Labs

Many Personal Genome Project (PGP) participants attend the GET Conference each year. These individuals include some of the most well-characterized humans on earth. An increasing number of research groups are organizing phenotyping sessions, specimen collection, recruitment booths, information sessions, workshops and other activities at the GET Conference to take advantage of this special opportunity.

• Brain Genomics Superstruct Project Gsp
  

  The goal of the Brain Genomics Superstruct Project (GSP) is to enable large-scale exploration of how genes affect the brain and the role they may play in brain development, structure and function. Specifically, we study questions related to the brain and diseases of the brain; for example, what causes, helps prevent, treat, or cure a disease, and how it may be passed on in families. To probe such questions, the GSP has built a data repository over the last 3 years of structural and functional MRI scans linked to genetic information from over 3,000 healthy individuals. This repository will be made widely available to researchers across the research community and is structured to enable targeted as well as exploratory analyses. Understanding the genetic underpinnings of normal brain variation will illuminate human nature; understanding genetic risk factors for brain disorders will shed light on neuropsychiatric, neurologic and other diseases with tremendous emotional and financial costs.

  This research is being conducted by the laboratory of Dr. Randy L. Buckner at the Center for Brain Science, Harvard University, Cambridge MA. In order to measure brain activity, you will be asked to lie inside a magnetic resonance (MR) scanner so that images of your brain can be obtained. You will also be asked to provide a saliva sample. We anticipate your appointment lasting approximately 1.5 hours including approximately 40 minutes in the scanner and twenty minutes of questionnaires. You will receive payment of $25 per hour for the scan and saliva sample and compensation for travel expenses. In addition, we offer an optional computer based take-home portion of the study, which can be done at home and will take approximately three hours. You will receive an additional $60 for completing this portion. If you would like to volunteer or if you have questions about the study, you may contact the project coordinator Marisa Hollinshead by email: mhollins@wjh.harvard.edu or phone: 617-496-7039. Please plan on scheduling your appointment by April 15th. Download the flyer (PDF)

  

• Circles In Human Biology The Areola
  

  The age of personalized genomics offers an unprecedented chance to understand the biology of uniquely human traits. One interesting and understudied human-specific trait is the areola, a circle of specialized, pigmented skin surrounding the human nipple. Areolas have been proposed to play an intriguing role in human evolution; differences in areola morphology have been linked to sexual attractiveness, nursing behavior, and infant weight gain. Developmentally, circular markings have a simple genetic architecture, making the areola both an interesting and a practical case study into the genetic underpinnings of distinctively human traits.

  The Tabin Laboratory at Harvard Medical School invites all PGP participants (both male and female) to join us in our effort to learn about the causes and consequences of diversity in the human areola. Our goal is to identify the genes responsible for variation in the appearance and glandular structure of the areola. Participation takes place in two parts. First, participants will fill out an online survey about health factors that could influence areola appearance, including weight, parity and breastfeeding history, hormonal status, etc. Next, participants will perform a breast and areola self-characterization wherein they will take measurements and photographs of their areolas (self-characterization can be performed at home). Measurements and images will be uploaded to our secure server for analysis. All results will be made available to participants at the conclusion of the study.

  Please visit us at the 2013 GET Conference to pick up your areola self-characterization kit and to learn more about the fascinating human areola.

  

• Diy Physiological Sensors Towards The Arduino Of Physiology
  

  Technologies for rudimentary physiological sensing are becoming cheaper and easier to implement, leading to a proliferation of start-ups in the quantified self and body sensor spaces. To accelerate progress, we are developing well-documented open-source hardware and software platforms to enable the integration and customization of multiple sensing modalities for long-term monitoring. We will present a functional open source EKG which can be adapted for EEG or EMG measurements, as well as early prototypes of a BlueTooth compatible Bio-Glasses (www.bioglasses.org) platform that integrates three or more physiological sensors, as well as motion monitoring, into a pair of glasses. These systems are fully open and are designed allow creative modification by non-engineers.

