Browsing by Subject "Genes"

Now showing 1 - 18 of 18

Open Access
Can you really anonymize the donors of genomic data in today’s digital world?
(Springer, 2016-09) Alser, Mohammed; Almadhoun, Nour; Nouri, Azita; Alkan, Can; Ayday, Erman
The rapid progress in genome sequencing technologies leads to availability of high amounts of genomic data. Accelerating the pace of biomedical breakthroughs and discoveries necessitates not only collecting millions of genetic samples but also granting open access to genetic databases. However, one growing concern is the ability to protect the privacy of sensitive information and its owner. In this work, we survey a wide spectrum of cross-layer privacy breaching strategies to human genomic data (using both public genomic databases and other public non-genomic data). We outline the principles and outcomes of each technique, and assess its technological complexity and maturation. We then review potential privacy-preserving countermeasure mechanisms for each threat. © Springer International Publishing Switzerland 2016.
Open Access
Cryptographic solutions for genomic privacy
(Springer, 2016-02) Ayday, Erman
With the help of rapidly developing technology, DNA sequencing is becoming less expensive. As a consequence, the research in genomics has gained speed in paving the way to personalized (genomic) medicine, and geneticists need large collections of human genomes to further increase this speed. Furthermore, individuals are using their genomes to learn about their (genetic) predispositions to diseases, their ancestries, and even their (genetic) compatibilities with potential partners. This trend has also caused the launch of health-related websites and online social networks (OSNs), in which individuals share their genomic data (e.g., OpenSNP or 23andMe). On the other hand, genomic data carries much sensitive information about its owner. By analyzing the DNA of an individual, it is now possible to learn about his disease predispositions (e.g., for Alzheimer’s or Parkinson’s), ancestries, and physical attributes. The threat to genomic privacy is magnified by the fact that a person’s genome is correlated to his family members’ genomes, thus leading to interdependent privacy risks. In this work, focusing on our existing and ongoing work on genomic privacy, we will first highlight one serious threat for genomic privacy. Then, we will present the high level descriptions of our cryptographic solutions to protect the privacy of genomic data. © International Financial Cryptography Association 2016.
Open Access
Data and model driven hybrid approach to activity scoring of cyclic pathways
(Springer, Dordrecht, 2010) Işık, Z.; Atalay V.; Aykanat, Cevdet; Çetin-Atalay, Rengül
Analysis of large scale -omics data based on a single tool remains inefficient to reveal molecular basis of cellular events. Therefore, data integration from multiple heterogeneous sources is highly desirable and required. In this study, we developed a data- and model-driven hybrid approach to evaluate biological activity of cellular processes. Biological pathway models were taken as graphs and gene scores were transferred through neighbouring nodes of these graphs. An activity score describes the behaviour of a specific biological process was computed by owing of converged gene scores until reaching a target process. Biological pathway model based approach that we describe in this study is a novel approach in which converged scores are calculated for the cellular processes of a cyclic pathway. The convergence of the activity scores for cyclic graphs were demonstrated on the KEGG pathways. © 2011 Springer Science+Business Media B.V.
Open Access
Differential privacy with bounded priors: Reconciling utility and privacy in genome-wide association studies
(ACM, 2015-10) Tramèr, F.; Huang, Z.; Hubaux J.-P.; Ayday, Erman
Differential privacy (DP) has become widely accepted as a rigorous definition of data privacy, with stronger privacy guarantees than traditional statistical methods. However, recent studies have shown that for reasonable privacy budgets, differential privacy significantly affects the expected utility. Many alternative privacy notions which aim at relaxing DP have since been proposed, with the hope of providing a better tradeoff between privacy and utility. At CCS'13, Li et al. introduced the membership privacy framework, wherein they aim at protecting against set membership disclosure by adversaries whose prior knowledge is captured by a family of probability distributions. In the context of this framework, we investigate a relaxation of DP, by considering prior distributions that capture more reasonable amounts of background knowledge. We show that for different privacy budgets, DP can be used to achieve membership privacy for various adversarial settings, thus leading to an interesting tradeoff between privacy guarantees and utility. We re-evaluate methods for releasing differentially private χ2-statistics in genome-wide association studies and show that we can achieve a higher utility than in previous works, while still guaranteeing membership privacy in a relevant adversarial setting. © 2015 ACM.
