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Harmanci A, Gerstein M. Quantification of private information leakage from phenotype-genotype data: linking attacks. Nat Methods 2016; 13:251-6. [PMID: 26828419 PMCID: PMC4834871 DOI: 10.1038/nmeth.3746] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 11/13/2015] [Indexed: 12/28/2022]
Abstract
Studies on genomic privacy have traditionally focused on identifying individuals using DNA variants. In contrast, molecular phenotype data, such as gene expression levels, are generally assumed to be free of such identifying information. Although there is no explicit genotypic information in phenotype data, adversaries can statistically link phenotypes to genotypes using publicly available genotype-phenotype correlations such as expression quantitative trait loci (eQTLs). This linking can be accurate when high-dimensional data (i.e., many expression levels) are used, and the resulting links can then reveal sensitive information (for example, the fact that an individual has cancer). Here we develop frameworks for quantifying the leakage of characterizing information from phenotype data sets. These frameworks can be used to estimate the leakage from large data sets before release. We also present a general three-step procedure for practically instantiating linking attacks and a specific attack using outlier gene expression levels that is simple yet accurate. Finally, we describe the effectiveness of this outlier attack under different scenarios.
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Affiliation(s)
- Arif Harmanci
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Computer Science, Yale University, New Haven, CT, USA
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Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC. Toward clinical genomics in everyday medicine: perspectives and recommendations. Expert Rev Mol Diagn 2016; 16:521-32. [PMID: 26810587 PMCID: PMC4841021 DOI: 10.1586/14737159.2016.1146593] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Precision or personalized medicine through clinical genome and exome sequencing has been described by some as a revolution that could transform healthcare delivery, yet it is currently used in only a small fraction of patients, principally for the diagnosis of suspected Mendelian conditions and for targeting cancer treatments. Given the burden of illness in our society, it is of interest to ask how clinical genome and exome sequencing can be constructively integrated more broadly into the routine practice of medicine for the betterment of public health. In November 2014, 46 experts from academia, industry, policy and patient advocacy gathered in a conference sponsored by Illumina, Inc. to discuss this question, share viewpoints and propose recommendations. This perspective summarizes that work and identifies some of the obstacles and opportunities that must be considered in translating advances in genomics more widely into the practice of medicine.
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Affiliation(s)
- Susan K Delaney
- a Coriell Institute for Medical Research , Camden , NJ , USA
| | - Michael L Hultner
- b Lockheed Martin , Information Systems & Global Solutions , Rockville , MD , USA
| | - Howard J Jacob
- c HudsonAlpha Institute for Biotechnology , Huntsville , AL , USA
| | | | - Jeanette J McCarthy
- e Duke University , Center for Applied Genomics and Precision Medicine , Durham , NC , USA
| | | | - Kenneth B Beckman
- g University of Minnesota , Genomics Center ,, Minneapolis , MN , USA
| | - John W Belmont
- h Baylor College of Medicine , Children's Nutrition Research Center , Houston , TX , USA
| | - Cinnamon S Bloss
- i University of California, San Diego , School of Medicine , La Jolla , CA , USA
| | | | | | - Stephen A Damiani
- k Mission Massimo Foundation , Elsternwick , VIC , Australia .,l Mission Massimo Foundation Inc ., Westlake Village , CA , USA
| | | | | | - Michael J Dougherty
- o The American Society of Human Genetics , Bethesda , MD , USA.,p Department of Pediatrics , University of Colorado School of Medicine , Aurora , CO , USA
| | - Joel T Dudley
- q Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | | | - Jennifer R Friedman
- r University of California, San Diego , Departments of Neurosciences and Pediatrics and Rady Children's Hospital , San Diego , CA , USA
| | | | - Tom S Hays
- t University of Minnesota , Department of Genetics, Cell Biology and Development , Minneapolis , MN , USA
| | | | - Jeff Huber
- u Google Inc ., Mountain View , CA , USA
| | | | | | | | - Elissa Levin
- q Icahn School of Medicine at Mount Sinai , New York , NY , USA
| | | | | | | | - David C Magnus
