Start a human genomics project with a few lines of code
This post is by Tomaz Berisa and Joe Pickrell.
Here they are (in python, after installing the open source seeq package):
Since Seeq launched a few months ago, we have heard one word loud and clear: sharing. Users have asked us how they can share their data with different projects, and researchers have asked us how they can recruit research participants through Seeq. We’ve heard you.
We started out by making it easy for users to access their raw data. Today, we’re announcing a set of features that allow users to easily share their data with projects outside of Seeq. We’re calling it Seeq Research [1].
In this post, we want to explain our motivation for building these tools, and describe how they can be used from the perspective of a researcher and a Seeq user.
Why?
Fundamentally, human genomics research requires large numbers of people in order to make progress. For example, a landmark study of the genetics of schizophrenia involved around 150,000 participants.
To a new researcher, these numbers are daunting — if you lead a five-person lab that studies schizophrenia, you likely don’t have the money or time to run a 100,000 person study. And even if you did, where would you find 100,000 people?
Further, even if I were excited to participate in your hypothetical study, it’s inconvenient for me to get involved. For one, I probably don’t live anywhere near your lab. And if I do, the simple fact is I’m probably not going to take a day off of work just to help you out.
These problems — a researcher with limited resources who wants to interact with many participants, and participants who are geographically-distributed and pressed for time — immediately suggest a simple solution: human genomics studies should be set up and run on the Internet. So let’s build the infrastructure to make that possible.
For researchers
If you’re a researcher, you can start collecting genomic data by creating a website like this:
When a user clicks on the “Participate with Seeq” link, the Seeq app is opened and the user is asked to confirm their participation. If the user does not have the app installed (or is not on their phone), they are taken to a web app to confirm their participation.
Once a user agrees to participate in the study, the researcher gains access to their genomic data when it becomes available.
We’ve published instructions and code for the above website in a public repository here. Of course, this is a simple example; larger studies will probably want to integrate this into an existing website or mobile app.
If you have questions about integration or need help getting set up, feel free to reach out to support@seeq.io and we will do our best to get you up and running ASAP!
For participants
If you’re a Seeq user, we aimed to make it easy for you to control how your data is used. If there’s a new study you’re interested in, joining should be a couple of taps on a smartphone.
To enable this, once you click on a researcher’s link, you can review details about who is requesting access to your data and what they plan on doing with it, and confirm your participation (see example screenshot below). If you change your mind, you can flip a switch in the app to revoke access to your data [2].
Our hope is that infrastructure like this can enable a new generation of human genomics studies, where disease communities or social networks can collectively pool their data to drive new discoveries.
We look forward to hearing your feedback!
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[1] Though this is called Seeq “Research” because the first use cases will be in the context of scientific studies, this isn’t just for researchers. For example, if you’re a developer interested in building an app or a feature using genomic data, you could use this API as well.
[2] Note, however, that if you revoke access, this means that the researcher can no longer access your Seeq data from that moment on. If they’ve already accessed it (and thus presumably have a copy of it) and you would like them to no longer use your data for research, they should have a mechanism set up to allow you to opt out. If they do not, let us know and we will completely remove their study’s access to Seeq.