Open Access
Environmental effect and genetic influence: A regional cancer predisposition survey in the Zonguldak region of Northwest Turkey
(Springer-Verlag, 2008) Kadir, S.; Önen-Hall, A. P.; Aydin, S. N.; Yakicier, C.; Akarsu, N.; Tuncer, M.
The Cretaceous-Eocene volcano-sedimentary units of the Zonguldak region of the western Black Sea consist of subalkaline andesite and tuff, and sandstone dominated by smectite, kaolinite, accessory chlorite, illite, mordenite, and analcime associated with feldspar, quartz, opal-CT, amphibole, and calcite. Kaolinization, chloritization, sericitization, albitization, Fe-Ti-oxidation, and the presence of zeolite, epidote, and illite in andesitic rocks and tuffaceous materials developed as a result of the degradation of a glass shards matrix, enclosed feldspar, and clinopyroxene-type phenocrysts, due to alteration processes. The association of feldspar and glass with smectite and kaolinite, and the suborientation of feldspar-edged, subparallel kaolinite plates to fracture axes may exhibit an authigenic smectite or kaolinite. Increased alteration degree upward in which Al, Fe, and Ti are gained, and Si, Na, K, and Ca are depleted, is due to the alteration following possible diagenesis and hydrothermal activities. Micromorphologically, fibrous mordenite in the altered units and the presence of needle-type chrysotile in the residential buildings in which cancer cases lived were detected. In addition, the segregation pattern of cancer susceptibility in the region strongly suggested an environmental effect and a genetic influence on the increased cancer incidence in the region. The most likely diagnosis was Li-Fraumeni syndrome, which is one of the hereditary cancer predisposition syndromes; however, no mutations were observed in the p53 gene, which is the major cause of Li-Fraumeni syndrome. The micromorphology observed in the altered units in which cancer cases were detected may have a role in the expression of an unidentified gene, but does not explain alone the occurrence of cancer as a primary cause in the region. © 2007 Springer-Verlag.
Open Access
GenoGuard: protecting genomic data against brute-force attacks
(IEEE, 2015-05) Huang, Z.; Ayday, Erman; Fellay, Jacques; Hubaux, J-P.; Juels, A.
Secure storage of genomic data is of great and increasing importance. The scientific community's improving ability to interpret individuals' genetic materials and the growing size of genetic database populations have been aggravating the potential consequences of data breaches. The prevalent use of passwords to generate encryption keys thus poses an especially serious problem when applied to genetic data. Weak passwords can jeopardize genetic data in the short term, but given the multi-decade lifespan of genetic data, even the use of strong passwords with conventional encryption can lead to compromise. We present a tool, called Geno Guard, for providing strong protection for genomic data both today and in the long term. Geno Guard incorporates a new theoretical framework for encryption called honey encryption (HE): it can provide information-theoretic confidentiality guarantees for encrypted data. Previously proposed HE schemes, however, can be applied to messages from, unfortunately, a very restricted set of probability distributions. Therefore, Geno Guard addresses the open problem of applying HE techniques to the highly non-uniform probability distributions that characterize sequences of genetic data. In Geno Guard, a potential adversary can attempt exhaustively to guess keys or passwords and decrypt via a brute-force attack. We prove that decryption under any key will yield a plausible genome sequence, and that Geno Guard offers an information-theoretic security guarantee against message-recovery attacks. We also explore attacks that use side information. Finally, we present an efficient and parallelized software implementation of Geno Guard. © 2015 IEEE.
Open Access
Genomic landscape of the Greater Middle East
(Nature Publishing Group, 2016-09) Özçelik, T.; Onat, O. E.
Study of the Greater Middle East (GME), home to approximately 10% of the world's population, has made invaluable contributions to the characterization of rare genetic disease, especially recessive conditions arising from the tradition of consanguinity and large families with multiple children. A new study now reports 1,111 unrelated exomes from the GME and provides a comprehensive view of genetic variation for enhanced discovery of disease-associated genes.
Open Access
HER2 and proliferation of wound-induced breast carcinoma
(The Lancet Publishing, 2003-11-01) Tez, M.; Göçmen, E.; Özçelik, T.
