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Inference Attacks against Kin Genomic Privacy

Erman Ayday, Mathias Humbert
2017 IEEE Security and Privacy  
Methods attackers use to infer genomic information, as well as recent proposals for enhancing genomic privacy, are discussed.  ...  members) than previously. 6 Membership Inference in Genomic Databases In 2008, Nils Homer and his colleagues identified an attack against genomic privacy that determined a targeted individual's membership  ...  In particular, DNA methylation, one of the most important epigenomic elements, was recently shown to be reidentifiable through genotype inference, 33 because parts of the DNA methylation are influenced  ... 
doi:10.1109/msp.2017.3681052 fatcat:uz5tck3alzalbgmtrkfu4au3zm

Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons [article]

Kerem Ayoz and Erman Ayday and A. Ercument Cicek
2020 arXiv   pre-print
However, beacon protocol was recently shown to be vulnerable against membership inference attacks.  ...  In this paper, we show that privacy threats against genomic data sharing beacons are not limited to membership inference.  ...  They proposed a beacon system for sharing DNA methylation data (an epigenetic mechanism to regulate transcriptional activity) and then showed that it is possible to successfully launch a membership inference  ... 
arXiv:2001.08852v2 fatcat:6nkz5pocsvhn7ok53hrmioywaa

Aging effects on DNA methylation modules in human brain and blood tissue

Steve Horvath, Yafeng Zhang, Peter Langfelder, René S Kahn, Marco PM Boks, Kristel van Eijk, Leonard H van den Berg, Roel A Ophoff
2012 Genome Biology  
Several recent studies reported aging effects on DNA methylation levels of individual CpG dinucleotides.  ...  DNA methylation data sets and clinical data description Although many platforms exist for measuring methylation levels [22] , the 16 DNA methylation data sets considered here were measured on the Illumina  ...  To protect against spurious artifacts due to batch effects, we used the following approaches.  ... 
doi:10.1186/gb-2012-13-10-r97 pmid:23034122 pmcid:PMC4053733 fatcat:5odes5hxtfh67ic7tmhmixfdqu

Panomics: New Databases for Advancing Cardiology

Dara Vakili, Dina Radenkovic, Shreya Chawla, Deepak L. Bhatt
2021 Frontiers in Cardiovascular Medicine  
We identified 104 omic databases, of which 72 met the inclusion criteria: genomic and clinical measurements on a subset of the database population plus one or more omic datasets.  ...  Of those, 65 were methylomic, 59 transcriptomic, 41 proteomic, 42 metabolomic, and 22 microbiomic databases.  ...  Methylome: Deoxyribonucleic acid (DNA) methylation data available as methylation arrays or deep sequencing.  ... 
doi:10.3389/fcvm.2021.587768 pmid:34041278 pmcid:PMC8142819 fatcat:7nergkdtgbfgxdwrao7gftym6e

The UCSC Interaction Browser: multidimensional data views in pathway context

Christopher K. Wong, Charles J. Vaske, Sam Ng, J. Zachary Sanborn, Stephen C. Benz, David Haussler, Joshua M. Stuart
2013 Nucleic Acids Research  
High-throughput data sets such as genome-wide protein-protein interactions, protein-DNA interactions and gene expression data have been published for several model systems, especially for human cancer  ...  (A) Left matrix represents DNA methylation data; right matrix mRNA expression data for the same genes (rows) and 10 samples (columns) as for the DNA methylation data.  ...  For example, most genes have increasing DNA methylation and decreasing mRNA expression (left to right orientation in the heatmap), an anti-correlation relationship that is expected because DNA methylation  ... 
doi:10.1093/nar/gkt473 pmid:23748957 pmcid:PMC3692096 fatcat:gtkifbnbf5chdd52x3kajzcpla

Identification of Five Hub Genes as Key Prognostic Biomarkers in Liver Cancer via Integrated Bioinformatics Analysis

