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Wednesday, July 29, 2020

A HiFi View: Sequencing the Gut Microbiome with Highly Accurate Long Reads

Whether you are seeking to characterize microbial diversity in the gut, or distinguish between pathogenic and commensal bacteria on the skin, full-length 16S rRNA sequencing using PacBio systems is a valuable tool for metagenomics studies, according to microbiology researchers in a recent webinar. The HiFi advantage. With HiFi sequencing, every read yields 7-9 complete genes. PacBio microbiology expert Meredith Ashby (@AshbyMere) began the webinar by highlighting some of the strengths of the Sequel II System in metagenomics research.  One of the biggest advantages is the ability to do gene prediction directly on high-quality HiFi reads, without the need for any…

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Tuesday, July 21, 2020

Review: How Long-Read Sequencing Is Revealing Unseen Genomic Variation

“We are now embarking on an era where all genetic variation in an individual will be completely discovered,” write Glennis Logsdon (@glennis_logsdon), Mitchell Vollger (@mrvollger), and Evan Eichler in a recent Nature Reviews Genetics paper. “Hundreds and ultimately thousands of new human reference genomes will be produced.”  A decade ago that would have sounded impossible, but today this bold proclamation is widely accepted in the genomics community — a telling sign of the remarkable innovation that has driven genome sequencing in recent years. In their review, the University of Washington scientists give credit for much of these accomplishments to advancements in…

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Friday, July 17, 2020

New Isoform Phasing Technique Traces Parental-Progeny Differences in Maize

It’s not unusual for progeny to outperform their parents, and it’s often the goal in plant breeding. But tracing the molecular basis of such heterosis can be difficult, especially in diploid species with high genetic diversity and allele-specific expression like maize. Cold Spring Harbor scientists have tackled the challenge using the PacBio Iso-Seq method and a new tool, IsoPhase. As reported in Nature Communications Biology, Bo Wang, Doreen Ware, and colleagues performed an isoform-level phasing study in maize using the temperate line B73 and the tropical line Ki11, as well as their reciprocal crosses (B73 × Ki11; Ki11 × B73),…

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Wednesday, July 1, 2020

Don’t Sweat The Small Stuff: Low DNA Input Workflow Enables Sequencing of the Smallest Species

Tackling larger and larger genomes has been an attractive pursuit for many scientists as sequencing technologies improve at rapid rates. But what about the other end of the spectrum — the tiny organisms that comprise much of the diversity of life?  An obvious obstacle to decoding the DNA of small organisms such as insects, nematodes and other arthropods is collecting enough of it to actually sequence (usually multiple micrograms worth). Until recently, the solution was to pool DNA from many of these tiny creatures to create a representative sample, and extrapolate the biology of the individual constituents from there. But…

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Wednesday, June 17, 2020

Webinar: Increasing Solve Rates for Rare and Mendelian Diseases with Long-Read Sequencing

It’s well known that finding the genetic cause of rare diseases can be complex — that’s why so many remain unsolved. But researchers are beginning to get a grasp on just how complex these conditions can be, thanks to the heightened power of PacBio. PacBio principal scientist Aaron Wenger kicked off a recent webinar with a quote from University of Washington scientist Evan Eichler, who said “there are three key aspects to genetic disease associations: comprehensive variant discovery, accurate allele-frequency determination, and an understanding of the pattern of normal variation and its effect on expression.”  Wenger explained how HiFi reads…

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Monday, June 1, 2020

Webinar: Using SMRT Sequencing to Understand SARS-CoV-2 and the Host Immune Response

As the flurry of research around the SARS-CoV-2 virus continues at an unprecedented pace, scientists are beginning to tackle some of the more complex immunological responses with the help of Single Molecule, Real-Time (SMRT) sequencing. Hundreds of people tuned in live to a special May 7 webinar, “Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing.” Meredith Ashby, Director of Microbial Genomics at PacBio, described some of the resources being generated by both PacBio and our users in order to help labs who are using SMRT Sequencing technology to investigate SARS-CoV-2 and COVID-19. These include two microbial sequencing…

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Monday, May 11, 2020

The Pathologist: Solving Rare Disease with SMRT Sequencing

The strides scientists have made in rare disease research lately is truly impressive. For an overview of recent progress, we encourage you to check out a new article in The Pathologist from our own Luke Hickey (@Luke_Hickey), Senior Director of Strategic Marketing. It offers a great overview of how scientists have used long-read sequencing to find the genetic explanations for elusive rare diseases. “Never before have our laboratory techniques been so successful at identifying rare diseases and elucidating their underlying biological causes,” Hickey writes. “The knowledge we obtain today opens the door to new treatments, giving hope to people who…

