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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

UPDATE: We’re proud to have released the next evolution of the Sequel System: The Sequel IIe. Launched in October 2020, the new system features advanced on-instrument data processing and cloud enablement to deliver HiFi data faster, with significant reduction in compute and data storage costs. Details available here.   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…

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