building a platform to accelerate kidney disease research
Goldfinch Bio is a leading biotech company that is conducting critical research to discover precision therapies for patients with kidney disease. They are collecting samples from affected patients, sequencing them, and enrolling them into a Kidney Genome Atlas (KGA) to build a data set large enough that the company can use statistical methods to identify potential drug targets with genetic evidence. Together with Dept, we built a dynamic web-based application that allowed them to surface all of the data they were collecting and producing as part of the KGA. This allows their researchers to simplify their complex workflows and create efficient data visualizations which enables them to do better work, faster.
Accelerating the company’s growth to further kidney disease research
Chronic kidney disease (CKD) is a growing health epidemic affecting an estimated 37 million people in the U.S. Given this large number, there is a fast-growing need for new treatment options to help this underserved patient population. Goldfinch Bio is focused on discovering and developing precision therapies for patients with kidney disease. We partnered together to accelerate the company’s innovative approach to kidney disease treatment by automating the processing of large scale genomic and longitudinal patient data, streamlining complex workflows while reducing repetitive tasks.
automating the processing of large scale patient data
Creating a holistic, interconnected system
Goldfinch researchers and computational biologists were operating under a highly complex, disconnected workflow in order to be able to receive, process, and analyze a massive amount of data coming from various sources, such as analyzed biopsies, tests, patient samples, etc. Goldfinch had multiple systems and software suites being used to look at the data, compare cohorts and test compounds in the lab. The company needed a way to create connective tissue between systems to be able to quickly go from curating to examining to validating their data.
To solve this problem, we started off by kicking off the project with a design sprint and rapidly moved into development while conducting extensive user research amongst Goldfinch’s biologists and medical researchers. We did this to better understand their workflow and what they needed from the data. This enabled us to clearly articulate the workflows that were needed for each team. We moved toward a vision of creating a software platform that could connect disparate workflows with visualizations that would make each team’s work quicker.
We quickly built a prototype of the platform so we could begin testing and iterating based on feedback from the research team. We learned that the interconnectedness of the platform was enabling the researchers and the biologists to take data, examine it, and be confident in what they found, all in a much more efficient way. This was crucial, as it allowed the team to move faster in pursuing which gene mutations they wanted to pursue further research on. From there, the prototype evolved into a powerful software application with a tremendous set of features and visualizations for the Goldfinch team.
Three environments wrapped in one application
The result? Three distinct environments for development, staging, and production of the overall application. We used a simple storage service (Amazon S3) that talks to an API which is built on a mostly serverless stack in AWS. Backing the API is an event-driven pipeline that produces everything the app needs on-demand. Therefore, this means that when someone uploads a new study from the app, the pipeline is kicked off. The data presented to users is derived from petabytes of raw data. This data is processed, refined, and distilled to a much smaller, more manageable data set. It is also supplemented, enriched, and annotated with public data to try to give the end-users everything they need to better understand the genetic drivers of kidney disease and identify potential new drug targets that will help these patients that so desperately need new treatments. In short, this enabled the company’s various researchers to work in a more efficient manner while unearthing important patterns that will inform further research.
Enhancing the company’s innovative approach
Goldfinch’s vision is to eradicate kidney disease through precision medicine. The ability to evaluate large amounts of data, automate processes with technology, and ultimately speed up their workflow is a big deal in reaching that vision. With our help, the company is able to work more efficiently by doing less manual work and easily see complex data visualizations through the platform that would have previously required third-party tools and manual efforts to pull together. These visualizations allow the team to unearth important patterns that will inform further research and ultimately treatment in the future.