With Open Humans we are not only working to empower you to decide with whom to share your personal data – but also to explore your own data. With our latest project addition – the Personal Data Notebooks – we are taking a further step in that direction. Based on the increasingly popular Jupyter Notebooks they bring together data analysis code, documentation and data visualization. With the added twist that the Personal Data Notebooks also easily provide simple and private access to your personal data that is stored in Open Humans. Which not only makes it easy to write and use a data analysis – it also makes it easy to share your results without having to share your personal data with someone else. That way you can not only learn about yourself and your data, but also about how data analyses are performed.
If you want to write your own data analysis for the notebooks from scratch you can get started in Python, R or Julia. Or if you want to tweak or run existing data analysis you can use and adapt existing notebooks. In the simplest case you don’t even have to write/edit any code, as the input data are standardized according to their Open Humans data source. So for example you can easily run a Fitbit analysis notebook written by someone else right away on your own Fitbit data. To get you started we have a step-by-step guide on how to use the Personal Data Notebooks, along with a set of ready-to-use data analysis notebooks for Fitbit, Apple Health,Moves, 23andMeand Twitter archive data.
Full vote tallies of the community election were as follows: Dana M Lewis (92), Alexander (Sasha) Wait Zaranek (60), Embriette Hyde (53), James M Turner (33), Katarzyna Wac (28), Richard Sprague (23), Chris Gorgolewski (16)
We are also thrilled to introduce two new board-elected directors!
Board-elected Seat: James Turner
James is one of the earliest and most active members of the Open Humans community, and has been profiled on our blog as well! Having joined through participation in the Personal Genome Project, James went on to create some of the first projects in our site – including an Apple Health import app that has been used in downstream academic research. In addition to his long commitment to this community, James brings valuable practical experience in managing nonprofit organizations, having created and managed his own charitable 501(c)3 for several years.
Board-elected Seat: Chris Gorgolewski
Chris is an academic in the field of neuroscience, interested in expanding the use of Open Humans among traditional researchers. Chris has promoted neurological research data sharing through his work with Neurovault, OpenNeuro, and reusable data sharing language for consent forms. Chris brings to the board a new facet of research, and an interest in promoting the use of Open Humans in studies — including the return of valuable data to participants to enable both individual access as well as re-use in new research.
Finally, I want to thank the candidates who volunteered to become members of our board. Candidates took time to communicate with us and with the community, and we are honored by the visions you shared with us. There were more excellent candidates than we had seats to fill! But there will be seats again, and we hope you continue to be part of Open Humans as some of our most brilliant members, colleagues, and advocates.
At our annual meeting on March 26, two board-elected seats will be determined from these candidates. And following this, members of Open Humans will be invited to elect the third “community” seat! We invite you to learn more about the candidates by reading the introductions and further links below.
I am a national nonprofit leader, educator and researcher. I bring a
fascination for the applications of computation in biology –
through both bioinformatics and digital health to a an
My experiences range from leading companies, serving on institutional
steering committees, designing university coursework, creating
research experiences and influencing educational policy.
My vision for Open Humans is for it to also be used as a tool used by
other institutions to expose graduate students, underclassmen and
K-12 students alike to participatory methods of initiating and
conducting collaborative computational research.
I have always had a passion for science, especially genetics. I ended up in software instead, but have continued to follow the field as an adult. I joined the Personal Genome Project in January 2011, and have been an activate participant ever since.
I organized and ran the PGP Participant’s Forum. I have also created several tools for the Open Humans API, including the HealthKit Uploader app.
I also have a second career as a freelance writer. I have written for publications such as the Christian Science Monitor, and have also written 3 books on software development. I also am the president and chairman of the board of a 501(c)3 public charity that has raised over $250,000 for cancer research, among other causes.
I think that I could leverage both my experience in journalism and in fundraising to assist the board in it’s duties. I would like to see OH work to expand the number of participants with active datasets so that the statistical power of the data would be increased.
I am passionate about open source and open science efforts. I’m one of the creators and the first users of an open source artificial pancreas (e.g. hybrid closed loop) system to make life with type 1 diabetes easier. My skillset ranges from non-traditional technical skills to communication and strategy. I’m dedicated to taking what we’ve learned in the diabetes community & sharing these lessons learned with all communities. To that end, I’m also a RWJF grant-funded principal investigator, studying the processes of patient-driven and patient-led innovation research, with goals around scaling effective processes and collaborations between traditional and ‘new’ stakeholders. I’ve used OpenHumans for ~2 years now, and believe it plays an integral role in enabling individuals to share data and facilitate new research efforts. My vision is to help support and scale the organization to continue to meet the needs of these new stakeholders and communities.
I am an entrepreneur, open source advocate, and PGP participant. My interest in open humans centers around the profound impact of genetics on our future as a species. As a board member of the Human Rights Foundation, and with organizations in life and health insurance, I am also deeply interested in the societal impact of sharing information which may allow third parties to predict our traits available in the public domain. I believe my primary contribution, aside from experience in board governance, would be to offer the board due diligence capacities in better understanding these risks and opportunities and communicating them to external stakeholders in stewardship of the foundation. More details and background are available on my website.
