Progress in Whole Genome Sequencing (WGS) will soon allow a large number of individuals to have their genome fully sequenced. This lays the foundations to improve modern healthcare, enabling a new era of personalized medicine where diagnosis and treatment is tailored to the patient's genetic makeup. It also allows individuals motivated by personal curiosity to have access to their genetic information, and use it, e.g., to trace their ancestry. However, the very same progress also amplifies a number of ethical and privacy concerns, that stem from the unprecedented sensitivity of genomic information and that are not well studied. This paper presents an exploratory ethnographic study of users' perception of privacy and ethical issues with WGS, as well as their attitude toward different WGS programs. We report on a series of semi-structured interviews, involving 16 participants, and analyze the results both quantitatively and qualitatively. Our analysis shows that users exhibit common trust concerns and fear of discrimination, and demand to retain strict control over their genetic information. Finally, we highlight the need for further research in the area and follow-up studies that build on our initial findings.
@cite_42 compared the attitude of 279 patients from the United States and Spain who had volunteered to donate a sample for genomic research, and showed that 48 that genetic information poses special risks (69.7 @cite_35 explored the attitude of research participants and possible future participants regarding Genome-Wide Association Studies (GWAS): they found out that participants expressed a variety of opinions about the acceptability of wide sharing of genetic and phenotypic information for research purposes through large, publicly accessible data repositories. Most believed that making de-identified study data available to the research community was a social good to be pursued. Privacy and confidentiality concerns were common, although not necessarily precluding participation. Also, many participants voiced reservations about sharing data with for-profit organizations.
@cite_35 @cite_42
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Purpose: Sharing study data within the research community generates tension between two important goods: promoting scientific goals and protecting the privacy interests of study participants. This study was designed to explore the perceptions, beliefs, and attitudes of research participants and possible future participants regarding genome-wide association studies and repository-based research. Methods: Focus group sessions with (1) current research participants, (2) surrogate decision-makers, and (3) three age-defined cohorts (18‐34 years, 35‐ 50, 50). Results: Participants expressed a variety of opinions about the acceptability of wide sharing of genetic and phenotypic information for research purposes through large, publicly accessible data repositories. Most believed that making de-identified study data available to the research community is a social good that should be pursued. Privacy and confidentiality concerns were common, although they would not necessarily preclude participation. Many participants voiced reservations about sharing data with for-profit organizations. Conclusions: Trust is central in participants’ views regarding data sharing. Further research is needed to develop governance models that enact the values of stewardship. Genet Med 2010:12(8):486–495. The disclosure of individual genetic results has generated an ongoing debate about which rules should be followed. We aimed to identify factors related to research participants' preferences about learning the results of genomic studies using their donated tissue samples. We conducted a cross-sectional survey of 279 patients from the United States and Spain who had volunteered to donate a sample for genomic research. Our results show that 48 of research participants would like to be informed about all individual results from future genomic studies using their donated tissue, especially those from the U.S. (71.4 ) and those believing that genetic information poses special risks (69.7 ). In addition, 16 of research participants considered genetic information to be riskier than other types of personal medical data. In conclusion, our study demonstrates that a high proportion of participants prefer to be informed about their individual results and that there is a higher preference among those research subjec... Concerns about genetic privacy affect individuals’ willingness to accept genetic testing in clinical care and to participate in genomics research. To learn what is already known about these views, we conducted a systematic review, which ultimately analyzed 53 studies involving the perspectives of 47,974 participants on real or hypothetical privacy issues related to human genetic data. Bibliographic databases included MEDLINE, Web of Knowledge, and Sociological Abstracts. Three investigators independently screened studies against predetermined criteria and assessed risk of bias. The picture of genetic privacy that emerges from this systematic literature review is complex and riddled with gaps. When asked specifically “are you worried about genetic privacy,” the general public, patients, and professionals frequently said yes. In many cases, however, that question was posed poorly or only in the most general terms. While many participants expressed concern that genomic and medical information would be revealed to others, respondents frequently seemed to conflate privacy, confidentiality, control, and security. People varied widely in how much control they wanted over the use of data. They were more concerned about use by employers, insurers, and the government than they were about researchers and commercial entities. In addition, people are often willing to give up some privacy to obtain other goods. Importantly, little attention was paid to understanding the factors–sociocultural, relational, and media—that influence people’s opinions and decisions. Future investigations should explore in greater depth which concerns about genetic privacy are most salient to people and the social forces and contexts that influence those perceptions. It is also critical to identify the social practices that will make the collection and use of these