Spotlight on an Activity – Seeq

Open Humans is excited to announce our newest activity: Seeq, a phone app and sequencing study that helps people learn about their ancestry and microbiome. Seeq participants can now add and share their data in Open Humans!

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CLICK HERE TO CONNECT SEEQ 
Download their FREE app, order a $50 saliva kit!

 

Last week, I spoke to Joe Pickrell, PhD, geneticist at the New York Genome Center and co-founder of Seeq, about this venture, the future of genomics and microbiome research, and more.

Hope: What makes Seeq a unique way for people to learn about themselves?  joe_v1

Joe: I think of genome sequencing as this amazingly powerful microscope that we’re just figuring out how to use. We’re one of the only places where people can actually turn this microscope on themselves.

Right now, we give people a look back at their past with their ancestry, and at their current environmental surroundings with their microbiome.

But we also give people their own data, and the data itself contain much more information than that–in principle, there’s information on mutations that have arisen recently in your blood (DNA from saliva is mostly from white blood cells), traits you may pass on to your children, and more.

We’re constantly looking for ways to give participants more back, and we hope people will come up with things we haven’t even thought of ourselves.

Hope: Why did you want to partner with Open Humans?

Joe: I’ve been a part of Open Humans since the beginning! I think I joined at the time when the only connection was to PGP data (my profile: https://www.openhumans.org/member/joepickrell/).

Overall, I think there’s potential to completely change the way genomics research is done, using the Internet and cheap sequencing to empower different communities–disease communities, social networks, and so on–to collectively decide they would like to pool their data to solve major scientific problems.

Building up the infrastructure to make this work is seriously non-trivial, and it’s going to take a lot of experimentation with different models to get it right.

Open Humans is a neat model, and it seems like there’s a great community of people who share this type of vision. So it’s exciting to get a chance to be a part of it, and hopefully we can provide some data and tools that are useful.

Hope: What are you trying to learn from the genetic data Seeq collects?

Joe: We are collecting questionnaire information to go along with the genetic data, and have a whole bunch of analyses going on.

A couple questions I’m particularly interested in now are: are the microbes in your mouth associated with psychological phenotypes like your personality? And: how do genetic and environmental factors interact to influence human lifespan?

On this latter question, we’ve published some work in other large cohorts (http://biorxiv.org/content/early/2016/11/10/085969) but it will be really useful to have sequencing data from Seeq.

Hope: What is Seeq’s relationship with the New York Genome Center? nygenomelogo-color2

Joe: This project is run out of my lab, which is part of the New York Genome Center.

Hope: How do most of your participants find out about Seeq?

Joe: There’s a social aspect to Seeq–if you add someone as a friend, you can compare your ancestry and microbiomes, and see what the ancestry of your (hypothetical) child is likely to be. So the majority of people get to Seeq through social connections to existing users–initially this was just people that the three of us know (Seeq is run by myself, Tomaz Berisa, and Kaja Wasik), but now this has expanded considerably as we’ve gotten into the thousands of users.

Hope: Do you have a favorite story that you can share about someone who has been sequenced by Seeq?

Joe: In our microbiome reports, we also report other things (mostly food) that we see DNA from in your mouth.

imagesdog
Credit: flickr.bairdphotos.com

We’ve had a few people contact us a bit confused, wondering why “dog” showed up in their list of results. To be clear, we don’t think people are unknowingly eating dog! In most cases, these are people that live with dogs, so it’s probable that dog hair or something is in their mouth sometimes. In a couple of cases though, we’re not totally sure what’s going on.

Hope: What made you want to study genetics?

Joe: I’ve always been intrigued by what makes people see the world differently–sometimes literally, in the sense of how colorblind people see colors in a different way, and sometimes more figuratively, in the sense of how people with different personalities respond differently to stress.

We know that some of this variation is due to genetics, and genetics is currently tractable–that is, we now have the tools to tell people they see colors differently (maybe people don’t realize this until they’re relatively old) or respond to foods differently, and the tools to discover part of the reason people vary in their personalities.

