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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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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, 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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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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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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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 8, 2021

PacBio Sequencing Uncovers Large Deletions in RSV Vaccine Candidate Under Selective Pressure

Scanning electron micrography of human respiratory syncytial virus (RSV) Vaccine safety is of the utmost importance. Respiratory syncytial virus (RSV) is the most common cause of severe lower respiratory tract illness in infants and young children.  Much like the flu, it can also cause severe disease in the elderly or immunocompromised adults, making it an important target for vaccine development. In a recently published study, researchers used PacBio long-read sequencing to evaluate the genetic stability of a live-attenuated RSV vaccine candidate and observed previously unknown adaptation mechanisms that was missed by short-read sequencing. Codon-pair deoptimization involves recoding of open reading…

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Tuesday, April 6, 2021

SMRT Grant Winners – Collaboration Reaches New Heights in Global Science Challenge

Today we’re pleased to announce the three winners of our latest SMRT Grant which called for teams of researchers and collaborative projects that could be addressed using the power of HiFi sequencing. The winners are seeking to solve a diverse set of questions from mussel-hopping transmissible cancer to the power of pistachios to help tackle climate change, and sex determination in bearded dragons.     The 2020 HiFi for All – Collaborations SMRT Grant Program was open to scientists worldwide and offered three winning projects awards of up to 10 SMRT Cells 8M and sequencing on the Sequel II or…

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Friday, February 12, 2021

LeafGo: A Workflow That Enables High-Quality Seven-Day Plant Genome Assembly 

  UPDATE — September 3, 2021: This paper is now published in Genome Biology. ORIGINAL POST A team of scientists from KAUST used a new rapid de novo assembly workflow to create genomes of the Eucalyptus species E. camaldulensis What does the ideal genome assembly look like? High-quality, free of errors, with no gaps, and all haplotypes resolved. It’s a big ask, especially with challenging genomes like plants that are rich in repetitive content with high levels of heterozygosity and complex polyploidy. Moreover, such assemblies often require a combination of technologies, such as sequencing plus optical mapping. But a team…

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Thursday, December 10, 2020

Sequencing 101: Ploidy, Haplotypes, and Phasing – How to Get More from Your Sequencing Data

The ploidy or number of copies of each chromosome in a genome affects not only the size but also the complexity of the genome. Geneticists often point out that a human does not have “a” genome but rather two genomes, one inherited from the mother and another from the father. The number of complete sets of chromosomes in each cell, or haplotypes, is referred to as ploidy.  Humans and most other animals are diploid (2N), having two sets. Many plants have higher ploidy, for example, the hexaploid (6N) California Redwood has 6 copies of each chromosome. The number of chromosome…

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Monday, October 5, 2020

Meet the New Sequel IIe System: Delivering Fast & Affordable HiFi Sequencing

The new Sequel IIe System provides direct access to HiFi sequencing Still soaring from the success of last year’s launch of the award-winning Sequel II System, we’re excited to announce the next evolution of the instrument: the Sequel IIe System. This evolution includes increased computing power and advanced on-instrument data processing. This means the instrument can directly produce the widely coveted, highly accurate long reads, known as HiFi reads, that have made the original Sequel II System indispensable for many labs — and save users time and money in the process.  Just how much of an improvement does the new…

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Monday, August 31, 2020

Colombian SMRT Grant Winners Hope HiFi Sequencing Will Help Save Critically Endangered Toads

The ‘happy toad’ (Atelopus laetissimus) comes in a variety of colors. Meet the ‘happy toad’ Atelopus laetissimus, a harlequin toad found on the slopes of the Sierra Nevada de Santa Marta mountains of Colombia. This toad is brightly colored, with an almost comical slow walk and lots of other unique attributes. But the reason it is delighting scientists and conservationists is its ability to adapt and survive while its relatives are on the brink of extinction. The 2020 Plant and Animal Sciences SMRT Grant Program co-sponsored by PacBio and the DNA Sequencing Center at Brigham Young University will enable a…

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Thursday, July 23, 2020

Sequencing 101: What’s the Value of Sequencing Full-length RNA Transcripts?

The study of genomics has revolutionized our understanding of science, but the field of transcriptomics grew with the need to explore the functional impacts of genetic variation. While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing – using a full-length transcript approach – become clearer. Reaching for the Transcriptome Even before genome sequencing became commonplace, scientists were able to measure gene expression activity using hybridization…

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Thursday, May 21, 2020

Sequencing 101: Understanding Accuracy in DNA Sequencing

For scientists who utilize DNA sequencing in their research but are not experts in the underlying technology, it can be difficult to determine the accuracy of sequencing results — and even harder to compare accuracy across sequencing platforms. Furthermore, accuracy differs not only between technologies but also across genomic regions as some stretches of the genome are inherently more difficult to read. It is critically important to understand accuracy in DNA sequencing to distinguish important biological information from sequencing errors.   What are the Types of Sequencing Accuracy? HiFi reads are generated by combining multiple consecutive observations of a DNA…

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