data more trustworthy for participants as well as to identify the circumstances that lead people to set aside worries and decide to participate in research. Genome-wide association studies (GWAS) aim at discovering the association between genetic variations, particularly single-nucleotide polymorphism (SNP), and common diseases, which is well recognized to be one of the most important and active areas in biomedical research. Also renowned is the privacy implication of such studies, which has been brought into the limelight by the recent attack proposed by Homer's attack demonstrates that it is possible to identify a GWAS participant from the allele frequencies of a large number of SNPs. Such a threat, unfortunately, was found in our research to be significantly understated. In this paper, we show that individuals can actually be identified from even a relatively small set of statistics, as those routinely published in GWAS papers. We present two attacks. The first one extends Homer's attack with a much more powerful test statistic, based on the correlations among different SNPs described by coefficient of determination (r2). This attack can determine the presence of an individual from the statistics related to a couple of hundred SNPs. The second attack can lead to complete disclosure of hundreds of participants' SNPs, through analyzing the information derived from published statistics. We also found that those attacks can succeed even when the precisions of the statistics are low and part of data is missing. We evaluated our attacks on the real human genomes and concluded that such threats are completely realistic. 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. Recent advances in genome-scale, system-level measurements of quantitative phenotypes (transcriptome, metabolome, and proteome) promise to yield unprecedented biological insights. In this environment, broad dissemination of results from genome-wide association studies (GWASs) or deep-sequencing efforts is highly desirable. However, summary results from case-control studies (allele frequencies) have been withdrawn from public access because it has been shown that they can be used for inferring participation in a study if the individual's genotype is available. A natural question that follows is how much private information is contained in summary results from quantitative trait GWAS such as regression coefficients or p values. We show that regression coefficients for many SNPs can reveal the person's participation and for participants his or her phenotype with high accuracy. Our power calculations show that regression coefficients contain as much information on individuals as allele frequencies do, if the person's phenotype is rather extreme or if multiple phenotypes are available as has been increasingly facilitated by the use of multiple-omics data sets. These findings emphasize the need to devise a mechanism that allows data sharing that will facilitate scientific progress without sacrificing privacy protection. To describe consumers' perceptions of genetic counseling services in the context of direct-to-consumer personal genomic testing is the purpose of this research. Utilizing data from the Scripps Genomic Health Initiative, we assessed direct-to-consumer genomic test consumers' utilization and perceptions of genetic counseling services. At long-term follow-up, approximately 14 months post-testing, participants were asked to respond to several items gauging their interactions, if any, with a Navigenics genetic counselor, and their perceptions of those interactions. Out of 1325 individuals who completed long-term follow-up, 187 (14.1 ) indicated that they had spoken with a genetic counselor. The most commonly given reason for not utilizing the counseling service was a lack of need due to the perception of already understanding one's results (55.6 ). The most common reasons for utilizing the service included wanting to take advantage of a free service (43.9 ) and wanting more information on risk calculations (42.2 ). Among those who utilized the service, a large fraction reported that counseling improved their understanding of their results (54.5 ) and genetics in general (43.9 ). A relatively small proportion of participants utilized genetic counseling after direct-to-consumer personal genomic testing. Among those individuals who did utilize the service, however, a large fraction perceived it to be informative, and thus presumably beneficial. One concern in human genetics research is maintaining the privacy of study participants. The growth in genealogical registries may contribute to loss of privacy, given that genotypic information is accessible online to facilitate discovery of genetic relationships. Through iterative use of two such web archives, FamilySearch and Sorenson Molecular Genealogy Foundation, I was able to discern the likely haplotypes for the Y chromosomes of two men, Joseph Smith and Brigham Young, who were instrumental in the founding of the Latter-Day Saints Church. I then determined whether any of the Utahns who contributed to the HapMap project (the "CEU" set) is related to either man, on the basis of haplotype analysis of the Y chromosome. Although none of the CEU contributors appear to be a male-line relative, I discovered that predictions could be made for the surnames of the CEU participants by a similar process. For 20 of the 30 unrelated CEU samples, at least one exact match was revealed, and for 17 of these, a potential ancestor from Utah or a neighboring state could be identified. For the remaining ten samples, a match was nearly perfect, typically deviating by only one marker repeat unit. The same query performed in two other large databases revealed fewer individual matches and helped to clarify which surname predictions are more likely to be correct. Because large data sets of genotypes from both consenting research subjects and individuals pursuing genetic genealogy will be accessible online, this type of triangulation between databases may compromise the privacy of research subjects. The aim of this research was to understand what affects people's privacy preferences in smartphone apps. We ran a four-week study in the wild with 34 participants. Participants were asked to answer questions, which were used to gather their personal context