Joining Open Humans

Note: Cross-posted from my original post at http://ruleofthirds.de/joining-open-humans/

I am more than delighted to announce that I will join Open Humans. Supported by a fellowship I will assume the role of Director of Research in November. Open Humans as a platform connects individuals who want to participate in research with research studies and projects that can be run by academic and “citizen” scientists alike. As I make this transition, I’d like to take the opportunity to reflect a bit on path into all things open* and what my vision for future is.

Digging into the old archives of my first (German language) science blog I find what must be my first public writing about Open Access back in April of 2009 and it’s been quite a ride since then. Back then I was a frustrated life sciences undergrad student, annoyed by not being able to read all the primary literature that sounded interesting enough to read. Frustrated enough even to run for state parliament on the platform of the Pirate Party in 2010, campaigning for both Open Access in the narrow sense and open access to education in the broader sense. While I ultimately didn’t end up in parliament, little did this to deter me from being more involved in opening up how research can be conducted. After moving on to doing a master’s degree in ecology and evolution it wouldn’t be too long before the next hobbyist open* project should start.

Only a year later, in the summer of 2011, Philipp Bayer and I started to work on openSNP, an open source repository that allows people from around the world to donate their genetic and phenotypic information into the public domain. Thanks to the magic of open source we were quickly joined by the ever talented Helge Rausch. Being frustrated was yet again a big driver in the process. Ironically, my frustration at that time was with the same people who started Open Humans. I wanted to donate my 23andMe data to its intellectual predecessor, the Personal Genome Project, only to discover that accepted donors had to be US citizens or residents. What else could one do in such a situation but start an alternative data repository, right? And ultimately our completely unfunded grassroots approach of “people just doing things in their spare time” did pay off: So far over 3,700 data sets have been donated through openSNP – making it the largest open* data source for personal genomics data. Along the way this work has led to many fun collaborations and interesting data uses, including work on the ethics of participant-led research, studies on genomic privacy, crowdsourced machine learning competitions based on genetic data and even art installations.

My own work in open* over the years has focused a lot on how to break down barriers to participation in research at large, be it in who’s getting access to publications, supporting people who want to start their own open* projects or evaluating how we can improve research by including participants more in the process. But while open science may be slowly winning in who is getting access to publications and data, there is still a long way to go when it comes to who will actually participate in doing research: For a large part research is still heavily confined to the realm of academia, with all the biases that this entails that lead to a growing divide between researchers and the “general public” at large. We need to take the next step in opening up science, this time to larger audiences, involving people much earlier in the research process, transforming “citizen science” into an endeavour that’s actually participatory and gives participants much more agency.

And to me Open Humans is doing just that: Offering a space that is open to everyone or – as Madeleine Ball put it so succinctly in her introductory blogpost as the Executive Director of the Open Humans Foundation – an empty garden with everyone of you being the gardeners. As such, Open Humans allows you to design and execute research projects, regardless of whether you are coming from Academia or not. I think the big success of the Quantified Self movement is testament to the wish of people to study themselves and do research. The great idea is that by increasing inclusivity we will all win. When academic and participant-led research come together – informing each other in the process – we will all end up with new and better research, asking more relevant questions and getting more satisfactory answers. So, if you have an interesting idea you would like to research, then please go ahead and give it a try!

Now that I just handed in my PhD thesis (obviously doing some meta-research on my thesis writing that’s fully in the spirit of Open Humans along the way), I want to put all of my energy into making the shift to more inclusive and grassroots-style research happen. This is made possible by Madeleine Ball, who has years of experience leading this field. She was not only instrumental in the success of the Personal Genome Project, but also co-founded Open Humans. She is herself a fellow of the Shuttleworth Foundation, and it is funding from this fellowship – along with her own co-investment! – that gives me the chance to fully pursue this. I am extremely grateful for this and her guidance will offer an excellent learning opportunity for me. I also have to thank Chris Mungall and the whole Berkeley Bioinformatics Open Source Project (BBOP) group for their great support. Through it I will be able to do all of this in a great and supportive environment at the Lawrence Berkeley National Lab. My role during the fellowship will be to help you tend to this garden in the best way possible, hopefully building many new collaborations, projects, studies and friendships along the way. So, let’s together get the democratization of science started.