  

• Exploring Personal Genomics
  

  Rapid advances in high-throughput genome sequencing technologies foreshadow a near-future in which millions of individuals will gain affordable access to their complete genome sequence. This promises to offer unprecedented insights into the fundamental biological nature of ourselves and our species: where we came from, how we begin our lives, how we develop and grow, how we interact with our environment, how we get sick, how we get well, and how we age. Personal genomics is an essential component of the inevitable transition towards personalized and participatory health and medicine.

  This workshop explores a novel, inquiry-based approach to understanding and interpretation of the practical, medical, physiological, and societal aspects of personal genomic information. Participants will gain an understanding of the biology of human genomes, information on how to obtain and understand digital representations of personal genomic data, tools and techniques for exploring the personal genomics of ancestry and genealogy, discovery and interpretation of genetic trait associations, and the role of personal genomics in drug response. Participants will also explore advanced topics in personal genome analysis, such as drawing connections between a personal genome and the environment, connecting DNA to physiology, and assessing rare variants. Participants are encouraged to bring their own personal genomic information, as the instructors will demonstrate specific examples using the interpretome platform (http://www.interpretome.com) and other freely available tools for exploring personal genomes.

  

• Flu Near You
  

  Although the value of self-report systems such as Flu Near You have been demonstrated to engage individuals in the importance of influenza surveillance, enable them to access real-time information about what is directly happening in their community, and to generate detailed information about influenza risk for populations, none of the platforms have employed molecular techniques to rapidly verify the intelligence data garnered. Our goal is to enable Flu Near You participants who are willing to also provide samples for viral confirmation, to validate symptomatic reports as well as enable a better understanding of the representativeness of self-reported data and symptom profiles for different acute respiratory illnesses.

  New genetic variants of influenza and other pathogens are rapidly emerging. Since 2000, avian influenza viruses (H5N1, H7N7, and H7N3), human metapneumovirus, severe acute respiratory syndrome (SARS), coronavirus (CoV and human CoVs NL63 and HKU1, a new coronavirus (2012)), parvovirus types 4 and 5, mimivirus, H1N1 and initial cases of H3N2 and H1N2 in humans, have emerged and been identified. At the same time, global surveillance capacity has remained stagnant. Our current ability to estimate population-wide incidence of acute respiratory infection (ARI) and influenza-like illness (ILI) or measure the relative contributions of different pathogens to incidence are severely limited. Thus we at HealthMap, created Flu Near You (http://www.flunearyou.org), an online participatory influenza surveillance tool for the USA and Canada.

  

• Get Genomed In 2013
  

  Stop by and register for Understand Your Genome (UYG). UYG provides a unique 2-day learning experience where the focus is YOU. Have your own genome sequenced in Illumina’s CLIA laboratory and delivered to you on an iPad for viewing with the Illumina MyGenome app. Industry thought leaders will also review the adoption and clinical utilization of whole genome sequencing. Be a part of the genomics revolution – register today!

  

• Guide Future Exposome Studies
  

  Right now, the genes + environment = health equation is a fiddler crab – with a large and growing “gene arm” and only a tiny knowledge base about all the chemical exposures we encounter in a lifetime. We invite all Personal Genome Project participants to help us in a study about putting personal environmental exposure data online. Participation consists of a half-hour interview. As a PGP participant already helping to accelerate discoveries about the human genome, you can help inform a parallel effort to understand the human “exposome” – an individual’s environmental exposures, beginning in the womb.

  We want to learn about your experiences participating in a study that involved sharing genetic data on the web, your decision to join the study, and your views about how researchers should handle study data to both advance science and protect any data that study participants want to keep private. This study is being conducted by a team of researchers from Silent Spring Institute, Northeastern University, and Harvard University, and is funded by the National Institutes of Health. Your responses will be kept confidential. As a thank you, the first twenty people to schedule and complete an interview will receive a free Public Laboratory desktop spectrometer, an experimental device for citizen scientists to analyze and compare material spectra – “fingerprints”. You can sign up for an interview via our calendar. If you have any questions about the study, please contact Oscar Zarate at 617-332-4288 ext. 232 or zarate@silentspring.org.

