PtBio Inc.

PtBio Inc. adopted Retrieva’s GGGenome packaged version for the safety assessment feature of Genome Editing Cloud®, the open platform for genome editing support it is developing toward a full launch in 2023. Because the packaged version can use proprietary nucleotide sequence databases, it also supports safety assessment in commercial services.

Why the GGGenome packaged version

PtBio: opening the future through industry-academia genome editing

PtBio is a Hiroshima University spin-off whose vision is "opening the future with genome editing and digital technology," built around three themes: co-creation, social implementation, and bio × digital. The company was founded around PlatinumTALEN, the domestically developed genome editing technology from Professor Takashi Yamamoto and colleagues at Hiroshima University’s Genome Editing Innovation Center. It commercializes domestic genome editing technology and supports drug discovery through services for producing model animals and cells.

We are working with companies to bring solutions to a range of problems through genome editing to as many people as possible, as quickly as possible — what we call social implementation.

Keisuke Okuhara, President and CEO

Okuhara previously worked at the Japan Science and Technology Agency (JST), the Cabinet Secretariat’s Intellectual Property Strategy Promotion Office, and the City of Higashihiroshima. In 2016 he established the industry-academia genome editing consortium OPERA with Professor Yamamoto of Hiroshima University, and in 2019 the two co-founded PtBio.

In March 2021, PtBio announced the beta version of Genome Editing Cloud®, developed jointly with Toppan Printing and Hiroshima University. Genome Editing Cloud® is an open platform for genome editing support that uses AI to simplify the processing of genome editing data.

Genome editing has the potential to solve problems in many fields, but it requires analyzing enormous volumes of data, which places a heavy burden on researchers. We concluded that a platform was needed where genome editing data analysis could be done without having to think about programming languages.

Keisuke Okuhara

Adopting the GGGenome packaged version in the genome editing platform

The beta version of Genome Editing Cloud® used the GGGenome web edition published by the Database Center for Life Science (DBCLS) for safety assessment.

The DBCLS web edition can only search genomes listed in public databases, so it cannot handle genome information we have sequenced ourselves or that our clients hold privately. Genome editing is used in applications such as crop breeding, and without genome information for the variety in question, the risk of unintended genomic changes rises accordingly.

Kazuyasu Nakamae, Senior Researcher

Nakamae, who plays a central role in developing Genome Editing Cloud®, describes the need for safety assessment robust enough for commercial use. After consulting Professor Hidemasa Bono of Hiroshima University, who also serves as PtBio’s science and technology advisor, and comparing the options against other tools, the company adopted the GGGenome packaged version.

The GGGenome packaged version lets us add our own nucleotide sequence databases. It has a simple static API, so integrating it with a cloud service is straightforward, and it handles complex requirements such as degenerate base notation and searching for gap (bulge) type off-targets.

Kazuyasu Nakamae

After trialling the packaged version ahead of implementing it in Genome Editing Cloud®, Nakamae says: "It has a wide range of features and fully meets our expectations. The search support script for searching multiple sequences at once is especially valuable."

Genome Editing Cloud® offers several features supporting genome editing data analysis; the GGGenome packaged version is to be integrated with Designer, the feature for designing and evaluating guide RNAs.

Adding GGGenome’s capabilities, aiming to be the standard tool for genome editing

Toward its full launch in fiscal 2023, Genome Editing Cloud® will continue implementing features, the GGGenome packaged version among them. When researchers and companies used the closed and beta versions, the platform was rated highly: "It is excellent that genome editing can be done through a simple UI." There were also many requests for additional features, and the plan is to extend functionality while more companies put the platform to use.

What Genome Editing Cloud® ultimately aims to be is a standard tool. Not only for people already comfortable with genome editing: we want those just starting out to use it and see what genome editing design and analysis actually involve, and what is possible. We position it as the standard tool that serves as an entry point to the world of genome editing, and we will keep developing it on that basis.

The GGGenome packaged version handles nucleotide sequence search, which plays an important role in genome analysis, so our expectations of it are high. With Genome Editing Cloud® we are aiming above all for a tool that is easy and simple to handle. Many wet-lab researchers who work directly with cells find dry analysis on a computer hard to approach, and we want Genome Editing Cloud® to dispel that. We want it to be as simple as uploading data and pressing a button to get results, while the latest, highly reliable machinery runs behind the scenes. As PtBio, we plan to pursue a range of initiatives so that we can be a hub for removing the barriers between academia and industry as well.