PacBio Launches Sequel II System

By Allison Proffitt

April 26, 2019 | Pacific Biosciences has launched the Sequel II System. The system includes the new SMRT Cell 8M, as well as chemistry, instrument control software and the SMRT Link software package. Together, the latest product release further reduces project costs and timelines with approximately eight times the data output compared to the previous Sequel System, according to the company.

The Sequel II System is based on the technology and workflow underlying the previous version of the system, but contains updated hardware to process the new SMRT Cell 8M. Building upon the October 2018 release, which delivered highly accurate individual long reads (HiFi reads), the Sequel II System also produces these Sanger-quality reads (>99.9% accuracy), now at approximately eight times the scale.

The company has begun shipping the new commercial instruments following a successful early access program with five institutions: Wellcome Sanger Institute, HudsonAlpha Genome Sequencing Center, University of Maryland Institute for Genome Sciences, Broad Institute, and the Icahn Institute for Data Science and Genomic Technology at Mount Sinai. All five early access sites have subsequently purchased their first Sequel II Systems.

Luke Tallon, Scientific Director, Genomics Resource Center at the University of Maryland Institute for Genome Sciences, has been using the Sequel II system since February, and has completed 30-35 runs spanning human genome sequencing, metagenome and microbiome profiling, and non-model plant and animal genomes.

“We haven’t done any single application very deeply. We’ve evaluated several different applications with a few runs each to get a sense of how the instrument performs across different samples types, library sizes, and run lengths,” Tallon said. Across all applications he’s been pleased. “The yield and performance are, for the most part, meeting the expectations that PacBio set out at the start of the early access period,” he said.

In the long read applications, Tallon’s group is seeing comparable data quality with yields 8-9 times higher than that of the Sequel. “So far we’re pretty encouraged by the results, and hopefully it’ll continue to improve,” he said.

Using the Sequel II System, customers can comprehensively detect human variants ranging in size from single nucleotide changes to large, complex structural variants, PacBio says. The system is also ideal for standard applications such as de novo assembly of large genomes and whole transcriptome analysis using the Iso-Seq method. Extensive analyses of Sequel II data demonstrate that the system can provide equivalent or higher accuracy compared to the Sequel System. HiFi reads can enable comprehensive human variant detection with ≥95% precision and recall of structural variants, ≥99% precision and recall of single nucleotide variants, and ≥ 96% precision and recall of insertions and deletions with as little as 15-fold coverage.

Michael Hunkapiller, PhD, CEO of Pacific Biosciences, said: “We are pleased with the results of our early access testing, which confirmed our internal assessment of the system. By dramatically increasing throughput while continuing to deliver long reads with industry-leading accuracy, the Sequel II System is already driving science forward by allowing scientists to see elements that have long been intractable. The first SMRT Cell run during early access was a plant genome that resulted in a contiguity that was 10-fold greater than the current published reference. We look forward to seeing many first-of-a-kind results as more scientists gain access to this remarkable sequencing system.”