  

• How Active Are You
  

  Physical inactivity has been linked with a number chronic disease including obesity, hypertension and diabetes. Research has shown that engaging in regular physical activity can help people live longer, more productive and better lives. Despite the importance of engaging in regular physical activity, many people still find it difficult to initiate and sustain regular physical activity. A number of barriers which affects the level of peoples’ activity include time constraints, limited access to physical activity facilities and poor motivation to exercise.

  At the Center for Connected health, Partners Healthcare, we are committed to improving healthcare delivery and helping people engage in healthy behaviors by using simple technologies to deliver personalized interventions relevant to the individual. We want to find out if there are certain genetic traits that influence the pattern of peoples’ physical activity behaviors. This information will help us better understand how to design more engaging and relevant programs to help people engage in healthy behaviors. For this program we are looking for 20 volunteers who are overweight or obese (body mass index, BMI, 25 or greater) to use small wireless pedometers to monitor the level of their physical activity for 2 months. Participants must be a participant in the Personal Genome project (PGP), must be able to engage in moderate physical activity like walking and must also be willing to add their physical activity data to their public profile on a monthly basis for the 2 months duration of the program. If you are interested in participating or have questions about this program please contact Stephen Agboola, email: sagboola@partners.org; phone: 617-643-0291. Interested participants will be registered to use the pedometers at the 2013 GET Conference. Please stop by our booth if you are interested.(Image from flickr user seanvenn)

  

• Human Microbiome Meets The American Gut
  

  Ever since Antonie van Leeuwenhoek discovered a vast diversity of microbes between his own teeth in the 17th century using a primitive microscope, the microbes inhabiting our bodies have fascinated us. It is somewhat startling to realize that the human body has 10 times more non-human cells than 10 trillion human cells! It is only in the last few years that radical advances in DNA sequencing have allowed us to examine, for the first time, the full extent of microbial diversity on or in our bodies and to explore possible linkages between microbes and a wide range of health and disease states (including skin infections, neurological conditions, obesity, malnutrition, and inflammatory bowel disease).

  The sampling procedure is relatively simple. We are asking PGP volunteers to sample microbes from multiple sites in the body using sterile q-tips. We may also ask volunteers to record any features of diet, medications (e.g. antibiotics), and other factors that could influence the microbial communities.

  

• Map Ed Genetics Pin Yourself On Our World Map
  

  Go to Map-Ed.org and work your way through five questions about key concepts in genetics to pin yourself on a world map. No expertise in genetics needed! Questions are multiple-choice, and you will be provided with fun facts along the way to point you toward the correct answer. Then, get your friends to play this game and see more pins popping up in your neighborhood. And…this is just the beginning! We will be adding questions from time to time so that you can pin yourselves in new and fun ways. Check out our interactive map to see the pins that are there! Once you have pinned yourself, come back to this map as often as you’d like to watch the pins filling in. Brought to you by the Personal Genetics Education Project (pgEd; www.pgEd.org).

  

• Musical Pitch Perception
  

  Ever wonder about your sense of musical pitch? The research app, PitchMatch!, was created by Dr. Peter K. Gregersen at The Feinstein Institute for Medical Research in New York in order to understand variation in musical pitch perception and innate musical ability in the general population. Dr. Gregersen has been studying the epidemiology and genetics of absolute pitch (a rare musical ability) for over a decade.

  This free app, designed in a friendly game format, tests for the absolute pitch trait as well as overall pitch perception ability in the general population. This has never been done before. No musical training or experience is required – whether you play a musical instrument or not, you may be able to do well at PitchMatch! Those interested in learning more about the research behind the app (iPhone/iPad compatible), may contact us at our website, www.absolutepitchstudy.com/pitchmatch.html. Please visit us during the 2013 GET Conference near the PGP participant blood draw registration table to learn more about PitchMatch!. A demo will be available for anyone who would like to try it out. (Image thanks to flickr user horiavarian)

  

