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Thursday, December 27, 2018

An Outstanding Year of SMRT Science: 2018 Publication Review

Scientists were certainly sequencing with confidence in 2018, as evidenced by the number of significant and wide-ranging advancements made using SMRT Sequencing technology, several of which made the cover of high-impact journals. 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 that even captivated the popular press.   “It’s been a phenomenal year for science. We are proud of our partners and honored that our technology is helping to drive such discovery across all…

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Wednesday, December 26, 2018

SMRT Sequencing — The PacBio Spirit of Past, Present, and Future

In the rapidly evolving world of DNA sequencing, the community is often focused on what’s new and what’s next. There’s not much opportunity for retrospection. But two recent articles offer an insightful look at the history of SMRT Sequencing technology, from the time it was just a gleam in the eye of some Cornell University scientists to how it works and some exciting new applications. At Technology Networks, reporter Ruairi MacKenzie writes about the scientific beginnings of SMRT Sequencing with memories from PacBio CSO Jonas Korlach, one of the inventors of the technology. “Korlach concluded that if only you could…

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Monday, December 24, 2018

Looking Forward to Sequencing Advances and Novel Findings at PMWC 2019

Advances in personalized medicine — whether it’s the discovery of a new pathogenic variant or a success story about a patient treated with a tailored therapy — seem to be almost a daily occurrence. That’s why we’re particularly excited to attend the Precision Medicine World Conference (PMWC), co-hosted by Stanford, UCSF, Duke, Johns Hopkins & U. of Michigan, taking place January 20-23 at the Santa Clara Convention Center. The meeting brings together thought-leaders of business, government, healthcare-delivery, research and technology to share the latest developments, challenges, and triumphs in the field. PMWC is well known for giving out prestigious awards,…

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Friday, December 21, 2018

The Genomic Gift Worth Giving: New Assembly Could Help Conserve Declining Turtle Dove Populations

Turtle dove. Photo by Andy Morfew You may be more likely to get five gold rings or three French hens than two Turtle doves this Christmas. The subject of the famous holiday carol is in precipitous decline across Europe, with 94 percent of Turtle doves lost since 1995, and fewer than 5,000 breeding pairs left in the UK. In an attempt to save the species, geneticists at the Wellcome Sanger Institute identified it as a priority species to be sequenced as part of a year-long 25th anniversary project. Collaborators at the University of Lincoln sent samples (collected from live birds…

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Wednesday, December 19, 2018

New Low-Input Protocol Enables High-Quality Genome Created from Single Mosquito

Anopheles coluzzii mosquito UPDATED January 18, 2019 This paper is now available at Genes. ORIGINAL POST December 19, 2018 High-quality reference and de novo genomes have been celebrated by geneticists, population biologists and conservationists alike, but it’s been a dream deferred for entomologists and others grappling with limited DNA samples, due to previous relatively high DNA input requirements (~5 μg for standard library protocol). A new low-input protocol now makes it possible to create high-quality de novo genome assemblies from just 100 ng of starting genomic DNA, without the need for time-consuming inbreeding or pooling strategies. The targeted release date for…

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Monday, December 17, 2018

Alzheimer’s Study Reveals First Somatic Gene Recombination Found in Human Neurons

Scientists in California recently released exciting results that could offer an entirely new approach to treating the most common form of Alzheimer’s disease. The project, which was reported in a Nature publication, made extensive use of SMRT Sequencing data using targeted sequencing and some previously released full-length RNA sequencing data. “Somatic APP gene recombination in Alzheimer’s disease and normal neurons” comes from lead author Ming-Hsiang Lee, senior author Jerold Chun, and collaborators at the Sanford Burnham Prebys Medical Discovery Institute and the University of California, San Diego. The team aimed to determine whether somatic gene recombination, which is used throughout the genome to…

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Thursday, December 13, 2018

A Sweet Sequence: Sugarcane Genome Assembly After Five-Year Collaborative Effort

It took nearly 20 years until the technology was right, and five years of hard graft by more than 100 scientists from 16 institutions, but the result was worth it, according to University of Illinois plant biology professor Ray Ming. One of several authors of a paper published and featured on the cover of Nature Genetics reporting the assembly of a 3.13 Gb reference genome of the incredibly complex autopolyploid sugarcane Saccharum spontaneum L, Ming said he dreamed about having a reference genome for sugarcane while working on sugarcane genome mapping in the late 1990s. But sequencing technology was not…

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Monday, December 10, 2018

Targeted PacBio Sequencing Adds to Scientific Arsenal in Evolutionary Arms Race

Cotton crops the world over have benefited from the pest-killing protein from Bacillus thuringiensis (Bt), first used in sprays and then, in 1996, transgenic crops, resulting in reduced insecticide use, enhanced biological control, and increased farmer profits. But the precious plants are under threat once again by a tiny but mighty pest: pink bollworm (Pectinophora gossypiella). In India, where more than 7 million farmers have planted 10.8 million hectares of transgenic Bt cotton, the lepidopteran pest has developed resistance to two different forms of the toxin that made the transgenic crops so effective, creating catastrophic economic losses. Scientists have been…

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Monday, December 3, 2018

Barn Swallow Project Helps Introduce PacBio Long Read Technology to Italy

Its reliable return to the same spot year after year has made the barn swallow a beloved symbol of Spring and safe passage, for mariners and landlubbers alike. But our changing climate is altering the birds’ migratory behavior, and Italian ecologists are turning to genetics to figure out how. As reported previously in this blog, scientists at the University of Milan joined forces with researchers from the University of Pavia and California State Polytechnic University to create the first high-quality reference genome for the European barn swallow (Hirundo rustica rustica), using SMRT Sequencing and newly available Bionano Genomics optical mapping…

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