A note on the term “citizen science”: The term sucks. Of course true inclusivity needs to mean that everyone – regardless of their immigration status – should be able to be an active agent in the research process. While I think that “participatory science” makes for an excellent replacement for the activity itself, I still struggle to find a replacement for “citizen scientist”.

Announcing Bastian joining Open Humans!

IMG_9708_editI am thrilled and honored to announce an expansion to the Open Humans team!

Bastian Greshake Tzovaras will join us starting November 1 as Director of Research at the Open Humans Foundation. He is funded by a fellowship from the Open Humans Foundation to support his work pursuing our shared vision of advancing citizen science and open approaches to health and human subjects research. Before Bastian starts, I’d like to to tell you more about him – even if you think you know him well!

To many Bastian is best known for openSNP, a project he co-founded in 2011 with Philipp Bayer – and joined soonafter by Helge Rausch. OpenSNP invites individuals to donate and publicly share their genetic data (e.g. from 23andMe and AncestryDNA). OpenSNP members can also contribute additional data, including crowd-sourced trait surveys. It is a community and platform that matches the themes of the Personal Genome Project and Open Humans.

I think OpenSNP has been an impressive success. On a small crowd-funded budget, Bastian, Philipp, and Helge helped more than 3,700 individuals to publicly share their genotyping data. I believe this is more publicly shared human genotyping data than all other projects combined!

Finding some way to join forces with Bastian seemed obvious and overdue. And so, I reached out. Because for Open Humans to succeed as a shared vision, it needs more than just me.

And as I got to know Bastian better, I realized how profoundly dedicated he is to broad and resonant themes – of personal data sharing, citizen science, participatory research, open access, and open science. He has published research about personal data sharing behavior, participant-led research, analyses of Sci-Hub usage, open peer review, and open science tools – in addition to his thesis work with lichen metagenomics! He serves on the committees for the Bioinformatics Open Source Conference (BOSC), OpenCon Berlin, and a FORCE11 workgroup. He has worked with with Mozilla Science Lab to mentor open science projects, run workshop sessions, and teach participatory/open science approaches. He attends, speaks, and presents at numerous events and meetings – BOSC, MozFest, Creative Commons, Sage Assembly, OpenCon, and more.

In summary, OpenSNP was just one facet of Bastian’s prolific and wide-ranging dedication to open approaches and social change in how we perform research. His vision matches that of Open Humans, and his strengths complement mine.

Bastian’s work with Open Humans will focus on the following areas: sustainable approaches for citizen science and patient-engaged research, collaborations and outreach for participatory research projects, mentorship and support for projects, and academic engagement via collaborations, publications, and meetings. I suspect he’ll get involved in almost everything, as his skills and interests are so diverse!

It is an honor to have Bastian joining Open Humans. I am eager for him to begin, and I look forward to his work with Open Humans in the coming year – and, if all goes well, years to come. Together we can endeavor to grow an open ecosystem – one that is thriving, sustained, and expands the world with something powerful and new.

Introducing myself as Executive Director.

Today is my first day as Executive Director of Open Humans Foundation. I am honored and thrilled to be taking the helm! As Open Humans co-founder I’m a familiar face, but I’d like to take this opportunity to re-introduce myself – and to share my vision.

How I got here probably begins with my love for creating and sharing knowledge.

As an early biotech graduate student, I stumbled into Wikipedia. I edited articles, created diagrams, and improved knowledge. Genetics was a theme: a reflection of my graduate work, and a topic I’d loved since high school. I gave the Genetics page a complete remodel – featured article in 2008! I helped One Laptop per Child create an offline Wikipedia for hundreds of thousands of children. I also created a page for my favorite mutation, a thing of history and beauty: Double-flowered.

This love for knowledge sharing – and for genetics – drew me, belatedly, to another project in the lab: George Church’s Personal Genome Project (PGP). (I was already in George’s lab. My thesis was mostly about DNA methylation.) George’s vision for the PGP was radical: open sourcing ourselves. He invited individuals to publicly share their genomes, health records, cell lines, and more. Participants took on strange, unknown risks. It was provocative and transgressive, and George had volunteered as its pilot participant: PGP #1.

In the years that followed, the Harvard PGP publicly released hundreds of genomes and enrolled thousands of participants. I became Director of Research for George’s project, and I was involved in every facet of operations. I created the project’s trait surveys, rewrote its entrance exam, fielded a multitude of inquiries, and helped organize sample collection events. I evaluated hundreds of genomes to create the “research reports” participants received, which explained the potential impact of variants in their genome. I was also first author on key papers for the project.

