Patients with myotonic dystrophy type 1 (DM1) want to know their size — the size of the expansion of repeats of the unstable CTG sequences that cause the progressive deterioration of neuromuscular functions that they might face. Size matters to them, because it has been found to correlate with the severity and onset of symptoms, which can range from severe cardiac and respiratory abnormalities and intellectual impairment in children, to muscle weakness, hypersomnolence or cataracts in adults. The earlier the onset, the more severe the symptoms tend to be. The autosomal disorder, which is the most common form of inherited…
Two years ago, Carola Greve and colleagues at the Zoological Research Museum Alexander Koenig in Bonn, Germany, were seeking to #SeqtheSlug as part of the 2017 Plant and Animal SMRT Grant competition, and the popular project was a close runner-up. Greve didn’t give up on her quest to sequence the ‘solar-powered’ sea slug. We caught up with her recently at the SMRT Leiden Scientific Symposium, where her update on the sea slug project earned her a Best Poster award. Why the sea slug? Although Mollusca represents the second largest animal phylum with around 85,000 extant species, only 23 mollusc genomes…
Maya and her partner, Sgt. Nic Banuelos, of the UWPD K9 unit First there was Shadow, the poodle owned by gene-entrepreneur Craig Venter. Then there was Tasha, a female Boxer. Will the next de-coded dog be Maya, a German Shepherd Dog that helps police the campus at the University of Wisconsin-Madison? Maya has been basking in social media celebrity alongside her human companion Sgt. Nic Banuelos, PhD students Lauren Baker and Emily Binversie, technician Jorden Gruel, veterinary surgeon-scientists Susannah Sample and Peter Muir, and Peter’s woven likeness, after winning the 2019 Plant and Animal SMRT Grant, co-sponsored by Histogenetics. We…
Kristen Sund Please join us in congratulating Kristen Sund from Cincinnati Children’s Hospital Medical Center for winning our 2018 Structural Variation SMRT Grant Program! Her proposal to use SMRT Sequencing to pinpoint the genetic mechanism responsible for neurological disease in patients with complex structural rearrangements definitely captured our attention. We caught up with Kristen to learn more about her background, her research, and how she hopes to use the data generated through this grant. How did you get into this field? I have always had a very strong interest in research and patient care, so I decided to get training…
What has four legs, lots of fat and fur, and will possibly help uncover novel mechanisms to combat diabetes? Photo courtesy of WSU Bear Center Grizzly bears! If humans were to undergo regular, extended cycles of weight gain and inactivity, they’d likely end up with obesity, muscle atrophy, or type 2 diabetes. But grizzly bears experience no ill effects from their annual fat gain and sedentary hibernation. Somehow they are able to switch their insulin resistance between seasons, and researchers at Washington State University are hoping to figure out how, with possible therapeutic value for humans. We’re proud to support…
Mark Webber We’re pleased to announce the winner of the 2018 Microbial Genomics SMRT Grant. Mark Webber, Research Leader at Quadram Institute Bioscience in the UK, will get free SMRT Sequencing and analysis from our certified service provider, the Genomics Resource Center at the University of Maryland. His goal is to further a project designed to understand how bacteria on the skin of premature babies in neonatal intensive care units acquire resistance to the antiseptics used to prevent infections. We spoke with Mark to learn more about his work and how the SMRT Grant will make a difference. Q:…
From wild animals to perfect pets, dogs have undergone some interesting changes during their centuries-long domestication. Intent on unraveling some of the developmental secrets of the process, a team of scientists from the University of New South Wales in Sydney, Australia, is doing deep dives into the genomes of a range of canine cousins along the evolutionary chain. A desert dingo named Sandy has already provided some insight into the process after its genome was sequenced as part of the 2017 Plant and Animal SMRT Grant. Study leader Bill Ballard described in this presentation at PAG 2018 that pure dingoes…
We’re pleased to announce the winner of this year’s ‘Open Your Eyes to Isoform Diversity’ SMRT Grant, which was launched during the American Association for Cancer Research annual meeting. The grant program, co-sponsored by PacBio and GENEWIZ, received many compelling entries, and it was a challenge choosing just one winner. Congratulations to Andrew Ludlow, a new faculty member at the University of Michigan, who impressed reviewers with his proposal to investigate the splicing of transcripts regulated by the oncogene NOVA1. Ludlow notes that in lung cancer cells, NOVA1 acts as a splicing enhancer to produce full-length hTERT and promote telomerase…
