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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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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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Wednesday, February 3, 2021

Genomes vs. GenNNNes: The Difference between Contigs and Scaffolds in Genome Assemblies

This blog post has been updated, it was originally published September 2016. In recent interactions with the scientific community, we’ve seen a growing number of questions around scaffolding genome assemblies. We thought it might be useful to review the concepts behind contigs and scaffolds, as well as the circumstances in which one might want to scaffold a high-quality PacBio genome assembly. Contigs vs. Scaffolds Contigs are continuous stretches of sequence containing only A, C, G, or T bases without gaps. SMRT Sequencing has all of the necessary performance characteristics – long reads, lack of sequence-context bias, and high accuracy –…

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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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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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Tuesday, July 7, 2020

Sequencing 101: From DNA to Discovery – The Steps of SMRT Sequencing

Starting a sequencing project can be daunting. First of all, there are several types of sequencing technologies, each based on unique processes. At PacBio, we use a technology called Single Molecule, Real-Time (SMRT) Sequencing.   Learn how SMRT Sequencing works in this short video:   Although each sequencing project is unique, there are five main steps to go from DNA to discovery with SMRT Sequencing:   Step 1: Sample Prep Similar to cooking, for the best results, start with the best ingredients. The ideal sequencing starter is high molecular weight DNA. There are plenty of kits on the market that…

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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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Thursday, April 30, 2020

Sequencing 101: Looking Beyond the Single Reference Genome to a Pangenome for Every Species

What is a Pangenome? A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. Unless you have an identical twin, no other person has a genome that is identical to yours. The same is true for other animal, plant, and microbial species that reproduce sexually: the genomes of individuals are unique. Less well known, but equally true, is that individual members of a species do not always share even the exact same genes. Nevertheless, scientists mostly use a single reference genome to represent an entire species: one human genome, one…

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Wednesday, April 22, 2020

Sequencing 101: Why Are Long Reads Important for Studying Viral Genomes?

The COVID-19 pandemic has brought a sudden urgency to virus research and led many of us to dig more deeply into all the tools available for characterizing viral genomes, from RT-PCR to DNA sequencing. For all their outsized impact on human health, viruses have remarkably small and simple genomes, some just a few thousand bases in length, and most lacking any repetitive structures. With such tidy genomes, you may wonder, why would scientists want to sequence them with a long-read technology like PacBio HiFi reads? Quasispecies develop as variants are introduced to the viral genome through mutations. While it is…

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Tuesday, April 7, 2020

Sequencing 101: Video Introduction to PacBio Sequencing and the Sequel II System

We’re pleased to release a short video describing PacBio Sequencing and our latest platform, the Sequel II System. If you’ve ever wondered how Single Molecule, Real-Time (SMRT) Sequencing works, what the Sequel II System is, and what applications are available, this video is a great place to start. We are excited to share the capabilities of our Sequel II System as it makes SMRT Sequencing affordable for scientists in any lab and provides comprehensive views of genomes, transcriptomes, or epigenomes. The Sequel II System also produces highly accurate long reads, known as HiFi reads, to deliver the highest quality sequencing…

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Monday, March 23, 2020

AGBT 2020 Highlights: Reference-Grade Assemblies, Iso-Seq Data, and More

It was a pleasure to attend the annual Advances in Genome Biology & Technology meeting in sunny Marco Island, Fla., last month. The conference has a long history of supporting sequencing innovation, and during the 20th anniversary celebration this year, the tradition continued. Video and synopses from several presentations featuring SMRT Sequencing are below. Adam Ameur (@_adameur) from Uppsala University spoke about the use of long-read PacBio sequencing to detect off-target edits from CRISPR/Cas9. In a method known as SMRT-OTS, Ameur’s team used a clever adaptation of the standard PacBio library preparation to enrich for molecules bound by a guide…

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Wednesday, March 11, 2020

SMRT Grant Winners: Three Scientists Selected to Use HiFi Sequencing to Tackle Genomic Challenges

  PacBio highly accurate long reads, known as HiFi reads, offer all the benefits of long-read sequencing with accuracy comparable to short-read sequencing. To celebrate this new paradigm in sequencing technology, we hosted the 2019 HiFi for All SMRT Grant this past fall. This SMRT Grant was open to scientists worldwide and offered three winning projects each up to six SMRT Cells 8M and sequencing on the Sequel II System by our Certified Service Providers and co-sponsors. In response to our call for projects across the range of SMRT Sequencing applications, we received many truly compelling proposals, which made selecting…

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