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Wednesday, May 6, 2020

Data Release: HiFi Sequencing Results for Plants, Animals, and Microbes

It’s been more than a year since we introduced HiFi sequencing to generate highly accurate long reads. In that time, we’ve seen many PacBio users make HiFi sequencing their go-to setting because it’s simple, reliable, and cost-effective. For scientists who have yet to generate their own HiFi data, we thought it might be helpful to publish a few data sets for exploration and analysis. In a new preprint, we have released HiFi data sets for five samples: mouse, frog, maize, strawberry, and a mock metagenome community. We like to think there’s a data set for everyone here, whatever your research…

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Tuesday, April 28, 2020

Delivering New Insights into Cancer Research: SMRT Sequencing Case Studies

Will the next big cancer breakthrough be in immunotherapy? Therapeutic modification of the tumor microenvironment or microbiome? Or early detection and screening?  Whatever the result, long-read sequencing technology can play a pivotal part in the discovery process, according to Meredith Ashby, PacBio’s director of Market Strategy for Microbial Genomics, Cancer and Immunology. In a recent article for Lab Compare, Ashby highlighted some of the ways Single Molecule, Real-Time (SMRT) Sequencing has given researchers a deeper understanding of tumors at the genomic and transcriptomic level. The benefits of applying long-read sequencing to cancer research By spanning very large structural variants in…

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Wednesday, April 15, 2020

Go Big or Go Home — Tackling a Giant Genome

California redwoods: Not only are they giants in height and age (up to 379 feet high, 29 feet round, and thousands of years old), but the famous towering trees are also derived from a massive 27 Gb genome. Seeking a sequencing challenge for the Sequel II System, we picked the California redwood, or Sequoia sempervirens as it’s known to scientists. There also happened to be several fine specimens at nearby Stanford University. A small crew of PacBio scientists — Emily Hatas (@EmilyHatas), Greg Young (@PacbioGreg), and Michelle Vierra (@the_mvierra) — headed to campus to acquire samples equipped with ice, scissors,…

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Monday, April 13, 2020

How Long-read Sequencing Can Help Researchers Address Pressing Questions in COVID-19 Pandemic

Herculean efforts are being made by scientists around the world to respond quickly to the COVID-19 crisis in a race to understand the virus causing the pandemic and develop diagnostics, vaccines, and therapeutics. But many research questions remain. How can long-read SMRT Sequencing technology help fill the gaps? PacBio microbiology expert Meredith Ashby highlighted several opportunities to support coronavirus research in a recent webinar as part of a day-long virtual conference hosted by LabRoots.    Sequencing the viral genome Understanding the basic biology of the virus is essential, and the more detailed our investigation, the better.  Highly accurate, long-read sequencing…

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Wednesday, April 8, 2020

In Battle Against COVID-19 Pandemic, Scientists Turn to PacBio Sequencing

Image by Miroslava Chrienova from Pixabay Our team is proud to announce that PacBio has been working closely with customers to help in the fight against the COVID-19 pandemic. Scientists in commercial, academic, and government research teams are using highly accurate SMRT Sequencing data to resolve variants of the SARS-CoV-2 virus that exist within one individual or across a population of patients, which is critical to developing and maintaining effective diagnostics, vaccines, and therapeutics. Many of these efforts are powered by our HiFi reads, which are both long and highly accurate. Such reads are well-suited for applications like viral sequencing,…

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Wednesday, April 1, 2020

HiCanu for HiFi Reads Produces First Assembly of Human Segmental Duplications and Centromeres

UPDATE — September 1, 2020: This paper is now published in Genome Research. ORIGINAL POST — April 1, 2020 In a new preprint, scientists from the National Human Genome Research Institute, the University of Washington, and other institutions describe HiCanu, a modified version of the Canu assembler designed specifically for PacBio HiFi reads. The team put the new assembler through its paces, reporting that it significantly outperformed traditional assembly methods — even getting through centromeres, segmental duplications, and other notoriously difficult regions. As lead authors Sergey Nurk (@sergeynurk) and Brian P. Walenz, corresponding authors Sergey Koren (@sergekoren) and Adam Phillippy…

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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 18, 2020

Prokaryotic Methylation Detection on the Sequel II System

Since the first PacBio instrument was released in 2011, methylation detection has been one of the advantages of SMRT Sequencing. The kinetics of nucleotide incorporation change as the DNA polymerase moves across a methylated position on the DNA template strand, producing distinctive perturbation patterns (Figure 1) that can be recognized by methylation-calling software. Figure 1: The arrows indicate the methylated positions on a 199 bp circular template. Bars indicate the ratio of the average intra-pulse distance (IPD) on the methylated template to that of the control template. Each methylation type produces a unique fingerprint. With the advent of a simple…

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