and to measure their privacy preferences by varying app name and purpose of data collection. Our results show that participants shared the most when no information about data access or purpose was given, and shared the least when both of these details were specified. When just one of either purpose or the requesting app was shown, participants shared less when just the purpose was specified than when just the app name was given. We found that the purpose for data access was the predominant factor affecting users' choices. In our study the purpose condition vary from being not specified, to vague to be very specific. Participants were more willing to disclose data when no purpose was specified. When a vague purpose was shown, participants became more privacy-aware and were less willing to disclose their information. When specific purposes were shown participants were more willing to disclose when the purpose for requesting the information appeared to be beneficial to them, and shared the least when the purpose for data access was solely beneficial to developers. This qualitative study examines privacy practices and concerns among contributors to open collaboration projects. We collected interview data from people who use the anonymity network Tor who also contribute to online projects and from Wikipedia editors who are concerned about their privacy to better understand how privacy concerns impact participation in open collaboration projects. We found that risks perceived by contributors to open collaboration projects include threats of surveillance, violence, harassment, opportunity loss, reputation loss, and fear for loved ones. We explain participants' operational and technical strategies for mitigating these risks and how these strategies affect their contributions. Finally, we discuss chilling effects associated with privacy loss, the need for open collaboration projects to go beyond attracting and educating participants to consider their privacy, and some of the social and technical approaches that could be explored to mitigate risk at a project or community level. 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. The continuous decrease in cost of molecular profiling tests is revolutionizing medical research and practice, but it also raises new privacy concerns. One of the first attacks against privacy of biological data, proposed by in 2008, showed that, by knowing parts of the genome of a given individual and summary statistics of a genome-based study, it is possible to detect if this individual participated in the study. Since then, a lot of work has been carried out to further study the theoretical limits and to counter the genome-based membership inference attack. However, genomic data are by no means the only or the most influential biological data threatening personal privacy. For instance, whereas the genome informs us about the risk of developing some diseases in the future, epigenetic biomarkers, such as microRNAs, are directly and deterministically affected by our health condition including most common severe diseases. In this paper, we show that the membership inference attack also threatens the privacy of individuals contributing their microRNA expressions to scientific studies. Our results on real and public microRNA expression data demonstrate that disease-specific datasets are especially prone to membership detection, offering a true-positive rate of up to 77 at a false-negative rate of less than 1 . We present two attacks: one relying on the L_1 distance and the other based on the likelihood-ratio test. We show that the likelihood-ratio test provides the highest adversarial success and we derive a theoretical limit on this success. In order to mitigate the membership inference, we propose and evaluate both a differentially private mechanism and a hiding mechanism. We also consider two types of adversarial prior knowledge for the differentially private mechanism and show that, for relatively large datasets, this mechanism can protect the privacy of participants in miRNA-based studies against strong adversaries without degrading the data utility too much. Based on our findings and given the current number of miRNAs, we recommend to only release summary statistics of datasets containing at least a couple of hundred individuals. Deciphering the genetic basis of human diseases is an important goal of biomedical research. On the basis of the assumption that phenotypically similar diseases are caused by functionally related genes, we propose a computational framework that integrates human protein–protein interactions, disease phenotype similarities, and known gene–phenotype associations to capture the complex relationships between phenotypes and genotypes. We develop a tool named CIPHER to predict and prioritize disease genes, and we show that the global concordance between the human protein network and the phenotype network reliably predicts disease genes. Our method is applicable to genetically uncharacterized phenotypes, effective in the genome-wide scan of disease genes, and also extendable to explore gene cooperativity in complex diseases. The predicted genetic landscape of over 1000 human phenotypes, which reveals the global modular organization of phenotype–genotype relationships. The genome-wide prioritization of candidate genes for over 5000 human phenotypes, including those with under-characterized disease loci or even those lacking known association, is publicly released to facilitate future discovery of disease genes. As consumers are increasingly using the Internet to manage their finances, there has been a concomitant increase in the risk of theft and fraud by cybercriminals. Hackers who acquire sensitive consumer data utilise information on their own, or sell the information in online forums for a significant profit. Few have considered the organisational composition of the participants engaged in the sale of stolen data, including the presence of managerial oversight, division of labour, coordination of roles and purposive associations between buyers, sellers and forum operators. Thus, this qualitative study will apply Best and Luckenbill's framework of social organisation to a sample of threads from publicly accessible web forums where individuals buy and sell stolen financial information. The implications