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      Harvard Personal Genome Project: lessons from participatory public research

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          Abstract

          Background

          Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment.

          Discussion

          Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project.

          Summary

          We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants.

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          Most cited references 6

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          Identifying personal genomes by surname inference.

          Sharing sequencing data sets without identifiers has become a common practice in genomics. Here, we report that surnames can be recovered from personal genomes by profiling short tandem repeats on the Y chromosome (Y-STRs) and querying recreational genetic genealogy databases. We show that a combination of a surname with other types of metadata, such as age and state, can be used to triangulate the identity of the target. A key feature of this technique is that it entirely relies on free, publicly accessible Internet resources. We quantitatively analyze the probability of identification for U.S. males. We further demonstrate the feasibility of this technique by tracing back with high probability the identities of multiple participants in public sequencing projects.
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            From genetic privacy to open consent.

            Recent advances in high-throughput genomic technologies are showing concrete results in the form of an increasing number of genome-wide association studies and in the publication of comprehensive individual genome-phenome data sets. As a consequence of this flood of information the established concepts of research ethics are stretched to their limits, and issues of privacy, confidentiality and consent for research are being re-examined. Here, we show the feasibility of the co-development of scientific innovation and ethics, using the open-consent framework that was implemented in the Personal Genome Project as an example.
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              A public resource facilitating clinical use of genomes.

              Rapid advances in DNA sequencing promise to enable new diagnostics and individualized therapies. Achieving personalized medicine, however, will require extensive research on highly reidentifiable, integrated datasets of genomic and health information. To assist with this, participants in the Personal Genome Project choose to forgo privacy via our institutional review board- approved "open consent" process. The contribution of public data and samples facilitates both scientific discovery and standardization of methods. We present our findings after enrollment of more than 1,800 participants, including whole-genome sequencing of 10 pilot participant genomes (the PGP-10). We introduce the Genome-Environment-Trait Evidence (GET-Evidence) system. This tool automatically processes genomes and prioritizes both published and novel variants for interpretation. In the process of reviewing the presumed healthy PGP-10 genomes, we find numerous literature references implying serious disease. Although it is sometimes impossible to rule out a late-onset effect, stringent evidence requirements can address the high rate of incidental findings. To that end we develop a peer production system for recording and organizing variant evaluations according to standard evidence guidelines, creating a public forum for reaching consensus on interpretation of clinically relevant variants. Genome analysis becomes a two-step process: using a prioritized list to record variant evaluations, then automatically sorting reviewed variants using these annotations. Genome data, health and trait information, participant samples, and variant interpretations are all shared in the public domain-we invite others to review our results using our participant samples and contribute to our interpretations. We offer our public resource and methods to further personalized medical research.
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                Author and article information

                Contributors
                Journal
                Genome Med
                Genome Med
                Genome Medicine
                BioMed Central
                1756-994X
                2014
                28 February 2014
                : 6
                : 2
                : 10
                Affiliations
                [1 ]Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02215, USA
                [2 ]PersonalGenomes.org, 423 Brookline Avenue, #323, Boston, MA 02215-5410, USA
                [3 ]Curoverse, Inc., 51 Melcher Street, Boston, MA 02210, USA
                [4 ]TeloMe Inc., 1393 Main Street, Waltham, MA, USA
                [5 ]Section Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands
                Article
                gm527
                10.1186/gm527
                3978420
                24713084
                Copyright © 2014 Ball et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Categories
                Open Debate

                Molecular medicine

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