Thong Ba Nguyen, Duy Ngoc Do, Tung Nguyen-Thanh, Vinay Bharadwaj Tatipamula, Ha Thi Nguyen
2021 Biology  
The weighted gene co-expression network analysis (WCGNA) was performed on the main data attained from the GEO (Gene Expression Omnibus) database.  ...  Based on the results of protein–protein interaction, gene co-expression network, and survival analyses, DNA topoisomerase II alpha (TOP2A), ribonucleotide reductase regulatory subunit M2 (RRM2), never  ...  DNA methylation is an important early event in tumor growth and progression [49] .  ... 
doi:10.3390/biology10100957 pmid:34681056 fatcat:rctplcvianhjvbt52uuyjbxgwy

A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

S. Saxonov, P. Berg, D. L. Brutlag
2006 Proceedings of the National Academy of Sciences of the United States of America  
The overall depletion of CpGs throughout the genome is thought to be a consequence of the methylation of some germ-line CpGs and their susceptibility to mutation.  ...  A comparison of the frequencies of inferred deamination mutations at CpG and GpC dinucleotides in the two classes of promoters using SNPs in human-chimpanzee sequence alignments shows that CpGs mutate  ...  CpG islands ͉ DNA methylation ͉ epigenetics ͉ gene expression I n vertebrates, the postreplication addition of methyl groups to the 5-position of cytosine in certain CpG dinucleotides and the maintenance  ... 
doi:10.1073/pnas.0510310103 pmid:16432200 pmcid:PMC1345710 fatcat:olympthlerfstkhctnrd5hienu

Development and Evaluation of the Ancestry Informative Marker Panel of the VISAGE Basic Tool

María de la Puente, Jorge Ruiz-Ramírez, Adrián Ambroa-Conde, Catarina Xavier, Jacobo Pardo-Seco, Jose Álvarez-Dios, Ana Freire-Aradas, Ana Mosquera-Miguel, Theresa E. Gross, Elaine Y. Y. Cheung, Wojciech Branicki, Michael Nothnagel (+7 others)
2021 Genes  
which combines 41 appearance predictive SNPs and 112 ancestry predictive SNPs (three SNPs shared between sets) in one massively parallel sequencing (MPS) multiplex, whereas blood-based age analysis using methylation  ...  These SNPbased tests have now been supplemented with DNA analyses that measure the methylation status of carefully chosen CpG sites showing age-correlated methylation patterns in order to estimate a donor's  ...  detected in the gnomAD 3.1 database.  ... 
doi:10.3390/genes12081284 pmid:34440458 pmcid:PMC8391248 fatcat:4bbcmemerffv7mzxkqzgt2yo74

Gene set enrichment; a problem of pathways

M. N. Davies, E. L. Meaburn, L. C. Schalkwyk
2010 Briefings in Functional Genomics  
Currently, the gene sets used for GSE are derived from annotation or pathway databases, which often contain computationally based and unrepresentative data.  ...  sequence variation and gene expression) and epigenetic (DNA methylation) variation accounts for individual differences in behaviour during childhood and adolescence.  ...  In reality, the complex nature of the genome is such that there is no way to establish a precise cut-off point that would determine membership or non-membership of any given set.  ... 
doi:10.1093/bfgp/elq021 pmid:20861160 pmcid:PMC3080747 fatcat:pibyiwieonazvmgmwpv6kijnyy

Epigenetic mediation of the onset of reproduction in a songbird [article]

Melanie Lindner, Veronika N. Laine, Irene Verhagen, Heidi M. Viitaniemi, Marcel E. Visser, Kees van Oers, Arild Husby
2020 bioRxiv   pre-print
Here, we used genome-wide DNA methylation profiles of individual great tit (Parus major) females that we blood sampled repeatedly throughout the breeding season.  ...  We demonstrate rapid and directional variation in DNA methylation within the regulatory region of genes known to play key roles in avian reproduction that are in line with observed changes in gene expression  ...  Each tested CpG site (n=5,097) is displayed as 107 dot and plotted against the location of the associated CpG site within the genome.  ... 
doi:10.1101/2020.02.01.929968 fatcat:z4bmj4pcqjgfplde4kvevou7ta

Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments

Y. Wang, R. S. van der Hoeven, R. Nielsen, L. A. Mueller, S. D. Tanksley
2005 Theoretical and Applied Genetics  
A collection of 9,990 single-pass nuclear genomic sequences, corresponding to 5 Mb of tomato DNA, were obtained using methylation filtration (MF) strategy and reduced to 7,053 unique undermethylated genomic  ...  This result indicates that, while most genes reside in the euchromatin, a significant portion of euchromatin is methylated in the intergenic spacer regions.  ...  library for non-methylated DNA fragments.  ... 
doi:10.1007/s00122-005-0107-z pmid:16208505 fatcat:dbn5rcevrreqlahmqyostv6rfi

Modular dynamics of DNA co-methylation networks exposes the functional organization of colon cancer cells' genome [article]

Izaskun Mallona, Susanna Aussó, Anna Díez-Villanueva, Víctor Moreno, Miguel A. Peinado
2018 bioRxiv   pre-print
DNA methylation profiles are variable and are extensively altered in most cancers.  ...  We show that DNA methylation variability follows a transchromosomal modular dynamics in both normal and colon cancer cells.  ...  B, Distribution of probes according to the mean 553 DNA methylation values in normal tissue (Y-axis) against the tumor-normal delta value (X-554 axis).  ... 
doi:10.1101/428730 fatcat:a2o25opthfdrxistslsxv7rhke

Evolution of an Epigenetic Gene Ensemble within the Genus Anopheles

Adam M. Jenkins, Marc A.T. Muskavitch
2015 Genome Biology and Evolution  
Epigenetic control of gene expression through histone acetylation and methylation, and DNA methylation, mediates compaction and decompaction of DNA within euchromatic and heterochromatic chromatin (Guil  ...  In contrast, evolution of DNA methylation within the genus Drosophila has been investigated based on the presence of a single methyltransferase gene, Dmnt2, compared with the multiple DNA methyltransferases  ... 
doi:10.1093/gbe/evv041 pmid:25724208 pmcid:PMC5322554 fatcat:4wro4ezpvrazpdstzwkeadu6ay

Cell death upon epigenetic genome methylation: a novel function of methyl-specific deoxyribonucleases

Eri Fukuda, Katarzyna H Kaminska, Janusz M Bujnicki, Ichizo Kobayashi
2008 Genome Biology  
A methyl-specific deoxyribonuclease, McrBC, of Escherichia coli cuts invading methylated DNAs.  ...  To our knowledge, this represents the first report of a defense system against epigenetic systems through cell death.  ...  Acknowledgements We are grateful to Mikihiko Kawai, Robert Blumenthal, and Chihiro Sasakawa for the gift of plasmids, Issei Narumi, Toshiaki Fukui, and Yutaka Kawarabayashi for the gift of genomic DNA,  ... 
doi:10.1186/gb-2008-9-11-r163 pmid:19025584 pmcid:PMC2614495 fatcat:auaftjkt4ndbxlq56ozyttntxu

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

A. Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D. Cherniack, Toshinori Hinoue, Peter W. Laird, Katherine A. Hoadley, Rehan Akbani, Mauro A.A. Castro, Ewan A. Gibb (+201 others)
2017 Cell  
B values range from zero to one, with scores of "0" indicating no DNA methylation and scores of "1" indicating complete DNA methylation.  ...  We dichotomized the DNA methylation data using a β value of >0.3 as a threshold for positive DNA methylation and eliminated CpG sites methylated in fewer than 3% of the tumor samples.  ... 
doi:10.1016/j.cell.2017.09.007 pmid:28988769 pmcid:PMC5687509 fatcat:fwsc7zoecvbetcpnmumlpyfdw4
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