- y Stanford Center for Biomedical Ethics , Stanford School of Medicine , Stanford , CA , USA
| | | | | | | | - Helen Messier
- ab Healix Health, Ltd , West Vancouver , BC , Canada
| | | | | | | | | | | | | | - Michael M Su
- ai Anthem Blue Cross , Woodland Hills , CA , USA
| | | | - Steven Tucker
- ak Novena Specialist Center , Singapore , Republic of Singapore
| | | | - Robert C Green
- am Division of Genetics, Department of Medicine, Brigham and Women's Hospital , the Broad Institute, Harvard Medical School and Partners Healthcare Personalized Medicine , Boston , MA , USA
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Shringarpure SS, Bustamante CD. Privacy Risks from Genomic Data-Sharing Beacons. Am J Hum Genet 2015; 97:631-46. [PMID: 26522470 PMCID: PMC4667107 DOI: 10.1016/j.ajhg.2015.09.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/23/2015] [Indexed: 12/21/2022] Open
Abstract
The human genetics community needs robust protocols that enable secure sharing of genomic data from participants in genetic research. Beacons are web servers that answer allele-presence queries—such as “Do you have a genome that has a specific nucleotide (e.g., A) at a specific genomic position (e.g., position 11,272 on chromosome 1)?”—with either “yes” or “no.” Here, we show that individuals in a beacon are susceptible to re-identification even if the only data shared include presence or absence information about alleles in a beacon. Specifically, we propose a likelihood-ratio test of whether a given individual is present in a given genetic beacon. Our test is not dependent on allele frequencies and is the most powerful test for a specified false-positive rate. Through simulations, we showed that in a beacon with 1,000 individuals, re-identification is possible with just 5,000 queries. Relatives can also be identified in the beacon. Re-identification is possible even in the presence of sequencing errors and variant-calling differences. In a beacon constructed with 65 European individuals from the 1000 Genomes Project, we demonstrated that it is possible to detect membership in the beacon with just 250 SNPs. With just 1,000 SNP queries, we were able to detect the presence of an individual genome from the Personal Genome Project in an existing beacon. Our results show that beacons can disclose membership and implied phenotypic information about participants and do not protect privacy a priori. We discuss risk mitigation through policies and standards such as not allowing anonymous pings of genetic beacons and requiring minimum beacon sizes.
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Grande D, Asch DA, Wan F, Bradbury AR, Jagsi R, Mitra N. Are Patients With Cancer Less Willing to Share Their Health Information? Privacy, Sensitivity, and Social Purpose. J Oncol Pract 2015; 11:378-83. [PMID: 26265174 PMCID: PMC4575401 DOI: 10.1200/jop.2015.004820] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Growing use of electronic health information increases opportunities to build population cancer databases for research and care delivery. Understanding patient views on reuse of health information is essential to shape privacy policies and build trust in these initiatives. METHODS We randomly assigned nationally representative participants (N = 3,336) with and without prior cancer to six of 18 scenarios describing different uses of electronic health information. The scenarios varied the user, use, and sensitivity of the information. Participants rated each scenario on a scale of 1 to 10 assessing their willingness to share their electronic health information. We used conjoint analysis to measure the relative importance of each attribute (ie, use, user, and sensitivity). RESULTS Participants with and without a prior diagnosis of cancer had a similar willingness to share health information (0.27; P = .42). Both cancer and noncancer participants rated the purpose of information use as the most important factor (importance weights, 67.1% and 45.6%, respectively). For cancer participants, the sensitivity of the information was more important (importance weights, 29.8% v 1.2%). However, cancer participants were more willing to share their health information when the information included more sensitive genetic information (0.48; P = .015). Cancer and noncancer respondents rated uses and users similarly. CONCLUSION The information sharing preferences of participants with and without a prior diagnosis of cancer were driven mainly by the purpose of information reuse. Although conventional thinking suggests patients with cancer might be less willing to share their health information, we found participants with cancer were more willing to share their inherited genetic information.
