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Friday, July 30, 2021

Announcing the Winners of Our Clinical Research SMRT Grant – Two Scientists at the Forefront of Discovery

Here at PacBio, we have had the privilege of awarding many SMRT Grants to intrepid scientists who believe that HiFi sequencing data can help them achieve their goals. Recently, we invited people to apply for our Clinical Research SMRT Grant for projects with a link to potential clinical utility. We believe these projects could benefit tremendously from the value of HiFi reads, which offer both high accuracy and long reads to reveal genomic insights often missed by short-read sequencing. Narrowing these applications down to just one winner is always challenging, but this time we found it to be impossible. So,…

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Thursday, July 22, 2021

For Metagenomic Studies, HiFi Reads Deliver Higher-Quality Data

  A new paper from scientists at the Max Planck Institute offers a great look at how HiFi sequencing delivers significantly improved results for metagenome studies compared to short-read data. In this project, HiFi reads led to higher-quality assemblies with less coverage and gave more insight into these complex microbial communities. Bathymetric map of sampling locations In the PeerJ publication, lead author Taylor Priest (@taylorpriest2), senior author Rudolf Amann, and collaborators report the analysis of 11 seawater samples collected from the Fram Strait, which connects the Arctic and Atlantic oceans and offers a unique view of how climate change is…

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Wednesday, July 14, 2021

Iso-Seq Analysis Provides Insights into Feats of Physiology of Hibernating Bears

  Hibernating bears have heart rates of 10-15 beats per minute, yet they do not develop congestive heart failure. Despite accumulating enormous amounts of fat and acquiring insulin resistance, they do not suffer metabolic diseases. And they maintain muscle strength in the near absence of weight-bearing activity.Iso-Seq study has revealed differential tissue-specific isoform changes in brown bears If we could crack these feats of physiology, perhaps we could apply the knowledge towards therapeutic targets for the prevention and treatment of numerous human diseases. The Project that Shed Light on the Metabolic Mystery of Brown Bears Washington State University researchers have…

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Tuesday, July 13, 2021

Iso-Seq Analysis Enthusiasts Share Research Wins at Virtual Social Event

Been itching to talk about your latest single-cell experiments, your favorite differentially expressed isoforms, or your latest and greatest software for visualizing alternative splicing, but thwarted by a worldwide pandemic preventing in-person scientific events? We were too, so we organized a virtual social club to easily enable scientists to geek out together. And we weren’t disappointed by our first event, which attracted dozens of self-proclaimed Iso-Seq analysis geeks and other curious researchers to share their work (published, unpublished and in progress) and discuss the benefits and challenges of incorporating long-read transcript sequencing into their research. Welcome to the Iso-Seq Analysis…

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Thursday, July 1, 2021

In Case You Missed It — Sequel IIe System Users Share Their First Time Experiences

The new kid on the PacBio block — The Sequel IIe System — has been receiving high marks from universities and sequencing centers around the world. What’s it like using the instrument, which was introduced in October 2020? Several users have spoken about their experiences in a series of recent online events. Launching PacBio Sequencing Services in a New Lab Bringing SMRT Sequencing to the BlueGrass State Melissa L. Smith (@SmithLab_UofL), spoke about her experience transferring her lab from New York City to the “PacBio naive” Bluegrass State in the Unleashing the Power of HiFi webinar. Smith admitted she faced…

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Friday, June 25, 2021

Minding the Gaps: International Team Creates First Two Gapless Rice Reference Genomes

Rice was the first crop genome ever completed almost two decades ago. However, the rice reference has never been truly complete. Even improved versions of the major food staple and breeding model system Oryza sativa have contained gaps and missing sequences. An international team of scientists from China, the United States and Saudi Arabia, has finally closed those gaps to produce two gap-free reference genome sequences of the elite O. sativa xian/indica rice varieties Zhenshan 97 (ZS97) and Minghui 63 (MH63). How Long-Read Sequencing Fills the Gaps As reported in Molecular Plant, Jianwei Zhang (Huazhong Agricultural University, Wuhan), Jesse Poland…

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Thursday, June 24, 2021

Sequencing 101: How Does Whole Genome Sequencing Help Us Understand Rare Diseases?

  Rare diseases are defined as diseases that affect a small number of people – fewer than 1 in 2,000 in the European Union and fewer than 200,000 total people (about 1 in 1,500) in the United States. For example, Tay-Sachs disease affects 1 in 300,000 while Cystic Fibrosis is more common and affects 1 in 10,000. Though individual rare diseases affect very few people, collectively they are common and affect over 300 million people worldwide. Advances in Sequencing Technology for Improved Understanding of Rare Diseases With more than 70% of rare diseases being genetic in origin, scientists around the…

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Tuesday, June 8, 2021

NIH Scientists Chart SARS-CoV-2 Evolution Within an Individual Over Time

An exciting new paper from scientists at the National Institute of Allergy and Infectious Diseases and the NIH Clinical Center reports on the evolution of the SARS-CoV-2 virus within individuals. The team used HiFi sequencing to make this work possible. The paper, which was published in PLoS Pathogens, comes from lead authors Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, senior author Eli Boritz, and collaborators. They conceived the project to overcome a key challenge in tracking viral adaptation. “An important obstacle to understanding intra-individual evolution of SARS-CoV-2 is that standard sequencing and analytical procedures yield a single consensus sequence…

