All posts by hk

About hk

Admin at Open Humans Foundation

Harvard PGP data in Action!

As an Open Humans member, we wanted to share some news and updates from one of our partner studies – the Harvard Personal Genome Project!

About Harvard PGP

The Harvard Personal Genome Project (or PGP) is, in many ways, the spiritual parent of the Open Humans project. The PGP began in 2005 with a proposal by George Church. Its mission is to advance personal genomic research – the study of everything in our DNA – through public data sharing. It hosts genomic and health data from thousands of participants who understand that their data, by its very nature, is potentially identifiable.

Interested in participating? You can sign up here:

Breaking the $1000 genome barrier!

This fall, Veritas debuted an offer for $1000 genome sequencing exclusive to Harvard PGP participants! The PGP’s resources are limited, and it has many more volunteers than it can sequence at the moment. Now participants have a faster way to get their genome in the hands of researchers: By getting a genome through Veritas, then donating it to the PGP and/or Open Humans.

Data visualization

Earlier this year, Abram Connelly developed an interactive tool called “Untap” to explore Harvard PGP data. Abram is a PGP participant, a member of the PGP staff, and a researcher at Curoverse, and he wanted to make the PGP data more accessible to all. His coworker Nancy Ouyang, also a PGP staff member, wrote a great summary of using Untap for the blog.

Genome interpretation

A community of genomic researchers called the Critical Assessment of Genome Interpretation (or “CAGI”) launched an experiment using PGP data. This experiment challenges researchers to match PGP participant genomes to health and trait profiles. The challenge is open until December 7th. CAGI is a great match for PGP data because the methods can be “open source”: both algorithms and data can be completely open and available to all.

Celebrating 10 years at GET

The PGP celebrated its 10th anniversary in September at the GET Global Conference in Vienna, Austria. “GET” stands for “Genomes Environments and Traits”, and the conferences are traditionally very participant-centric: the GET Labs events invite attendees to work with other research groups and were an inspiration for Open Humans. In 2015, GET went farther afield and was hosted by a PGP member site (Genom Austria), reaching out to the global community. Open Humans’ co-founder Madeleine Ball also spoke about data access and sharing as part of the session on Society. We’re looking forward to meeting participants – and Open Humans members – at the next GET Conference in Boston, in April 2016.

What We’re Reading

Be a part of GoViral’s third season!

October is not only the month of witches, vampires, zombies and pumpkin spice lattes…

It’s also the start of flu season –- and a great time to join the GoViral study!

GoViral is a study for testing viruses. Participants are sent kits and, when they get sick, can use these kits to collect and send in virus specimens. Both aggregate and individual results are returned: Find out what viruses were in your area – and which virus got you sick.

Entering its third year this season, the project is led by Rumi Chunara at New York University. GoViral is an Open Humans Research Partner, and we wanted to give you some updates on their work. The research has seen important progress so far. Back in 2013, Dr. Chunara wasn’t even sure whether participants could collect specimens at home and ship them to a lab in a timely manner without contamination. One of her first discoveries: They can! Check out the GoViral site for video demonstrations of how to collect saliva and nasal swabs – the whole process takes just a few minutes.

Due to this success, the GoViral team made further discoveries. For example, they discovered that they can detect viruses in samples taken as late as six days after symptoms first present themselves. This means that we all shed viruses – and therefore are contagious – for a longer period than most of us always assumed. So do your coworkers a favor and take that extra sick day from work!

By now, GoViral has processed over 500 specimens. What has been uncovered has largely corresponded with what is known from clinical data: Up to 20% of the population gets influenza each year and preventative measures – such as getting the flu vaccine and frequent hand-washing – are beneficial. The study has also shown, for the first time, a definitive concordance between nasal and saliva specimens. For more details, you can read the research report that the GoViral team published earlier this year: “Surveillance of Acute Respiratory Infections Using Community-Submitted Symptoms and Specimens for Molecular Diagnostic Testing”

GoViral continues to expand. One of the variables GoViral studies is geography, and in past seasons it has been concentrated on the Northeast United States. Whether it expands to new areas depends on how many people in that area sign up. Interested in having them join your area? Don’t just sign yourself up, let others know about it too!

The study is ongoing – and the more people involved, the richer the data.

Interested in contributing? Click here to join GoViral

What We’re Reading

What We’re Reading

What We’re Reading

What We’re Reading