I am head of quantified biology at Veritas Genetics, the first company to introduce whole genome sequencing and interpretation to consumers and their physicians for under $1,000. My current research is focused on the delivery of real-time, biomedical insights from massive data sets, spanning millions of individuals across collaborating organizations, eventually encompassing exabytes of data. I am also a co-founder of the Harvard Personal Genome Project.
My hope is that Open Humans becomes a central, global hub for participatory research and participant led data sharing much as Wikipedia has become a hub for sharing facts. Specifically, I will use my relationships with the Global Alliance for Genomics and Health (GA4GH), the NIH data commons pilot, the NIST “Genome In a Bottle” reference material consortium, and the global Personal Genome Project (PGP) organizations to further the integration of Open Humans with other local, national and international biomedical data sharing efforts.
My passion for sharing science with the public started in graduate school, when I realized that scientists do a bad job of explaining their work to the broader community. This is critical — public perception of science has downstream effects on funding. A major roadblock is a misunderstanding of the scientific process and timeline. Citizen science projects help fill this knowledge gap by giving people the opportunity to contribute to science and experience it first hand. One of my most fulfilling experiences was managing the American Gut Project, which is part of Open Humans. Open Humans encourages people to support citizen science, and the dataset integration it promotes is critical for making precision medicine a reality in healthcare. My vision for Open Humans includes establishing educational efforts such as more regular and varied blog posts, short video blogs, and online courses — including a hands-on course on how to interpret scientific papers.
For decades, I’ve managed consumer-focused software products at places like Apple, Microsoft, and numerous startups because I believe technology is a great equalizer, transforming society by putting powerful computing tools within the reach of everyone. An early and active fan of OpenHumans, I think science too can be transformed if we make personal health and self-tracking data openly accessible to all curious people.
Like most OpenHumans users, my background is outside the world of professional science or academia. As a former product developer, big company exec, and entrepreneur, I want OpenHumans to appeal to all ranges of expertise, in every part of the world, because the ability to do science shouldn’t depend on your background or your current skill level. To do this, I’d like to help OpenHumans (1) improve its visibility through world-class marketing and promotion, (2) expand internationally and (3) remain the best place for sharing, exploring, and analyzing humans.
Katarzyna Wac is an Associate Professor of Computer Science at University of Copenhagen (DK) University of Geneva (CH), affiliated with Stanford University. Her research appears in more than 100 to date peer reviewed proceedings and journals in computer science, human-computer interaction and health informatics. She is a (co)-PI in several European, Swiss and Stanford Medicine projects. Dr. Wac leads Quality of Life Technologies lab researching how emerging sensor/actuator-based mobile and wearable technologies can be leveraged for a personalized assessment of the individual’s behavior and Quality of Life (QoL), as they unfold naturally over time and in context, and improvement of the latter. The vision for Open Humans is to enable individual’s short-term behavior and long-term QoL assessment and improvement based on the crowdsourced efforts of the donors, social and behavioral, as well as data scientists and practitioners leveraging the results for better QoL-enabling services.
My life’s mission is to accelerate the progress of science by making as much data accessible to as many researchers as possible. Most of my work has focused on brain imaging data. I built a platform for sharing results of neuroimaging experiments (https://NeuroVault.org), as well as one for sharing raw neuroimaging data (https://OpenNeuro.org – formerly known as OpenfMRI). I have also been promoting ethical data sharing by providing ready to use text for participant content forms (http://open-brain-consent.readthedocs.io/en/latest/ultimate.html). I would work with the Open Humans Foundation to help integrate it with existing open neuroimaging databases and getting their participants involved in additional follow-up data collection via the Open Humans platform.
I have been involved in the world of bioinformatics for decades. I have a master’s degree in Medical AI. Most of my work experience has been in bioinformatics rather than medical informatics, but I would love to get involved with something more directly relevant to health.
I have chaired BOSC (the Bioinformatics Open Source Conference) for the last 8 years. Under my leadership, BOSC has flourished and become more diverse in both content and attendance. I am also a board member for the Open Bioinformatics Foundation.
In addition to helping OHF communicate using social media and other online mechanisms, I’d like to help organize events to bring OHF community members together to exchange ideas and meet face-to-face.
This might uncover reports about to rare variants with potentially dramatic effects: people typically carry several “recessive diseases”, and this report might uncover some of yours. But it might also uncover mistakes in the literature! Research is messy, and so is this. To help everyone sort through the evidence, Genevieve also invites users to edit collaborative notes regarding reported effects.
As such, the tool is not a clinical tool, no more than Wikipedia is! It’s open source, freely shared, and intended for collaborative learning. It’s my own personal project – and I’ve extended it to enable private data analysis, and empower more folks to explore their data.
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.
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.
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.
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.
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.
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?
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!
Open Humans is now a community of 3,000 members…And counting!
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).
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:
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!
Keeping Pace uses personal sensor data for its research. Along with data from the free Runkeeper app, it is now accepting data from the free Moves app
Movesis 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.
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!
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: 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?
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?
Hope: What is Seeq’s relationship with the New York Genome Center?
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.
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.
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?
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?
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.