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Thursday, June 3, 2021

Reaching a Genomics Milestone – The First Complete Human Genome

It’s a moment three decades in the making: the first complete human genome assembly is here! Reading this you will no doubt feel some sense of déjà vu. After all, the human genome reference was pronounced “done” in 2000, 2001, and again in 2003. But any scientist who has used the reference since then knows that there has never been a single fully sequenced human genome. Until now. HiFi Sequencing Enables the First Complete Sequence of a Human Genome The Telomere-to-Telomere (T2T) Consortium, a large team of scientists from the National Human Genome Research Institute and dozens of other institutions,…

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Wednesday, May 19, 2021

Scientists Use PacBio Sequencing to Discover Likely Pathogenic Structural Variants Linked to ALS

May is ALS Awareness Month, and we’re hoping to help raise awareness by shining a spotlight on two deserving publications from scientists at the University of Washington and at the Mayo Clinic. In both studies, researchers used PacBio technology to sequence targeted genomic regions and to discover and characterize complex pathogenic variants associated with ALS. ALS, short for amyotrophic lateral sclerosis and commonly known as Lou Gehrig’s disease, is a progressive disease of the nervous system that causes loss of muscle control. The mean survival time for patients with ALS is just three to five years from diagnosis, and there…

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Monday, May 10, 2021

Sequencing 101: DNA Extraction – Tips, Kits, & Protocols

If you are like most of us at PacBio you likely learned how to extract DNA in a high school or college biology class, or maybe even in your kitchen. But as you moved on to more high stakes experiments, you may have found that extracting DNA for sequencing in your lab isn’t always as straightforward as lyse, precipitate, wash, suspend. In this introduction to DNA extraction, we will share tips, tricks, and protocols to help make your DNA isolation easier! For optimal results to power biological discovery, sample prep is a critical step in any sequencing project. And with…

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Tuesday, May 4, 2021

Pandemic Preparedness: PacBio and Labcorp Team Up On a Global Pan-Pathogen Surveillance Network

If only we could track COVID-19 like we track the weather, with satellites and weather stations placed around the globe monitoring and sounding the alarm about potential storms, floods, droughts and other severe weather events. A global pathogen surveillance network would save countless lives, and lessons learned from the current coronavirus pandemic could help make it possible, PacBio Chief Scientific Officer Jonas Korlach told Mendelspod host Theral Timpson (@theraltweet). Korlach joined Brian Caveney, President and Chief Medical Officer of Labcorp, in a recent podcast to discuss SARS-CoV-2 viral surveillance and the trajectory of COVID research, vaccination and treatment.   PacBio has…

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Monday, April 26, 2021

New HiFi Sequencing Workflow and Software Update Streamlines Whole Genome Sequencing

Today we’re pleased to announce the launch of a new HiFi Sequencing workflow along with a software update for the Sequel II and Sequel IIe Systems that will increase the number of HiFi reads at or above 99.9% accuracy (QV30) for whole genome sequencing-based applications. Together, these advances will improve the quality of HiFi Sequencing while providing​ an efficient and scalable workflow for sequencing hundreds to thousands of whole human genomes per year on Sequel Systems. This high-throughput sequencing and analysis workflow release includes a new HiFi library prep protocol offering a three-fold reduction in DNA input, enabling HiFi sequencing with limited sample quantities (neonatal…

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Thursday, April 22, 2021

Conservation is For Life, Not Just For Earth Day

  By Jonas Korlach, Chief Scientific Officer   Grapy dusks over tangerine fields. Potato-patch fog over beds of coral. Mountains, glaciers, forests, deserts, fertile farmland and seas with both Arctic and tropical biomes.  One of the most geographically and biologically diverse states, California is home to both the highest (Mount Whitney) and lowest (Death Valley) points in the 48 contiguous states, as well as to some of the world’s most exceptional trees — the tallest (coast redwood), most massive (Giant Sequoia), and oldest (bristlecone pine). At PacBio, we are extremely fortunate to have this biodiversity in our back yard —…

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Wednesday, April 21, 2021

SMRT Sequencing Detects Clinically Significant Repeat Changes In Triplet Expansion Disorders

When size matters and you need to be able to detect both single nucleotide changes as well as large repeated sequences, SMRT Sequencing on the Sequel II System is the way to go, concluded rare disease researchers at Centre de Recherche en Myologie at Sorbonne Université/INSERM  Stéphanie Tomé (@TomeStephanie) and colleagues used the highly sensitive, comprehensive long-read sequencing to investigate myotonic dystrophy type 1 (DM1), the most complex and variable trinucleotide repeat disorder, caused by an unstable CTG repeat expansion that can reach up to 4,000 triplets in those affected most severely with the disease. Myotonic dystrophy type 1 (DM1)…

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