In addition, I became a liaison for the Harvard PGP and other projects that wished to work with it. When Jason Bobe expanded the GET Conference to add “GET Labs”, I was there as an interface between the researchers, the PGP, and the participants. My ongoing collaborations, through GET Labs and otherwise, have included American Gut (Rob Knight, UCSD), GoViral (Rumi Chunara, NYU), Critical Assessment of Genome Interpretation (Steven Brenner, UC Berkeley & John Moult, U of Maryland), the Personal Genomics Human Computer Interaction group (Orit Shaer, Wellesley & Oded Nov, NYU), and the PeopleSeq Consortium (Robert Green, Partners).

Through these, I started to see the bigger picture of what it means to study ourselves.

Genomes hold larger lessons. We have entered a world of data, where personal and meaningful information is being aggregated about us. But data sharing is foundering on privacy concerns. Silos of control have divorced individuals from their data, and reinforce a divide between the roles of participant and researcher.

This matters, because our data matters – it has the potential to make discoveries, to improve our health, and to empower us. But achieving these visions has begun to seem like an unreachable mirage.

By Michael Gwyther-Jones, CC-BY-SA.

I see a design problem. Our system for research was built in a pre-digital world. Open Humans is a redesign, restructuring how we aggregate data and perform research.

In Open Humans, individuals are the aggregators and data sharers.

And anyone can create a project on the site to work with members.

Projects can be citizen-led as well as traditional academic studies. Projects can provide data analysis tools, or can add new data. Data can come from anywhere – from research studies to third party APIs. A project can also invite members to share data broadly, e.g. in a “commons”, managed by a trusted entity. Researchers can build upon existing data streams. And studies can return their data – where it becomes a resource for personal discovery and future research.

It unlocks new opportunities for longitudinal research, for citizen science, for individual exploration, and for innovations that transcend any single study.

Our role is to be stewards: we have built an empty garden. You are its gardeners.

In this role, I hope you can trust us. Open Humans Foundation is a nonprofit, and my work as steward is supported by my Shuttleworth Foundation Fellowship. This funds me as an individual – and more – it grants me access to $250,000 in project funding each year. But for each $10 in project funding I seek from the Shuttleworth Foundation, I must give $1 of my own income. This is their bargain, and I’m taking it. I’m investing in this dream, and in this community garden.

What has grown already is full of serendipity and innovation. When we started, we seeded this with data we supported: genomic, microbiome, activity tracking, GPS. But now it grows beyond us. James Turner – a PGP participant – created an open source app to add Apple iOS “HealthKit” data. Continuous glucose monitor data has come from the Nightscout Project, a type 1 diabetes community. The Nightscout Foundation is creating a patient-led “data commons”. And Dana Lewis invites data donations from her own amazing community – the Open Artificial Pancreas System (OpenAPS) – and is bringing aggregated OpenAPS data to research teams at Stanford and Johns Hopkins. Newcomers wander in regularly now, bearing the seeds of nascent projects.

And so I invite you. Come, build. Plant your seeds – your data – your projects and ideas. Let’s grow something amazing together.

Announcing our new Executive Director: Madeleine Ball

A message from George Church, President of Open Humans Foundation Board of Directors, and Misha Angrist, John Cammack, Esther Dyson, Juan Enriquez, Steven Keating, and Michelle Meyer.

Photo of Madeleine Ball

On behalf of the Open Humans Foundation Board of Directors we are thrilled to announce a new Executive Director for the Open Humans Foundation: Madeleine Ball.

Madeleine Ball is co-founder of Open Humans, and our previous Director of Research. In recognition of her vision for opening human health data – and her talents in pursuing this vision – Madeleine was recently awarded a Shuttleworth Foundation Fellowship. We are thrilled with her recognition with this award, as it publicly confirmed what we privately knew: Madeleine is an enormously talented individual that balances thoughtful strategy with bold vision. We are confident that she will lead OHF to new innovations and achievements.

Our organization has undergone exciting changes in recent years, and we have had a rich history since our start. Founded by Jason Bobe and George Church in 2008, our organization was originally called “PersonalGenomes.org” to reflect its focus on George Church’s Personal Genome Project.

