The following is a guest post by Alan Oppenheimer. The Alan and Priscilla Oppenheimer Foundation seeks to advance humanity through scientific research and education and has been a long-time supporter of the Harvard Personal Genome Project. The views of this guest post, and responses from participants reported upon here, do not necessarily reflect the views of the Harvard Personal Genome Project. It is important to keep in mind that the Harvard Personal Genome Project study is not intended nor expected to help participants diagnose or improve personal health issues.
Following up on our previous blog post, here’s a quick summary of the results of the Harvard Personal Genome Project enrollee survey “What are you looking for in your genome, and how can we help you find it?” There were about 280 respondents.
The first questions were about the participant’s background. The “average” participant has been in PGP about 3 years, may or may not have donated a sample, is most interested in inherited disease risk, has 23andMe or FamilyTree/Ancestry DNA data, and is very computer savvy, reading articles/journals.
In terms of the key question in the title of the survey, participants would slightly prefer their genome analysis through either current tools like GET-Evidence and Promethease or an easy-to-use overview tool, versus raw data or a genome browser (see figure below). Primary important factors in exploring their genome include medical analysis and broad, flexible in-depth data, both slightly favored over ease-of-use and accessibility of an overview (and significantly favored over the ability to share/compare with family members).
The most interesting items from the survey were the comments, mainly in the free-form “What else would you like to tell us” question at the end (entered by about 1/3 of the respondents). Most prevalent of those were:
- “here’s what’s wrong with me that I’m hoping my genome will help me find/understand/fix” (which is thus the number one answer to the title of the survey)
- “I wish there was a blood collection event in my area.”
Thanks to everyone who took part. Our next step after this survey: decide on what tool(s) we here at the Oppenheimer Foundation should start building (or assisting the Personal Genome Project with) to best address the survey responses.
At the 2014 Get Conference, Robert Green described how medical genetics is being integrated into primary care, Michael Linderman spoke on how to prepare the next generation of genomicists, and Diana Bianchi presented on how prenatal screening using sequencing of cell-free fetal DNA is revolutionizing prenatal care. Afterwards, they were led in a moderated discussion by Boston Globe reporter Carolyn Johnson. Watch the video.
If a major goal of genomics research is to understand the underlying molecular causes of beneficial phenotypes, for purposes of promoting overall health in society, then perhaps sports, in many regards, can help facilitate this process. The canonical athletic phenotype, with highly desirable physical traits, may serve as a model for understanding optimal fitness. And certainly professional athletes, at the pinnacle of their respective sport, have tremendous social and economic influence by inspiring everyday athletes and fans alike to emulate their performances. Therefore, a deeper understanding (or at least discussion) of what makes an “elite” athlete, or who has the potential to become one, is warranted. With 99% percent of the human genome being identical, is it plausible to think we all have the inherent ability to become elite athletes? Or, do the remaining 30 million divergent nucleotides of our genetic code determine who can or cannot become an Olympian? At the annual Genes, Environment, and Traits (GET) conference, a sports genomics panel was held to discuss this provocative topic. Invited speakers were:
- David Epstein. Investigative reporter at ProPublica, former senior writer for Sports Illustrated, author of the New York Times best seller The Sports Gene.
- Heidi Rehm, PhD. Chief Lab Director at Partners’ Laboratory for Molecule Medicine, associate professor of Pathology at Brigham & Women’s Hospital, expert on genomic medicine & integrating genetic discovery into clinics
- Mark Gerstein, PhD. Professor of Bioinformatics at Yale University, expert in human genome mining & annotation, author on over 400 computational biology research publications.
- Jonathan Scheiman (moderator), a research fellow in the genomics laboratory of George Church, former Division I athlete, and NBA correspondent for an international radio show.
In a lively debate at the 2014 GET Conference – which included moments of scientific inquiry, levity, and moral contemplation – panelists engaged in discourse over the inheritability and trainability of athletic traits as well as selective pressure from society to enrich for performance phenotypes. Additional topics discussed included:
- Evolution of athletic body types
- Performance enhancing polymorphisms
- Genetic tests and specialization of athletes at a young age
- Genetic tests for ensuring athlete health – requisite or optional?
- Whole genome sequencing of elite athletes for beneficial allele discovery
- Professional athlete salaries vs. science funding – can we collaborate?!?
- Quantified self and advanced analytics in professional sports
- The future and potential of genomics in sports analytics
- Competition, fairness, and genetic engineering
Practice vs. genetics. Nature vs. nurture. A timeless debate, with a new quantitative spin from current cutting edge advances in next generation genomics technologies. Never before has society had access to such powerful tools to read and write DNA. And athletes, with a history of transcending sport, are as are as popular as ever in mainstream culture. Perhaps the next revolution in science will entail a sports star allowing us all to peak into their biological greatness. Scientists vs. athletes? Why? As the sports genomics panel at the GET conference displayed, these are two communities that stand to benefit from playing on the same team.
(special thanks to moderator Jonathan Scheiman for this written summary)
The following is a guest post from Alan and Priscilla Oppenheimer.