of this study for criminologists, law enforcement, the intelligence community and information security researchers will be discussed in depth. Increasingly, software developers are using a wide array of social collaborative platforms for software development and learning. In this work, we examined the similarities in developer’s interests within and across GitHub and Stack Overflow. Our study finds that developers share common interests in GitHub and Stack Overflow; on average, 39 of the GitHub repositories and Stack Overflow questions that a developer had participated fall in the common interests. Also, developers do share similar interests with other developers who co-participated activities in the two platforms. In particular, developers who co-commit and co-pull-request same GitHub repositories and co-answer same Stack Overflow questions, share more common interests compare to other developers who co-participate in other platform activities. The rapid and continuous growth of social networking sites has led to the emergence of many communities of communicating groups. Many of these groups discuss ideological and political topics. It is not uncommon that the participants in such discussions split into two or more subgroups. The members of each subgroup share the same opinion toward the discussion topic and are more likely to agree with members of the same subgroup and disagree with members from opposing subgroups. In this paper, we propose an unsupervised approach for automatically detecting discussant subgroups in online communities. We analyze the text exchanged between the participants of a discussion to identify the attitude they carry toward each other and towards the various aspects of the discussion topic. We use attitude predictions to construct an attitude vector for each discussant. We use clustering techniques to cluster these vectors and, hence, determine the subgroup membership of each participant. We compare our methods to text clustering and other baselines, and show that our method achieves promising results. Citizen participation in online communities of scientific investigations has recently become more popular. Enhancing the engagement of citizens within these communities is a focus of attention for researchers and practitioners who want to amplify the impact on learning, science and society. This study investigates the relationship between engagement factors and behaviour patterns in an online community that requires high levels of citizen participation. While other studies explore engagement in communities where citizens contribute data, the current research investigates a community to support citizens in facilitating their own scientific investigations. Data were collected from log files and questionnaires, and multiple measures of engagement were examined: engagement metrics, roles, motivation, attitude, satisfaction and belonging to the community. The results allowed comparison of the engagement levels among different types of citizen participation communities and categorised members in engagement profiles, according to their behaviour patterns. Findings indicate a need for differing design approaches based on the type of citizen participation community and individual engagement profiles. Researchers who develop new home technologies using connected devices (e.g. sensors) often want to conduct large-scale field studies in homes to evaluate their technology, but conducting such studies today is quite challenging, if not impossible. Considerable custom engineering is required to ensure hardware and software prototypes work robustly, and recruiting and managing more than a handful of households can be difficult and cost-prohibitive. To lower the barrier to developing and evaluating new technologies for the home environment, we call for the development of a shared infrastructure, called HomeLab. HomeLab consists of a large number of geographically distributed households, each running a common, flexible framework (e.g., HomeOS [4]) in which experiments are implemented. The use of a common framework enables engineering effort, along with experience and expertise, to be shared among many research groups. Recruitment of households to HomeLab can be organic: as a research group recruits (a few) households to participate in its field study, these households can be invited to join HomeLab and participate in future studies conducted by other groups. As the pool of households participating in HomeLab grows, we hope that researchers will find it easier to recruit a large number of households to participate in field studies. Since there is, in principle, no reason why third parties should not pay individuals for the use of their data, we introduce a realistic market that would allow these payments to be made while taking into account the privacy attitude of the participants. And since it is usually important to use unbiased samples to obtain credible statistical results, we examine the properties that such a market should have and suggest a mechanism that compensates those individuals that participate according to their risk attitudes. Equally important, we show that this mechanism also benefits buyers, as they pay less for the data than they would if they compensated all individuals with the same maximum fee that the most concerned ones expect. As genomic data becomes widely used, the problem of genomic data privacy becomes a hot interdisciplinary research topic among geneticists, bioinformaticians and security and privacy experts. Practical attacks have been identified on genomic data, and thus break the privacy expectations of individuals who contribute their genomic data to medical research, or simply share their data online. Frustrating as it is, the problem could become even worse. Existing genomic privacy breaches rely on low-order SNV (Single Nucleotide Variant) correlations. Our work shows that far more powerful attacks can be designed if high-order correlations are utilized. We corroborate this concern by making use of different SNV correlations based on various genomic data models and applying them to an inference attack on individuals' genotype data with hidden SNVs. We also show that low-order models behave very differently from real genomic data and therefore should not be relied upon for privacy-preserving solutions.