Jason, our organization’s co-founder and outgoing Executive Director, was pivotal in reifying George’s pioneering vision for open science, genomes, and health data. After helping to establish the Harvard Personal Genome Project (PGP), Jason set-up a global network including sites at Sick Kids Hospital in Toronto, Canada; University College London in the United Kingdom; and Center for Molecular Medicine in Vienna, Austria. Simultaneously, Jason’s support for the pilot PGP site – at George’s lab in Harvard Medical School – helped it achieve many noteworthy successes.

Jason organized the Harvard PGP’s study protocols, consents and operations, including an innovative quiz format for testing and improving understanding in the informed consent process. He also led the effort to integrate the Harvard PGP platform with Google Health (sadly discontinued), and, with Jason’s guidance, Harvard PGP was the first participatory study to adopt “Creative Commons Zero” for public domain human health data, releasing an unprecedented set of public genome and health data, cell lines, and official “genome reference material“, as well as sparking numerous ground-breaking papers.

In 2010, Jason’s work extended to the Genomes Environment and Traits conference (GET), an annual conference exploring the frontiers of understanding about human biology that uniquely brought together research participants and scientists to debate the technical, commercial, and societal impacts of advances in our ability to measure and understand people and their traits. (At the first conference, a dozen pioneers of personal genomes – like James Watson, Esther Dyson and Skip Gates – were interviewed by Robert Krulwich and Carl Zimmer, while a desktop DNA sequencer hummed away in the back, analyzing the microbial DNA extracted from a dollar bill donated by a conference participant.) In recent years, the conference itself became a laboratory: GET Labs invited attendees to participate directly with studies. This led to some interesting shared experiences – like armpit swabs, sampling face mites, and the sounds of sterile kit packaging being unwrapped in the restrooms stalls.

Most recently, in March 2015 Jason and Madeleine launched a new program, Open Humans, with support from the Robert Wood Johnson Foundation and the John S. and James L. Knight Foundation. Its transformative, participant-centered approach unlocks new opportunities for research – including longitudinal data aggregation and a cohort shared between studies. The success of this program led us to change the organization’s name to “Open Humans Foundation” in 2016. While we continue to support PGP and GET programs, we believed this new name would better reflect the organization’s overarching vision, as well as expressing our confidence in the Open Humans program itself.

Madeleine is expected to begin as Executive Director on June 1. We are sorry to see Jason leave the Executive Director position, as he shifts to focus more on his work with the Icahn Institute at Mount Sinai where he leads the Resilience Project and other cutting edge clinical research endeavors at the newly formed Institute for Next Generation Healthcare. Jason will continue his leadership of the organization by joining the Board of Directors later this year.

New GoViral website + get a prize for contributing!

ONE OF OUR FIRST PARTNERS HAS UNDERGONE A REBOOT!

GoViral.
Using crowdsourcing to track the spread of viruses.

Join now to help impact the future of public health.
If you haven’t been to their new site, check it out
– it went live in September 2016! –
and sign up

Join GoViral

BONUS:
Get a $5 Amazon gift card
if you are one of the first 1000 participants
to receive your flu test kit & fill in 4 weekly symptom surveys

 


Meet a GoViral Team Member

Ingrid Spielman is the research associate and data scientist who built GoViral’s new website.

Hope: Why did you think GoViral would benefit from having a new website? 14379714_10211042321037579_7715615894899053292_o (1)

Ingrid: GoViral, as it stood, had a website interface without any means to interact with users. The new site makes it easy for us to engage with participants. We can remind them to submit kits, and also show them more of the data they input in the form of cool, interactive visualizations.

Hope: Can you describe your typical workday?

Ingrid: While working on the website, I kept a detailed list of project goals. I took a certain amount of time to learn how to accomplish each goal, then went ahead and implemented it. Basically, it broke down to 40% search, 20% asking smart people for help, 40% trying … That adds up right? … If I had known exactly what we needed to do when I started, I bet this project would have happened much more quickly!

Hope: You received your Master’s in Material Science in 2012. What exactly is ‘material science’ and how does it relate to your current work?

Ingrid: It’s a multidisciplinary field where we look at material failure, and discover and engineer materials that have very specific and/or enhanced properties. By looking at how materials degrade over time due to stress, strain failure, or corrosion from sunlight or chemicals, we learn how to improve them. So you have people in material science who are engineering composites that are made up many types of materials – your shoes, for example. Others look at ways to use PTFE (poly tetra fluoro ethylene) – which most people know of as Gore-Tex – in clothing.