We’re excited to be heading to Washington, DC, for the annual meeting of the American Association for Cancer Research. The PacBio team always enjoys hearing about the latest in cancer translational research at AACR, along with thousands of leading scientists in the field. Many of those scientists have already learned that SMRT Sequencing provides a unique view into cancer, revealing structural variation, phasing distant variants, and delivering full-length isoform sequences. With uniform coverage, industry-leading consensus accuracy, and reads extending to tens of kilobases, PacBio long-read sequencing gives researchers the ability to monitor and make sense of even the most complex…
Blog readers may recall that last year’s SMRT Grant winner was Renying Zhuo from the Chinese Academy of Forestry. We’re pleased to report that the project is now complete! Zhuo proposed sequencing the genomes of two strains of the Sedum alfredii plant from the same ecosystem — one that accumulates cadmium ions from polluted soil and one that doesn’t. The goal was to use high-quality assemblies for comparative genomic analysis to determine the genetic mechanisms responsible for this remediation effect. Plant DNA was sequenced on the Sequel System by RTL Genomics, and genome assembly was performed by Computomics. (We’re also grateful…
Our team of scientist reviewers has considered hundreds of submissions for the latest SMRT Grant award and narrowed the selection to five finalists. Now it’s your turn! We welcome the community to vote for their favorite project now through April 5th. The winner will receive SMRT Sequencing and genome assembly or Iso-Seq analysis sponsored by PacBio and our partners, the Arizona Genomics Institute and Computomics. Here’s a look at the entries from our five finalists: Project: Temple Pitviper Principal investigators: Mrinalini Mrinalini, National University of Singapore; Ryan McCleary, Utah State University; Manjunatha Kini, National University of Singapore #SeqtheViper The highly venomous snake…
We’re pleased to announce the winner of this year’s SMRT Grant, which launched during the American Society for Microbiology annual meeting this summer. The grant program, co-sponsored by PacBio and the Institute for Genome Sciences (IGS), was very competitive, with over 100 submitted proposals. From this broad range of entries, our judges faced quite a task choosing just one recipient for the grant. Congratulations to Jessica Sieber from the University of Minnesota Duluth, who impressed reviewers with her proposal, “Metagenomic analysis of the gut microbiota of the 13-lined ground squirrel, a model fat storing hibernator.” Ground squirrels have been models…
You may remember the firefly genome sequencing project, which was a finalist in our recent SMRT Grant competition and ultimately was crowdfunded through the Experiment site and our Genome Galaxy Initiative. We’re thoroughly enjoying the lab updates on this project, and couldn’t resist sharing this latest one from Team Firefly. In a jubilant note, the scientists report to their funders: “Good News! PacBio long-read sequencing data received.” The update is written with lots of great explanation about the basics of sequencing, analysis, and more for science enthusiasts. Our favorite part is the visualization of read length: the team included the…
We’re pleased to launch the latest opportunity to have your favorite microbe sequenced on a PacBio System. The SMRTest Microbe Grant Program, kicking off at this year’s American Society for Microbiology annual meeting in Boston, will give one scientist a free genome sequence for his or her chosen microbe. For those folks unable to make it to the meeting this year, don’t worry — you do not need to attend ASM Microbe to enter the program. To enter, simply submit a short application describing your microbe or microbial community and how it would benefit from the long read lengths, high…
Congratulations to the winner of the first-ever SMRT Grant program decided by the community: Renying Zhuo of the Chinese Academy of Forestry! We ran polling through our Genome Galaxy Initiative on the Experiment crowdfunding platform and were amazed to see much how it galvanized the genomics community. There were 30,000+ responses to the competition across the five finalists for our “Explore Your Most Interesting Genome” grant opportunity. Zhuo garnered the most support for his project to sequence two highly related strains of Sedum alfredii for a comparative genomics investigation to identify key genes important for remediating soil contaminated by heavy…