PacBio Announces ML Methylation Calling, New Software, Consumables

April 21, 2022

By Bio-IT World Staff

April 21, 2022 | Pacific Biosciences announced broad updates to its Sequel IIe and Sequel II Systems today including new capabilities in DNA methylation detection and workflow improvements promising a 50% decrease in NGS sequencing workflow and a 40% decrease in needed sample.

The upgrades include a new version of SMRT Link (v11.0) software, new instrument control software for both the Sequel II and Sequel IIe systems, as well as new consumables. The new software is immediately available for download and the new consumables are immediately available to all Sequel II/IIe customers.

New Methylation Data

DNA methylation is a known biomarker of biological age and impacts how genes are expressed with implications for both health and disease. “Looking at methylation helps researchers understand how, when, and where genes are being regulated, which is foundational for everything from evolutionary and developmental biology, to ecology, to human health and disease, including common diseases of aging,” explained Dave Miller, Vice President, Product Marketing at PacBio.

But access to the epigenome has been difficult, often requiring sacrifices in read lengths, accuracy, and completeness while adding workflow complexity, according to PacBio. Now PacBio is using machine learning algorithms to make methylation calls during the sequencing process.

“In PacBio’s HiFi sequencing, we observe individual ‘live’ DNA polymerase molecules as they go about their work of copying DNA strands,” Miller said. “Subtle patterns of polymerase behavior report on properties of the DNA strand, such as methylation. In HiFi sequencing, we sequence the exact same molecules repeatedly and this is what leads to PacBio’s extraordinary read accuracy. But it also means that we get many observations of those subtle patterns of polymerase behavior. Using advanced machine learning techniques, we can tease out those signals and make accurate DNA methylation calls.”

Adding the machine learning calls creates no workflow additions or changes and adds no costs or time to the sequencing. The additional data processing takes only minutes, Miller said, and results in about a 5% increase in data volume.

Methylation calling will be turned on in the software upgrade by default, and Miller expects anyone studying organisms that have 5mC in CpG contexts—the vast majority of customers—to use and appreciate the new data. “I think this application has been so underserved historically with a good solution that we will see a considerable amount of learnings and discoveries come out quickly,” he said.

Already researchers at Children’s Mercy Kansas City have been using the methylation detection along with Iso-Seq full-length RNA sequencing in their study of genetic disease.

“We aim to expand sequencing from its interpretation of DNA alone to an integrated test of DNA sequence and its function—in the past we used multiple platforms to achieve the necessary genome characterization,” said Tomi Pastinen, MD, PhD, Director, Genomic Medicine Center, Children’s Mercy Kansas City in a press release. “The systematic application of RNA testing using Iso-Seq and direct methylation detection in HiFi-GS yields information about gene regulation and epigenetic state. We are now working on integrated analyses across hundreds of our unsolved cases and we hope to identify new, previously veiled genomic variants that may be associated with rare disease.”


Streamlining workflows is another focus of the announced updates. PacBio announced several kits and consumables aiming to ease HiFi sequencing. The company’s new SMRTbell prep kit 3.0 is capable of reducing workflow time for whole-genome sequencing applications by 50% or more and reducing required DNA inputs by 40% (to three micrograms per human genome). SMRTbell prep kit 3.0 is suitable for a wide range of applications and supports automation and batch processing of samples. PacBio also introduced a new single-reaction sequencing plate and SMRT Cell 8M tray that better enables customers to run samples at their convenience.

This update also includes a wide range of workflow improvements to enhance customer experience, such as simplified, unified, and accelerated library preparation workflows and consumables, live instrument performance monitoring, and on-instrument analysis support for recombinant adeno-associated virus (rAAV) genome sequencing, a rapidly growing biopharmaceutical application relevant to gene therapy and vaccine development research.

“With each product release we continue to improve the utility and value of the Sequel II and IIe platform, providing researchers with unique capabilities that differentiate PacBio HiFi sequencing from all other sequencing technologies,” said Christian Henry, President and Chief Executive Officer of PacBio, in a statement announcing the updates. “Our latest enhancements to the Sequel II and IIe platform, including 5-base sequencing and improved workflows are expected to both simplify the ability to generate high quality data and enable deeper insights into the complexity of the genome.”