Some material scientists look at biomaterials specifically, and solve polymer problems – in which case they’re half chemist! They apply fundamental physics and chemistry to understand the properties of materials and how they change over time. Practical applications are solar cells – how we improve their efficiency – or building computers with smaller, more delicate circuits. They might discover alloys with interesting electronic properties or design lightweight materials that respond better under stress – think of carbon fiber bikes. Perhaps they build materials with interesting reflective properties – which would be considered metamaterials.

Basically, as my professor used to say and probably still does, everything boils down to a materials science question!

With my research-oriented background, GoViral was a natural fit. But I’m so lucky Rumi said I could work on the website. I had to learn most of everything I did for it from scratch!

Hope: Is there another project you’ve worked on that you found to be particularly interesting and/or fulfilling?

Ingrid: Before I decided to focus on data science, I worked in a microbiology lab where we studied how bacteria move and adhere to surfaces. In particular, we studied the bacteria that causes gonorrhea. I used a software called ‘matlab’ to build a user interface so students could easily upload videos of the bacteria, track them, and then find out how fast they moved and how much they were able to pull on the elastic surface they were sitting on. Data like this has implications for how we sterilize surfaces, and also how we treat bacterial infections – which is obviously very important!

Hope: On your LinkedIn page, you mention that you participate in triathlon racing. How did you get involved in this, and what makes it so enjoyable to you?

Ingrid: Cool that you looked! This summer, I did an olympic distance triathlon race at Lake George. I started triathlons while I was in graduate school. I love all three sports – swimming, biking, and running. On weekends, I go out to Coney Island to do laps and to Piermont for cycling trips. The cycling is by far the most fun of the three – if you like exploring and feeling wind in your face!

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

Ingrid: There are so many wristwatch tools for tracking health related things. I’d like to measure people’s gate (walking) by putting sensors in the soles of their shoes that could help improve both posture and running / walking techniques.

It would be cool to track insulin levels without actual blood samples. It will be great when the cost of sequencing is low enough that people can have in-home devices, and start measuring their gut microflora and skin microflora on a daily basis. If we also keep track of what we eat, this can probably lead to many discoveries in how foods affect our immune system and health.

Additionally, I’d like us to be able to track cortisol levels so we can see how stressed we are at any given point in time.

Hope: I bet lots of people would track that. Thanks, Ingrid!


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Your data is more powerful
when you’re a part of it!

Celebrating Two Years and 3,000 Members!

Pop the champagne…It’s time to celebrate!

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Open Humans is now a community of 3,000 members…And counting!


FREE STICKERS

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As a token of our gratitude for your participation, we’d like to send you an Open Humans sticker. You can put it on your laptop, phone, luggage — wherever you want (but preferably somewhere that others will see it and know you’re cool).

Get a sticker: Email your address to support@openhumans.org

Please note: This promotion is valid through March 2017 only.

THEN, NOW & NEXT

When we launched in March 2015, we envisioned a platform where participants could ‘open-source’ their body for science. We’ve evolved into a community of researchers, citizen scientists, and individuals whose embrace of open values has indeed enabled new types of scientific study and innovation:

  • James Turner created an open source iOS app that exports “Health” app data (aka HealthKit) to Open Humans

  • Alex Biel and Eric Hekler, PhD  used James Turner’s app as a data source and created a Pokemon Go study pilot to gain a better understanding of how games might influence physical activity

  • Open Humans and developers from the Nightscout Project (type 1 diabetes + open source) created a tool to upload data to the Open Humans platform so it can be easily shared with researchers

  • Dana Lewis is using the Open Humans platform to collect data from DIY artificial pancreas users and facilitate research in partnership with the DIY “closed loop” community

  • …And there’s more! We invite you to check out all of our activities here.

We remain fully committed to sharing data that is centered on our greatest resource: YOU. Open Humans’ future is bright, and our current research pipeline includes diverse projects being developed by academic and citizen scientists who study genomics, toxins, viruses, and more.

Together, we will transform the status quo in humans subjects research!

This is all possible because of you so…

THANK YOU VERY MUCH!

(And we hope you like the sticker.)

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Your data is more powerful
when you’re a part of it!

Have an iPhone or Android? You can join Keeping Pace!

Any smartphone user can now contribute to Keeping Pace!

Whether you’re a marathon runner or only like marathons involving ‘Law & Order’ and the Simpsons…You have valuable data to share.

keeping-pace

Keeping Pace analyzes activity-tracking data in order to understand how seasons and the environment influence movement patterns.