Open Access
Inference attacks against kin genomic privacy
(Institute of Electrical and Electronics Engineers Inc., 2017) Ayday, E.; Humbert M.
Genomic data poses serious interdependent risks: your data might also leak information about your family members' data. Methods attackers use to infer genomic information, as well as recent proposals for enhancing genomic privacy, are discussed. © 2003-2012 IEEE.
Open Access
Inter-varietal structural variation in grapevine genomes
(Wiley-Blackwell Publishing Ltd., 2016) Cardone, M. F.; D'Addabbo, P.; Alkan C.; Bergamini, C.; Catacchio, C. R.; Anaclerio, F.; Chiatante, G.; Marra, A.; Giannuzzi, G.; Perniola, R.; Ventura M.; Antonacci, D.
Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent inï¿½situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties
Open Access
Mammalian telomeric DNA suppresses endotoxin-induced uveitis
(American Society for Biochemistry and Molecular Biology Inc., 2010) Yagci, F. C.; Aslan, O.; Gursel, M.; Tincer, G.; Özdamar, Y.; Karatepe, K.; Akcali, K. C.; Gursel, I.
Telomeric regions of mammalian chromosomes contain suppressive TTAGGG motifs that inhibit several proinflammatory and Th1-biased immune responses. Synthetic oligodeoxynucleotides (ODN) expressing suppressive motifs can reproduce the down-regulatory activity of mammalian telomeric repeats and have proven effective in the prevention and treatment of several autoimmune and autoinflammatory diseases. Endotoxin-induced uveitis (EIU) is an established animal model of acute ocular inflammation induced by LPS administration. Augmented expression of proinflammatory cytokines/chemokines such as TNFα, IL-6, and MCP1 and bactericidal nitric oxide production mediated by LPS contribute to the development of EIU. Suppressing these mediators using agents that are devoid of undesirable systemic side effects may help prevent the development of EIU. This study demonstrates the selective down-regulatory role of suppressive ODN after (i) local or (ii) systemic treatment in EIU-induced rabbits and mice. Our results indicate that suppressive ODN down-regulate at both the transcript and protein levels of several proinflammatory cytokines and chemokines as well as nitric oxide and co-stimulatory surface marker molecules when administrated prior to, simultaneously with, or even after LPS challenge, thereby significantly reducing ocular inflammation in both rabbit and mouse eyes. These findings strongly suggest that suppressive ODN is a potent candidate for the prevention of uveitis and could be applied as a novel DNA-based immunoregulatory agent to control other autoimmune or autoinflammatory diseases. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.
Open Access
On non-cooperative genomic privacy
(Springer, Berlin, Heidelberg, 2015) Humbert, M.; Ayday, Erman; Hubaux J.-P.; Telenti, A.
Over the last few years, the vast progress in genome sequencing has highly increased the availability of genomic data. Today, individuals can obtain their digital genomic sequences at reasonable prices from many online service providers. Individuals can store their data on personal devices, reveal it on public online databases, or share it with third parties. Yet, it has been shown that genomic data is very privacysensitive and highly correlated between relatives. Therefore, individuals’ decisions about how to manage and secure their genomic data are crucial. People of the same family might have very different opinions about (i) how to protect and (ii) whether or not to reveal their genome. We study this tension by using a game-theoretic approach. First, we model the interplay between two purely-selfish family members. We also analyze how the game evolves when relatives behave altruistically. We define closed-form Nash equilibria in different settings. We then extend the game to N players by means of multi-agent influence diagrams that enable us to efficiently compute Nash equilibria. Our results notably demonstrate that altruism does not always lead to a more efficient outcome in genomic-privacy games. They also show that, if the discrepancy between the genome-sharing benefits that players perceive is too high, they will follow opposite sharing strategies, which has a negative impact on the familial utility. © International Financial Cryptography Association 2015.
