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Wednesday, September 29, 2021

Long-read HiFi Sequencing is Helping Researchers Tackle Biggest ALS Challenges

  Seven years after the ALS Ice Bucket Challenge soaked the world, the pace of discovery in sporadic amyotrophic lateral sclerosis has increased tremendously, with more than $115 million dollars in donations funding research that has led to the identification of several genes implicated in both familial and sporadic cases of the neurodegenerative disease. While the social campaigns have generated much needed awareness around the disease, there are other challenges – one of which can be addressed with long-read sequencing. As detailed in a new, interactive case study, PacBio SMRT Sequencing is helping researchers at the University of Washington unravel…

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Thursday, September 23, 2021

ESHG 2021: How HiFi Sequencing is Closing the Gaps in Rare Disease Research

  It’s a challenge that has haunted rare disease researchers for years: how to increase solve rates in rare and Mendelian disease. Currently, the genetic cause of more than half of rare disease cases worldwide remain unexplained. In a series of talks and posters presented at the 2021 annual meeting of The European Society of Human Genetics (#ESHG21), PacBio experts and users described how HiFi sequencing could help close the gap by providing more comprehensive, accurate and high-definition coverage of the gaps in the human genome. Here is a summary of the discussions that took place and the posters that…

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Wednesday, September 8, 2021

UW Scientists Resolve Key Segmental Duplication Region with PacBio Sequencing

    A new Nature Communications paper shows how scientists continue to make progress elucidating some of the most complex regions of the human genome by deploying long-read PacBio sequencing technology. In this case, lead author PingHsun Hsieh (@phhBenson), senior author Evan Eichler, and collaborators at the University of Washington resolved the TCAF gene locus and identified more than 100 kb that had been missing in the human reference genome. Since the publication comes from the Eichler lab, it’s no surprise that the target genes in this project emerged in a segmental duplication (SD) region. The TCAF genes — which…

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Monday, August 23, 2021

SMRT Grant Winners: When Accuracy Matters Scientists Choose HiFi Sequencing

  At PacBio, we are passionate about accuracy in sequencing data. Our commitment to ensuring reliable results is why our HiFi reads are better than 99.9% accurate. Combined with the length of those reads — up to 25 kb — and it’s no wonder that our sequencing data generates complete, contiguous, and correct assemblies for even the most complex genomes.   While we’re proud of these technical accomplishments, our favorite thing is seeing how HiFi reads empower scientists to make new discoveries and reach novel insights. To that end, we launched our HiFi for Accuracy SMRT Grant program earlier this…

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Friday, August 6, 2021

Young Investigators Share Stellar Science, Career Advice and Bioinformatics Tools at SMRT Leiden 2021

  They spoke about omentum, chemosynthesis, chromothripsis, and… Tasmanian devils? This year’s virtual two-day SMRT Leiden Scientific Symposium and Informatics Developers Meeting was certainly educational. With the pandemic and increased difficulty in being able to connect in person, we wanted to provide a forum for young investigators, post docs, and faculty to come together and share their research experiences during these abnormal times. The result? 27 speakers—the majority of whom were young investigators—sharing data and discoveries, and their advice for early-career scientists. There was a great spectrum of presentations. The first keynote featured fun facts about Dominette (first Bos taurus…

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Monday, August 2, 2021

Data Release: Human Microbiome Samples Demonstrate Advances in HiFi-Enabled Metagenomic Sequencing

  As technology developers, one of our greatest joys is seeing how customers take our sequencing tools and deploy them for innovative and compelling new projects. Metagenomics has been one of those areas: our customers have recently been demonstrating the significant performance improvements enabled by our HiFi metagenome sequencing data and analysis pipelines. But since much of that work is protected by HIPAA regulations or has not yet been published, we are now releasing a metagenomic data set to help scientists see how HiFi data can make a difference for these types of studies. This information is now available for…

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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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