For far too long, rare disease patients and their guardians have had to wait “forever” for genetic information to be returned back to them. All of that is about to change: thanks to the convergence of mapping technologies and public genomic datasets, patients can now find other rare disease patients sharing the same mutations across the globe and research communities.
Recently, Muzaffar Anjum, whose son is inflicted with a rare genetic disease, approached me to learn more about the disease. Together we used genomic location data to convert his son’s genome into a map layer on the web. He made his son’s data available via this genome dashboard, mobile genome map (Figure 1), including – importantly – his exome data via federated JSON REST API. His accompanying request was clear: share this information widely along with his contact information“firstname.lastname@example.org” in the hope others will help analyze the data and direct him towards additional resources to help his son.
A step-wise approach towards building a patient-centric federated genome for a rare disease patient
We developed a three-step approach to achieve a federated patient-centric federated genome for rare disease genetic data as outlined here:
- Convert the genome into a federated web service: Upon the patient’s/guardian’s request the raw genomic data was submitted to a web service available via a REST API. This allows making the data available immediately to other researchers while remaining connected to the data source. There are lots of ways to create JSON web services. My favorite is the ESRI’s ArcGIS online earth mapping software because it’s built on a global federated location data infrastructure with existing human relationships between entities that successfully share health data (i.e., it’s the same platform used for John Hopkins Covid-19 dashboard). Earth mapping software can be converted into genome mapping software by making the background continents map layer transparent and using chromosome and position data to create points and lines for genetic markers that fit inside the coordinate system used to map the earth.
- Return a map of the patient’s genome to the patient/physician: Previously a patient’s raw data had little to no value, mostly because it was provided as a large zip file, which was not easy to engage with, especially as a patient/guardian. Our approach is different: by turning a patient’s genome into a map, we can let patients (and researchers/physicians) easily search for genes of interest in the same way we google maps to search for a city. Better yet, providing rare disease patients in a map format allows us to show the density of gene mutations at the entire genome level before ordering a bunch of expensive individual tests that might be returning reports for variants of unknown significance. One can easily envision how these interactive maps, containing dynamic information, have the potential to replace existing static PDFs, which often show outdated information. This would be of particular value for testing labs and genetic counselors when communicating genetic mutation information at the genome level to their patients/physicians as they begin their rare disease journey.
- Provide a list of the top ten gene clusters with links for gene-driven research: This is an opportunity to provide patients (and physicians) tools that allow them to engage with others using their own genome map. This can easily be achieved via introduction of a simple share button via the genome dashboard that includes the top ten gene clusters (based on the number of mutations) along with links to gene DNA guilds to help them find other patients with similar mutation clusters and move patient-driven research forward.
“Earth mapping software can be converted into genome mapping software by making the background continents map layer transparent and using chromosome and position data to create points and lines for genetic markers that fit inside the coordinate system used to map the earth.”
What the web does well is to establish fine-grain connectivity between persons (regardless of where they live on earth) based on specific content. In this context, the two most basic underlying data structures of the web are time stamps and location data with genomic data being location data. Extending this information with genomic location data would enable rare disease patients to find each other and self-organize at scale.
“The time of rare disease patients to passively wait for information is over.”
Alice Rathjen – enlightenbio Guest Blogger
Alice is the Co-founder of DNA compass which provides security and visualization for genetic data. DNA compass enable entities to have their own infrastructure for creating and publishing genomic maps. Their focus is on simple genome maps for customers embedded in their websites to help improve genomic literacy with a focus on rare disease.
Alice is passionate about innovation, mapping genomes, rare disease, and building regional genomics capacity.
Feel free to reach out to Alice Rathjen via email (email@example.com) or Twitter for additional information.