk on HiFi Reads

By Zev Kronenberg, Senior Engineer of Bioinformatics at PacBio   Since the introduction of HiFi reads the community has embraced these long and highly accurate reads for human genome assembly and paralog resolution [1-5]. At PacBio, the assembly team (Figure 1) is working to build on the accuracy of HiFi data for direct phasing during assembly. Figure 1. The PacBio assembly team. From left to right, James Drake, Zev Kronenberg (@ZevKronenberg), Derek Barnett (@DerekWBarnett), Chris Dunn, and Ivan Sović (@IvanSovic) In diploid organisms, phasing an assembly means separating the maternally and paternally inherited copies of each chromosome, known as haplotypes.…

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Wednesday, January 8, 2020

SMRT Grant Winner: Hunting for Answers in Spinocerebellar Ataxia

Cleo van Diemen, University Medical Center Groningen A hearty congratulations to Cleo van Diemen at the University Medical Center Groningen for winning the 2019 Neuroscience SMRT Grant! Van Diemen’s impressive proposal involves using PacBio long-read sequencing to find new genetic mechanisms associated with spinocerebellar ataxia (SCA). While some 70% of SCA patients can get clear diagnostic and prognostic information because they have one of the ~37 genes known to be associated with this condition, 30% of patients have no such clarity. In this project, van Diemen and her colleagues will use their SMRT Grant award to generate highly accurate long…

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Friday, January 3, 2020

Novel Workflow Produces Fully Phased Human Genome Assemblies Without Trio Sequencing

A new preprint from lead authors David Porubsky and Peter Ebert, senior authors Evan Eichler and Tobias Marschall (@tobiasmarschal), and collaborators reports a method for generating fully phased, de novo human genome assemblies without parental data. The approach combines PacBio HiFi reads (>99% accuracy, 10-20 kb) with the short-read, single-cell Strand-seq technique.  The authors provide a proof-of-principle through assembling the genome of a Puerto Rican female from the 1000 Genomes Project. The work extends a recent publication from many of the same authors in which HiFi reads were used to produce an accurate and contiguous assembly of the human haploid…

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Friday, December 27, 2019

SMRT Sequencing Highlights – Top Publications of 2019

With the release of the award-winning Sequel II System, 2019 was an exciting year for the SMRT Sequencing community. We were inspired by our users’ significant contributions to science across a wide range of disciplines. As the year draws to a close, we have taken this opportunity to reflect on the many achievements made by members of our community, from newly sequenced plant and animal species to human disease breakthroughs.   “It has been another phenomenal year for science. The introduction of the Sequel II System will accelerate discovery even more, and I can’t wait to see what 2020 will…

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Monday, December 23, 2019

Iso-Seq Analysis Sheds Light on Splicing Associated with Schizophrenia

Neurexin genes, which have been associated with certain neuropsychiatric disorders, are known to make heavy use of alternative splicing. In a recent study, scientists used the Iso-Seq method with SMRT Sequencing to better understand splice variants in neurons derived from human induced pluripotent stem cells (hiPSCs). The study, “Neuronal impact of patient-specific aberrant NRXN1α splicing,” was published in Nature Genetics. Lead authors Erin Flaherty (@erinkflaherty) and Shijia Zhu, senior author Kristen Brennand (@kristenbrennand), and collaborators at the Icahn School of Medicine at Mount Sinai and other institutions undertook the project to help shed light on disorders linked to exonic deletions in the…

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Thursday, December 19, 2019

Release of Six New Reference-Quality Genomes Reveals Superpowers of Bats

Photo of a pale spear-nosed bat (Phyllostomus discolor) courtesy of the Rossiter Lab (@rossiterlab) Bat lovers and animal researchers have been waiting for insights into the evolution and remarkable genetic adaptations of our winged mammalian friends, ever since the global Bat1K initiative announced its quest to decode the genomes of all 1,300 species of bats using SMRT Sequencing and other technologies. Now, the first six reference-quality genomes have been released on the Hiller Lab Genome Browser, and described in a pre-print by Sonja Vernes (@Sonja_Vernes), Michael Hiller (@hillermich) and Gene Myers (@TheGeneMyers) of the Max Planck Institute, Emma Teeling (@EmmaTeeling1) of…

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Tuesday, December 17, 2019

SMRT Sequencing Enables Discovery of Epigenetic Driver of C. diff Persistence

How do pernicious pathogens like Clostridioides difficile spread through hospitals and persist so tenaciously in the human gut, leading to about half a million infections and 30,000 deaths each year?  It’s a mystery scientists have been anxious to solve, and they’ve invested countless hours of research into the bacteria’s physiology, genetics and genomic evolution.   A team from Mount Sinai School of Medicine in New York City has uncovered an important new clue by studying an overlooked aspect of C. difficile’s biology: Epigenetics.  Using PacBio SMRT Sequencing and comparative epigenomics, Pedro H. Oliveira (@pholive81), Gang Fang (@iamfanggang), and colleagues mapped and…

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Wednesday, December 11, 2019

Long-Read Sequencing Could Improve the Sensitivity and Precision of 16S Studies Says Jackson Lab Study

It’s time to revisit the way scientists are using 16S rRNA gene sequencing to study microorganisms, according to a team of Jackson Laboratory researchers.  Popular targets for taxonomy and phylogeny studies because of their highly conserved nature, amplified sequences of the 16S ribosomal RNA genes can be compared with reference databases to determine the identity of the microorganisms that comprise a metagenomic sample. Sequences with a > 95% match are generally considered to represent the same genus, for example, while > 97% matches are considered the same species. However, these matches are often made by sequencing only part of the nine-region, ~1500 bp…

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Thursday, December 5, 2019

Two Review Articles Assess Structural Variation in Human Genomes

Two recent review articles discuss the idea that structural variants (SVs) — genetic differences that involve at least 50 base pairs — are numerous, important to human biology, and best detected with long reads. The authors review years of studies that have applied PacBio SMRT Sequencing to identify around 20,000 SVs per human genome. The reviews also report on cases in which SMRT Sequencing has helped scientists discover pathogenic variants that explain diseases for which there had previously been no clear genetic cause. In Nature Reviews Genetics, Steve Ho, Alexander Urban, and Ryan Mills from the University of Michigan and…

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Tuesday, December 3, 2019

Award-Winning Sequel II System Sets a New Standard for Long-Read Sequencing

Every year since 2008, The Scientist has canvassed the life-science community to find out which newly released products are having the biggest impact on research. We were proud to have the Sequel System selected as one of the Top 10 Innovations of 2016. And now we’ve been honored again, with the Sequel II System making the Top 10 Innovations of 2019 list. “Our goal is to identify those products and services that are poised to revolutionize research and advance scientific knowledge,” Scientist editors wrote.  As part of the competition, a carefully selected panel of expert, independent judges were asked to rank…

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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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