Open Access
Privacy and security in the genomic era
(ACM, 2016-10) Ayday, Erman; Hubaux, Jean-Pierre
With the help of rapidly developing technology, DNA sequencing is becoming less expensive. As a consequence, the research in genomics has gained speed in paving the way to personalized (genomic) medicine, and geneticists need large collections of human genomes to further increase this speed. Furthermore, individuals are using their genomes to learn about their (genetic) predispositions to diseases, their ancestries, and even their (genetic) compatibilities with potential partners. This trend has also caused the launch of health-related websites and online social networks (OSNs), in which individuals share their genomic data (e.g., Open-SNP or 23 and Me). On the other hand, genomic data carries much sensitive information about its owner. By analyzing the DNA of an individual, it is now possible to learn about his disease predispositions (e.g., for Alzheimer's or Parkinson's), ancestries, and physical attributes. The threat to genomic privacy is magnified by the fact that a person's genome is correlated to his family members' genomes, thus leading to interdependent privacy risks. This short tutorial will help computer scientists better understand the privacy and security challenges in today's genomic era. We will first highlight the significance of genomic data and the threats for genomic privacy. Then, we will present the high level descriptions of the proposed solutions to protect the privacy of genomic data and we will discuss future research directions. No prerequisite knowledge on biology or genomics is required for the attendees of this proposal. We only require the attendees to have a slight background on cryptography and statistics.
Open Access
Privacy in the genomic era
(Association for Computing Machinery, 2015) Naveed, M.; Ayday, E.; Clayton, E.W.; Fellay J.; Gunter, C.A.; Hubaux J.-P.; Malin, B.A.; Wang, X.
Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highlydetailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. © 2015 ACM 0360-0300/2015/08-ART6 $15.00.
Open Access
Privacy threats and practical solutions for genetic risk tests
(IEEE, 2015) Barman, L.; Elgraini, M.-T.; Raisaro, J. L.; Hubaux, J. -P.; Ayday, Erman
Recently, several solutions have been proposed to address the complex challenge of protecting individuals' genetic data during personalized medicine tests. In this short paper, we analyze different privacy threats and propose simple countermeasures for the generic architecture mainly used in the literature. In particular, we present and evaluate a new practical solution against a critical attack of a malicious medical center trying to actively infer raw genetic information of patients. © 2015 IEEE.
Open Access
Production and structural characterization of biosurfactant produced by newly isolated staphylococcus xylosus STF1 from petroleum contaminated soil
(Elsevier BV, 2015) Keskin, N. O. S.; Han, D.; Ozkan A.D.; Angun, P.; Umu, O. C. O.; Tekinay, T.
Petroleum-contaminated soil was used to isolate and characterize biosurfactant producing bacteria. The strain could produce higher amount of biosurfactant in medium supplemented with motor oil as sole source of carbon and energy. A new biosurfactant producing bacterium, designated as Staphylococcus xylosus STF1 based on morphological, physiological, biochemical tests and 16S rRNA gene sequencing. The isolated bacterium was first screened for the ability to produce biosurfactant. Partial sequence of STF1 strain of 16S rDNA gene was highly similar to those of various members of the family Staphylococcaceae. Biochemical characterizations including FT-IR, Raman spectroscopy and Mass spectroscopy studies suggested the biosurfactant to be lipopeptide. Study also confirmed that the cell free supernatant exhibited high emulsifying activity against the different hydrocarbons. Moreover, the partially purified biosurfactant exhibited antimicrobial activity by inhibiting the growth of several bacterial species. The strain could be a potential candidate for the production of polypeptide biosurfactant which could be useful in a variety of biotechnological and industrial processes, particularly in the food and oil industry. © 2015 Elsevier B.V.
Open Access
Quantifying genomic privacy via inference attack with high-order SNV correlations
(IEEE, 2015) Samani, S. S.; Huang, Z.; Ayday, Erman; Elliot, M.; Fellay, J.; Hubaux, J.-P.; Kutalik, Z.
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.
Open Access
Stability analysis of a dynamical model representing gene regulatory networks
(2012) Ahsen, M. E.; Özbay, Hitay; Niculescu, S. I.
In this paper we perform stability analysis of a class of cyclic biological processes involving time delayed feedback. More precisely, we analyze the genetic regulatory network having nonlinearities with negative Schwarzian derivatives. We derive a set of conditions implying global stability of the genetic regulatory network under positive feedback. As a special case, we also consider homogenous genetic regulatory networks and obtain an appropriate stability condition which depends only on the parameters of the nonlinearity function. © 2012 IFAC.