If you are enrolled in PGP Harvard, you probably received a recent email that mentioned a survey that we, the Alan & Priscilla Oppenheimer Foundation, are inviting you to take. We’d like to share more about who we are and why we’re inviting PGP Harvard participants to take this survey. Although this survey is limited to PGP Harvard participants, we invite others to keep reading. Big changes are ahead that will start affecting us all!
About our foundation
We are a small science-focused family foundation, started in 2007. We knew we were small, but we still wanted to think big. When we became aware of Dr. Church’s new Personal Genome Project, we realized that it provided a great opportunity for a foundation like ours to make a big difference. We felt quite privileged when Dr. Church and his team said we could work with them, helping out where we could.
A few of the areas in which we feel we have made a difference include:
- prototyping the current sequencing effort by sponsoring one of the first genomes beyond the original PGP 10
- creating the initial study guide which helped potential PGP participants learn about genomics and pass the entrance exam (a predecessor to the current one)
- helping out with a number of aspects of the GET conferences
- and, most recently, planning and putting together the current survey.
Our faith in the PGP in particular and personalized health in general has been validated through a number of recent developments, President Obama’s newly announced Precision Medicine initiative being the most visible. Also, as indicated in the recent email, it’s great to see that the PGP has been able to send out almost all submitted enrollee blood samples for sequencing, that the project has spread from Harvard to Canada, the UK, Austria, and beyond, and has spun off important related efforts such as Open Humans.
About our survey
As the cost of a complete human genome sequence falls towards the $1000 mark, and such sequencing begins to become commonplace, it’s now time to ask the gratifying but difficult question of “What’s next?”. For the foundation, the answer is related to understanding what our now-obtainable complete sequence means. Helping to address this question has always been an underlying goal of the PGP, but it is only with recent successes that we have been able to begin focusing on it.
The current survey is our attempt to understand the ways in which PGP enrollees (and by extension many others worldwide) want to try to learn about, explore and understand their genomes. With that data in hand we can then focus our limited resources on one or two key tools to aid in that exploration. If you’re enrolled in PGP, we’d thus very much appreciate your taking our 10-minute survey.
Thank you for your time and your interest in personal genomics.
Alan and Priscilla Oppenheimer
The Alan & Priscilla Oppenheimer Foundation
Some updates about PGP Harvard: (1) we’ve added a new feature to the website that allows participants to share their real name, and (2) we have more whole genomes on the way!
Our new “real name” feature
The Harvard Personal Genome Project has always emphasized that the genetic data our participants publicly share is “identifiable”. This means, even if you remove your name from the data, it’s possible for someone to determine your identity. Almost 4,000 people have enrolled knowing that privacy cannot be guaranteed, and many of them are proudly public about their data.
However, to an outside viewer, the data looks anonymous! PGP Harvard’s profiles have random identifiers (huID numbers). Even for the staff, we’re often unsure whether a participant considers their name to be publicly associated with the profile or not. Sometimes participants do things that seem to indicate they believe their information is public by including their real name in an upload, uploading a photograph, or mentioning their participant ID in another forum. Until now there has been no way for a participant to explicitly choose to associate their name with their data on our website .
We’d like the project to look less anonymous and we want to let participants be clear about when they consider their name to be a public fact associated with their data. So we’ve added to the website a feature that allows a participant to associate their real name. (This is based on their first and last name in our system, which they signed the consent form with.)
To share your real name as a PGP Harvard participant: (1) log in to your account on my.pgp-hms.org, (2) select “Public Profile” from the “Participate” menu, (3) edit the “Real Name” section at the top of this page. Here is a screenshot:
More genomes coming
In addition to providing the real names feature to PGP participants, we are also working on processing a new data set received from Complete Genomics, the company responsible for most of the sequencing done by PGP Harvard.
This data comes from around 200 blood samples collected in the past year and a half, including the 2013 GET conference. At this point the most of these genomes have been sequenced and are waiting to be analyzed and approved. We hope to start releasing these to participants soon.
Participants will have a 30- day period to review their data and decide whether or not to withdraw. For everyone that remains a participant, the data will then become public. We look forward to sharing this data and expanding our public resource!
 There are many participants that have publicly associated their names with their profiles, most notably the first ten participants in PGP Harvard (the “PGP-10″). However, these associations weren’t done within the participant website, but were done in other contexts (e.g. conferences, news articles, press releases, blog posts etc).
PGP Harvard is planning two more blood collection events. These events will take place in San Diego, CA on December 16, and in St. Louis, MO on December 29.
PGP Harvard participants who have completed the PGP Participant Survey and all twelve trait surveys are invited to apply to donate blood. Importantly, this event is NOT for those who already have a genome or gave blood at GET2013, GET2014, or at recent Boston or Mountain View collection events.
To apply, please log in to your participant account at my.pgp-hms.org and visit the San Diego collection event page or the St. Louis collection event page. You can complete surveys (or check if you’ve already done them) by visiting the trait surveys page.