So it’s a really exciting time, and frankly I just stumbled into it because I thought the topic was cool. I’ve been lucky in that it was the right time to do it.

Hope: What genetic, microbiome, or genomic discovery has surprised you the most?

Joe: Probably the most surprises in genomics recently have come from studies of ancient DNA. We now know that, for example, people in Europe today are descended from a mix of populations that existed a few thousand years ago–some related to European hunter-gatherers, some related to Middle Eastern farmers, and some related to population who were living in Siberia (see e.g. http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html).

The standard view in population genetics was basically that Europeans today are descended from the people who were there 10,000 years ago, so it was really surprising to me to see that the populations we call “European” in some genetic sense didn’t exist until recently.

This sort of dynamic seems to have been common across the world in recent history, I’ve written a bit about it here: http://genetics.med.harvard.edu/reichlab/Reich_Lab/Welcome_files/PIIS0168952514001206.pdf

Hope: What questions do you expect genomics and microbiome research to be able to answer in the next decade?

Joe: On the genomics side, it’s going to be possible to tell you what makes you and your family unique–we’re going to find the rare genetic variants that cause your family members to have early-onset heart disease, or why you and your dad happily sleep only four hours a night, or (on a more trivial note) why you and your mom burp when you yawn (no joke! https://www.reddit.com/r/NoStupidQuestions/comments/2lgjht/i_always_burpmake_a_burp_like_sound_when_i_yawn/). This is because the technology needed for this (genome sequencing) is only now cheap enough to get to the sample sizes necessary for these types of study. 

On the microbiome side, in ten years I’d hope we’ll figure out what the hell it means. There’s a lot of hype about microbiome research, but there’s a fundamental problem in that the microbiome is like any other epidemiological variable–it changes in response to your environment in a way the genome doesn’t. So when you see a study that says “Presence of microbe X is associated with obesity”, it’s hard to know if the microbe causes obesity, obese people are a better host for the microbe, or whether it’s just that obese people tend to have a diet that’s favorable to the microbe. These sorts of issues are really hard to tease apart, but I do think it’s a tractable problem.

Hope: How do you foresee engaged, data-sharing participants will impact research? open-humans-network-hand-300x300

Joe: I think this has the potential to completely change the way research in some fields is conducted. Specifically, the power to decide which research questions are “important” lies with the people who collect and fund data collection, and this is a fairly small number of people.

Once everyone has access to their own data, there’s the potential for a huge influx of new ideas and approaches and really exciting things can happen. But this is not a foregone conclusion, people have been saying this for years and it hasn’t really happened yet. There’s a lot of work that needs to be done on building infrastructure, making participation fun, and more. We hope to play a role in this, and it’s why I’ve been a member of Open Humans as well.

Hope: Do you do any regular health tracking?

Joe: I don’t.

Hope: Have you changed any of your lifestyle or dietary habits due to the information you’ve received from sequencing or health tracking?

people-scifaculty-pickrell1Joe: Not on a day-to-day basis, but finding out I’m an APOE4 heterozygote (discussed here: http://genomesunzipped.org/2011/07/visualizing-the-impact-of-apoe4-on-ageing.php) has motivated me to be more interested in the genetics of Alzheimer’s disease. That result and blog post ended up motivating the research I mentioned earlier (http://biorxiv.org/content/early/2016/11/10/085969).

Hope: What health-tracking technology do you wish existed?

Joe: One thing that would be really useful is a real-time measurement of your immune system–maybe a wearable that monitored expression levels of some important immune genes. Then if you saw some particular marker spiking, you might be able to say “Uh oh, that guy who sneezed on me in the subway had a bacterial infection, time to start a course of antibiotics”, or “Something I just ate seems to be triggering an autoimmune reaction, maybe I should talk to my doctor”, or things like that. Obviously it’s currently impossible to make these measurement non-invasively, but in the long term who knows.

To read Joe’s interview with Madeleine Ball, cofounder of Open Humans, CLICK HERE to go to Seeq’s blog.

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