• Olfactory Perception
  

  Humans have around 400 different odorant receptors which they use to sense the olfactory environment. The family of odorant receptors is the largest gene family in the human genome and its members are exceptionally genetically and functionally variable. As a consequence, everybody smells the world with a different set of functional odorant receptors and it therefore smells different to each individual. The most prominent variability is seen in a condition called specific anosmia. People with specific anosmia have a normal sense of smell but cannot smell a specific type of odors (like vanilla or musk). The most widely known case of specific anosmia is to an odor released by urine after asparagus ingestion: most people can smell this odors, but some cannot. The phenotyping for olfactory perception by Andreas Keller from the Rockefeller University is relatively simple. Participants will sniff a few odors and answer questions about them (“How strong is the odor?”, “How pleasant is the odor?”, etc.) on a computer screen. Watch a video showing the protocol. (Image from flickr user Caro’s Lines)

  

• Re Identification Research Can We Connect The Dots In The Data
  

  Before the GET conference we attempted to link names to PGP profiles. Drop by our table and see if we correctly identified you to your profile. We can tell you how we did it and what you can do to stop others from doing the same while still keeping your profile useful for research. We are the Data Privacy Lab at Harvard University.

  

• Testmybrain.org
  

  At TestMyBrain, we are interested in a few main questions: is a collaboration between psychologists and brain scientists at Harvard University and Massachusetts General Hospital aimed at understanding the human mind. TestMyBrain is dedicated to collaborating with citizen scientists around the world, by providing tools that allow people to test themselves on a range of cognitive functions. Scientists then use that data to learn more about cognition and how the brain works. Since 2008, 750,000 volunteers have taken part in TestMyBrain experiments and TestMyBrain has become an engine for research, education, and scientific discovery.

  (1) How do basic cognitive functions vary between individuals? (2) How do these differences impact us in our day-to-day lives? (3) What is the relationship between these variations and our personality, mental health, and who we are as individuals?

  We invite you to come and take some of our tests, either online at http://www.testmybrain.org or at the conference. For individuals attending the conference, we will provide tests of face recognition ability, emotion perception, mental quickness, visual memory, and/or sensitivity to visual changes. Come and visit us at the GET conference to get your brain profile and discuss your results! You can also contact Dr. Laura Germine at testmybrain@gmail.com for more information about the TestMyBrain project, our mission, and the discoveries we’ve already made based on the contributions of people like you. (Image thanks to flickr user waltjabsco

  

• The Cinematic Exploration Of The Human Genome
  

  is a film festival that will be part of the 2014 G.E.T. Conference. The festival will not only screen films that relate to genetic science but will reach out to filmmakers and actively encourage them to make new short films that explore the ideas, research, and issues being generated by modern genetics. These short films will be screened as part of next years festival and will be made public to provide a point of entry for anyone curious to learn more about this scientific frontier. The goal is to build a collection films that will help engage and educate the public.

  We are looking to collect ideas for short films from you and everyone attending this years G.E.T. Conference. Ideas that will give filmmakers a solid foundation to start from and clear direction as they explore this subject. We want as a diverse a collection of short films as possible: documentaries, speculative fiction, profiles or researchers, science fiction, history, drama, musicals, comedies…this a community wide brainstorming session, and there can be no bad ideas. Postcards will be available at the conference for you to write your suggestions on, and at any time you can send ideas to: filmfest@fieldtest.us

  

• Whose Genome Is It
  

  We recently developed a method to identify personal genomes through surname inference. This method relies on the fact that Y-chromosomes and surnames are usually inherited together. Online genetic genealogy databases post hundreds of thousands of profiles linking Y-chromosome short tandem repeat (Y-STR) profiles with surnames. We showed that using only publicly available resources, we can obtain high-quality Y-STR results from low-coverage whole genome sequencing datasets and use these profiles to infer the surname of the individual behind the dataset. The inferred surname combined with additional metadata, such as the state of residence and the age of the individual, is often enough for full identification. Sharing large-scale genomic data is vitally important to understanding the complexities of the human genome. Thousands of “anonymous” sequencing datasets are freely available over the Internet in order to facilitate research progress. However, as more and more data about our genomes and our lives accumulates online, promising “anonymity” of a personal genome becomes increasingly unrealistic.

  How identifiable is your genome? Come see how with some simple bioinformatics techniques and fast internet searches we attempt to discover the individual behind the genome. (image from flickr user davemorris)

  

Interested in featuring your research project or activity at the GET Conference? Send inquiries to Jason Bobe (jason at personalgenomes.org)