JOIN KEEPING PACE

Personal Sensor Data

Keeping Pace uses personal sensor data for its research. Along with data from the free download-4-39-20-pm Runkeeper app, it is now accepting data from the free Moves app

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  • Moves is an activity diary that passively tracks your movement and calories burned. Unlike other movement trackers, once installed on your smartphone, it runs all the time so you never have to remember to turn it on or off. 

JOIN AND CONNECT MOVES

Why use app-generated data?

  1. Participants have more control over their data.
  2. It’s cost-effective, so it’s sustainable over long periods.
  3. There’s no risk of “recall bias” ie. the mis-reporting that can happen when data is collected verbally.
  4. It makes it easy to focus on short timeframes and the impact of intra-city activities like street fairs, road closings, and snowstorms.

Through Keeping Pace,
your physical activity becomes a resource for the greater good.


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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.

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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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Love fermented foods? Hate them? Check out American Gut’s free new study!

amgut-logo-sticker   Fermented Foods Study

  • Why join?
    • It’s free and you do not have to be a current or former American Gut participant to join
    • You’ll get your gut microbiome profiled
  • What are fermented foods?
    • Yogurt, kefir, kimchi, kombucha, miso, sauerkraut, tempeh, pickles, and more
  • Requirements
    • Have a diet consisting of – or lacking – fermented foods (they need people in both groups!)
    • Must be <50 years of age
    • Must have a Body Mass Index >19 and < 30
    • Must not have taken antibiotics in the last year
    • Must have no history of IBD, IBS, or Diabetes
  • What you’ll do if you join
    • Once a week for a month, swab a used piece of toilet paper after going #2
    • Answer a survey with health and lifestyle questions

Interested?
Email Project Manager Embriette Hyde at ehyde@ucsd.edu

Holiday Exclusives & Gift Ideas

Searching for unique and memorable gifts?

We’ve collected options that teach people cool things about themselves…And produce data they can share!

SPECIAL OPPORTUNITIES FOR OPEN HUMANS MEMBERS

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Five Site Explorer Kit – $89 (~78% off regular price of $399)

  • Discover all the bacteria living in your mouth, nose, skin, genital AND gut microbiomes
  • Special offer for Open Humans – ‘5 sites for the price of 1’
  • Use discount code shared in our newsletter
  • Offer valid until Friday December 16 or while supplies last

detoxme
Detox Me Action Kit – $299

  • New crowdfunded study from the nonprofit Silent Spring Institute
  • Test your personal exposure to ten common household and environmental chemicals (e.g. bisphenol-A, aka “BPA”)
  • Get a personalized report comparing your results with others, including tips on how to reduce your exposures
  • Special bonus for Open Humans – they plan to return data to member accounts!

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Veritas myGenome Service – $899 (10% off regular price of $999)

  • Whole genome sequencing and health interpretation
  • Special bonus for Open Humans – they are opening their holiday special a week early for members! Use discount code shared in our newsletter
  • Offer valid until Saturday January 7 or while supplies last
  • NOTE: There is an additional $99 fee to receive your Variant Call Format (VCF) file. (You’ll need to contact support@veritasgenetics.com.) VCF raw data is needed for third-party interpretation and/or sharing on Open Humans.
OTHER HOLIDAY DEALS
AncestryDNA Test Kit – $89 (10% off regular price of $99)
  • DNA testing for family history
  • No special code required
  • Offer valid through December 14
Genos Whole Exome Sequencing – $374 (~6% off regular price of $399)
  • CLIA-compliant, 75x on-target coverage via a saliva spit sample
  • Analyzed with GATK best practices workflow
  • Download as a VCF file for sharing
  • Certified genetic counselors at preferred rate
  • 25% off select health-tracking products
  • 25% off your entire order through December 25 when you buy 2 or more devices
MORE GIFT IDEAS
23andMe Ancestry Service for $99 or Health+Ancestry Service for $199
American Gut Microbial Sampling Kit – $99
Fitbit health-tracking products, accessories, services and apparel (prices vary)

May you have a happy, healthy, and inspiring holiday season and New Year!
– The Open Humans team
Open Humans Foundation is a 501(c)(3) nonprofit organization. Contributions are welcome and tax-deductible to the extent permitted by law. You can also support us by shopping at AmazonSmile.
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