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Affiliation(s)
- David Grande
- University of Pennsylvania Perelman School of Medicine; Leonard Davis Institute of Health Economics, University of Pennsylvania; Center for Health Equity Research and Promotion, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA; and University of Michigan School of Medicine, Ann Arbor, MI
| | - David A Asch
- University of Pennsylvania Perelman School of Medicine; Leonard Davis Institute of Health Economics, University of Pennsylvania; Center for Health Equity Research and Promotion, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA; and University of Michigan School of Medicine, Ann Arbor, MI
| | - Fei Wan
- University of Pennsylvania Perelman School of Medicine; Leonard Davis Institute of Health Economics, University of Pennsylvania; Center for Health Equity Research and Promotion, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA; and University of Michigan School of Medicine, Ann Arbor, MI
| | - Angela R Bradbury
- University of Pennsylvania Perelman School of Medicine; Leonard Davis Institute of Health Economics, University of Pennsylvania; Center for Health Equity Research and Promotion, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA; and University of Michigan School of Medicine, Ann Arbor, MI
| | - Reshma Jagsi
- University of Pennsylvania Perelman School of Medicine; Leonard Davis Institute of Health Economics, University of Pennsylvania; Center for Health Equity Research and Promotion, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA; and University of Michigan School of Medicine, Ann Arbor, MI
| | - Nandita Mitra
- University of Pennsylvania Perelman School of Medicine; Leonard Davis Institute of Health Economics, University of Pennsylvania; Center for Health Equity Research and Promotion, Philadelphia Veterans Affairs Medical Center, Philadelphia, PA; and University of Michigan School of Medicine, Ann Arbor, MI
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Bull S, Cheah PY, Denny S, Jao I, Marsh V, Merson L, Shah More N, Nhan LNT, Osrin D, Tangseefa D, Wassenaar D, Parker M. Best Practices for Ethical Sharing of Individual-Level Health Research Data From Low- and Middle-Income Settings. J Empir Res Hum Res Ethics 2015; 10:302-13. [PMID: 26297751 PMCID: PMC4547207 DOI: 10.1177/1556264615594606] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Sharing individual-level data from clinical and public health research is increasingly being seen as a core requirement for effective and efficient biomedical research. This article discusses the results of a systematic review and multisite qualitative study of key stakeholders' perspectives on best practices in ethical data sharing in low- and middle-income settings. Our research suggests that for data sharing to be effective and sustainable, multiple social and ethical requirements need to be met. An effective model of data sharing will be one in which considered judgments will need to be made about how best to achieve scientific progress, minimize risks of harm, promote fairness and reciprocity, and build and sustain trust.
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Affiliation(s)
| | | | - Spencer Denny
- University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Irene Jao
- KEMRI Wellcome Trust Research Programme, Nairobi, Kenya
| | - Vicki Marsh
- University of Oxford, UK KEMRI Wellcome Trust Research Programme, Nairobi, Kenya
| | - Laura Merson
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Neena Shah More
- Society for Nutrition, Education and Health Action, Mumbai, India
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Communication is the key. : Part 2 : Direct to consumer genetics in our future daily life ? J Cell Commun Signal 2014; 8:275-87. [PMID: 25408105 DOI: 10.1007/s12079-014-0258-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 01/21/2023] Open
Abstract
The considerable advances of genome sequencing over the past decades have had a profound impact on our daily life and opened up new avenues for the public to have access to their genetic information and learn more about their ancestry, genealogy and other traits that make each of us unique individuals. A very large number of individual single nucleotide polymorphisms (SNPs) have been associated to diseases whereas others have no known phenotype. For example, among the SNPs mapped within ccn1(cyr61), ccn2(ctgf), ccn3(nov), ccn4(wisp-1), ccn5(wisp-2) and ccn6 (wisp-3), only mutations within ccn4 were associated to PPD (the autosomal recessive skeletal disorder Progressive Pseudorheumatoid Dysplasia). On the occasion of this JCCS special issue on the roles of hormetic responses in adaptation, and response of living species to the modifications of their environment, it appeared that it was a good time to briefly review a topic that has been the subject of passionate discussions for the past few years, that is Direct to Consumer genetic tests (DTC GT). Based on the use of DNA analysis and identification of polymorphisms, DTC GT have been developed by several companies in the USA and in countries where there was no legal obstacle for customers to have direct access to their genetic information and manage their healthcare. Problems that arose and decisions that have been taken by regulatory agencies are presented and discussed in this editorial. The « freeze » of health-oriented DTC GT in the USA neither implies the end of DNA analysis nor « fun » applications, which are not aimed at providing risks estimates for particular illnesses. As shown in the example which is discussed in this editorial, DTC GT for cosmetic applications might be considered a fun application of great interest for companies such as L'Oréal, who recently developed the Makeup Genius mobile application. Other fun applications of DTC GT are discussed but there is no doubt that nothing will stop progress and it is most probable than within a few years from now all the tensions raised about these procedures will vanish to the profit and benefit of consumers. In any case, this will only be possible through an intensive communication effort, because …communication is the key !
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