Open Source Joins Efforts to Create Gene Therapies for Rare Diseases

Some 400 million patients worldwide are affected by more than 7,000 rare diseases; yet treatments for rare genetic diseases remain an underserved area. More than 95 percent of rare diseases do not have an approved treatment, and new treatments are estimated to cost more than $1 billion.

Sanath Ramesh created the RareCamp project and the OpenTreatments Foundation to enable patients to create gene therapies for rare genetic diseases and then work with their doctors and nonprofit organizations to develop drugs. The Linux Foundation, the nonprofit organization enabling mass innovation through open source, is helping those efforts succeed.

Ramesh is the father of one such patient. His two-and-one-half-year-old son was born with a rare disease, Sedaghatian-type Spondylometaphyseal Dysplasia (SSMD), which is caused by a mutation in the GPX4 gene.

He has documented some of his personal story in this YouTube video:

Ramesh, a software developer, spearheaded a two-pronged attack to fight back using open-source software. He is the founder of the OpenTreatments Foundation and the creator of RareCamp.

The OpenTreatments Foundation enables treatments for rare genetic diseases regardless of rarity and geography. The RareCamp Project provides the source code and open governance for the OpenTreatments software platform to enable patients to create gene therapies for rare genetic diseases.

The Linux Foundation hosts the project to decentralize and accelerate drug development for rare genetic diseases. The project is supported by individual contributors, as well as collaborations from companies that include Baylor College of Medicine, Castle IRB, Charles River, Columbus Children’s Foundation, GlobalGenes, Odylia Therapeutics, RARE-X and Turing.

“OpenTreatments and RareCamp decentralize drug development and empowers patients, families, and other motivated individuals to create treatments for diseases they care about. We will enable the hand off of these therapies to commercial, governmental and philanthropic entities to ensure patients around the world get access to the therapies for years to come,” said Ramesh.

Open Source for the Greater Good

The RareCamp open-source project provides open governance for the software and scientific community to collaborate and create the software tools to aid in the creation of treatments for rare diseases.

The project uses the open-source Javascript framework NextJS for frontend, and the Amazon Web Services serverless stack — including AWS Lambda, Amazon API Gateway, and Amazon DynamoDB — to power the backend. The project also uses the open-source toolchain Serverless Framework to develop and deploy the software. The project is licensed under Apache 2.0 and available for anyone to use.

“If it’s not yet commercially viable to create treatments for rare diseases, we will take this work into our own hands with open-source software and community collaboration, [this] is the way we can do it,” said Ramesh.

“OpenTreatments and RareCamp really demonstrate how technology and collaboration can have an impact on human life. Ramesh’s vision is fueled by love for his son, technical savvy, and the desire to share what he is learning with others who can benefit. Contributing to this project was an easy decision,” Brett Andrews, RareCamp contributor and software engineer at Vendia, told LinuxInsider.

The OpenTreatments Foundation and RareCamp really represent exactly why open source and collaboration are so powerful, added Mike Dolan, executive vice president and general manager of projects at The Linux Foundation.

Creator’s View

The stark reality of dealing with his then-infant son’s diagnosis of an ultra-rare genetic condition 18 months ago drove Ramesh to seek an open-source solution where none existed in the proprietary software world. Since then, he has done a lot of work to repurpose existing drugs that have been used in other diseases to help treat his son’s condition.

Ramesh also started working on this new technology called gene replacement therapy. That technology essentially replaces a faulty gene with a good one, he explained.

“During this process, I discovered that the process of building a gene replacement therapy is targeted across a lot of diseases not specific to my son. It is something that a lot of patient foundations are trying to master by themselves; and quite honestly, they are failing,” he said. “Just like how I would have failed if I didn’t seek help.”

Ramesh realized a lot of people could benefit from this process. So he started thinking about ways to expand and share the knowledge and expertise with other patient foundations. That led Ramesh to create RareCamp and the Open Treatments Foundation.

What’s Involved

A lot more is going on, he continued. For instance, the big stack of the biotech world and all the activities that everyone is doing do not fully describe the extent of activity from the different players in the open-source collaborative space.

“What I am trying to do is sort of integrate all of that and provide a more streamlined simpler solution specifically focused on empowering individuals that typically are not already in the biotech space. That is something that has never been done before,” he said.

Until Ramesh started these two open-source projects, nothing comparable to providing the end game he seeks was available, he agreed.

It is also a different model because the activity is not based on a company structure. The endgame is not trying to sell a product. Instead, the nonprofit foundation is trying to create a sustainable ecosystem.

“So you are taking the open-source spirit and instilling it in an industry that has never seen this before. This is a completely different problem, a new problem,” said Ramesh.

That involves surmounting whatever other hurdles appear in order to get this project going to where it is now. Many of the hurdles exist because this is a new concept, he noted.

Implementing patients to build a treatment sounds sometimes ridiculous. But in reality, numerous instances of success and progress are growing.

Anniversary of Conference That Sparked the Idea

Building the software platform and getting the right scientific expertise aligned for the new project team were essential. Meeting those challenges at times seemed insurmountable. Pushing beyond them was part of the larger challenge of helping the patient community, Ramesh recalled.

“A lot of those challenges were primarily due to my lack of understanding of the space and secondarily, due to the lack of an established pattern in this phase, like no one has ever done this before. Which means there is always going to be a lot of resistance,” he shared.

Ramesh started having the first conversations about bringing open source into the gene therapy research field the first week of April last year. Ramesh said that occurred during a conference that happened the same week and set the stage for those conversations. It’s been a year in the making — pandemic and all. That surprisingly helped rather than hindered his efforts, he noted. Everybody was at home.

“I could reach the people that I wanted quite effectively because prior to the pandemic I would have to be flying. They would have given me four-week lead times before I could meet with them,” he explained.

Instead, all of their conferences and busy schedules were canceled. So Ramesh actually got a lot more time with people. Now he is feeling the difference because the world is starting to go back to the old normal. But in this pandemic period, Ramesh brought openness and collaboration into the biotech world.

“It is now a topic that everybody is discussing from the FDA to the NIH to academic institutions and to the biotech industry itself. Everybody’s talking about how we can bring more open collaboration to the space,” Ramesh said.

Jack M. Germain has been an ECT News Network reporter since 2003. His main areas of focus are enterprise IT, Linux and open-source technologies. He is an esteemed reviewer of Linux distros and other open-source software. In addition, Jack extensively covers business technology and privacy issues, as well as developments in e-commerce and consumer electronics. Email Jack.

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