Just DNA-Seq: Achieving and Expanding Our Vision with Web3 and Decentralization

Just DNA-Seq ( http://dna-seq.github.io/ ) is a suite of open-source libraries and pipelines to empower individuals to take control of their genetic information. Initially funded by GitCoin during the longevity funding round (end of 2021), we have successfully delivered on most of our promises: with 23 source code repositories ( see https://github.com/dna-seq ), 11 published Oak Var modules, several hack-your-own-genome workshops together with documentation and scientific research paper (yet, in a draft stage).

Now, we are excited to make our project:

• More decentralized - by incorporating Web3 and decentralization elements to further enhance its accessibility and utility by integrating our pipeline with PLEX ( https://docs.labdao.xyz/#about-plex ) developed by LabDAO ( https://labdao.xyz/ ) and allowing our Oakvar modules to run in a secure privacy-preserving DNA vault (collaboration with Genomes DAO).
• More interactive - we have already developed a prototype of the chatbot called LongevityGPT that utilizes large language models to answer (with verifiable references to avoid hallucinations of the model) users' questions about Longevity. We want to extend it to answer users' questions about genetic and genetic variants, including (if users allow) questions about her own genetic variations. Of course, it cannot compare in accuracy/robustness with personalized genomics consultants, but it should significantly improve understanding of the results by non-professionals.
• More actionable - at the moment, so-called “aging clocks” are used to measure the individual pace of aging, which are based on blood, methylation, glycosylation, and other parameters, and are used to correct lifespan interventions. However, non of them take into account patient genetics, so we want to investigate if our longevity scores can improve the aging clocks' accuracy. This project is done in collaboration with Healome; the proposal has recently been approved by UK biobank, which will provide the data.
• Easier to understand - we started developing “Hack your own genome” Massive Online Course to bring personalized genomics to more people. We will also work more with the user community to improve the overall user experience and robustness of the platform.

We invite the Gitcoin community to join us in this endeavor!

What you can already do with our existing codebase:

1. Realign your raw genome reads and perform variant calling using state-of-the-art tools and bioinformatics pipelines.
2. Annotate your own genome with the longevity-focused OakVar plugin, which also includes:

• Known longevity and cancer risks
• Known drug interactions
• Cardio hereditary disease risks
• Coronary artery disease risk variations

3. Receive a comprehensive and transparent open-source report featuring all the above information, as well as polygenic health risk predictions and personalized recommendations related to longevity. You can check out an example of such a report (computed from the genome of one of the project founders) is https://dna-seq.github.io/report_example/

You can deploy everything mentioned above on your laptop. You can also try our development server at http://agingkills.eu:8081/index.html , where you can either upload your data (note: as it is a development version, use at your own risk!) or use our demo account (login: jdnaseq@gmail.com, password: 123456) to explore already processed open-source genomes and generated reports.

Why Just DNA-Seq?

The first human genome sequencing project concluded on April 14, 2003, after more than 12 years of labor and costing approximately $3 billion. Since then, genome sequencing has become widely accessible and affordable, with commercial offerings priced between $400-$800. However, these services often lack transparency, privacy, and customization. Just DNA-Seq was born out of our team's passion for addressing these shortcomings. We recognized that commercial genetic testing services often rely on proprietary databases and algorithms, which limit users' understanding of the predictions they receive. Additionally, we identified a lack of commercial offerings for longevity-related predictions, despite the growing interest in this area. As a result, we developed Just DNA-Seq to harness the wealth of information generously shared by the scientific community through open-source solutions.

On decentralization and privacy:

At the Longevity round, we focused on our core features and science done right. However, our results lack the scale and degrees of freedom decentralization provides. Right now, you either deploy everything on your hardware or somebody runs a centralized server for you (you can also play with our development server, but we do not provide guarantees).

We want to remove that restriction and enable personalized genomics for everybody, including users with limited time, hardware (esp. RAM), or technical skill and expertise. For this, we partner with Lab DAO ( https://labdao.xyz/ ) to enable the running of our scientific workflows on a decentralized infrastructure with the PLEx Lab Exchange platform. It offers an opportunity to close a gap between invested DIY enthusiasts who can deploy and maintain computational nodes for tokenized compensation and the average Joe who only want the results delivered and does not want to dive in deep.

We also partner with Genomics DAO ( https://genomes.io/ ) to allow running our OakVar modules inside secure privacy-preserving DNA vaults.

We need this funding round to finish those developments and extend our longevity reports with new data that emerged since our first Gitcoin funding round.