Grundberg E, Meduri E, Sandling JK, Hedman AK, Keildson S, Buil A, et al. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet. 2013;93:876–90.
Article
CAS
PubMed Central
PubMed
Google Scholar
Erlich Y, Narayanan A. Routes for breaching and protecting genetic privacy. Nat Rev Genet. 2014;15:409–21.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lin Z, Owen AB, Altman RB. Genetics. Genomic research and human subject privacy. Science. 2004;305:183.
Article
CAS
PubMed
Google Scholar
Lee HY, Park MJ, Yoo JE, Chung U, Han GR, Shin KJ. Selection of twenty-four highly informative SNP markers for human identification and paternity analysis in Koreans. Forensic Sci Int. 2005;148:107–12.
Article
CAS
PubMed
Google Scholar
Joly Y, Zeps N, Knoppers BM. Genomic databases access agreements: legal validity and possible sanctions. Hum Genet. 2011;130:441–9.
Article
CAS
PubMed
Google Scholar
Greenbaum D, Sboner A, Mu XJ, Gerstein M. Genomics and privacy: implications of the new reality of closed data for the field. PLoS Comput Biol. 2011;7:e1002278.
Article
CAS
PubMed Central
PubMed
Google Scholar
National Institutes of Health. NIH Genomic Data Sharing Policy (NOT-OD-14-124). 2014. http://grants.nih.gov/grants/guide/notice-files/NOT-OD-14-124.html. Accessed 1 July 2015.
Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, et al. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2012;19:196–201.
Article
PubMed Central
PubMed
Google Scholar
Nietfeld JJ, Sugarman J, Litton JE. The Bio-PIN: a concept to improve biobanking. Nat Rev Cancer. 2011;11:303–8.
Article
CAS
PubMed
Google Scholar
Wolfson M, Wallace SE, Masca N, Rowe G, Sheehan NA, Ferretti V, et al. DataSHIELD: resolving a conflict in contemporary bioscience - performing a pooled analysis of individual-level data without sharing the data. Int J Epidemiol. 2010;39:1372–82.
Article
PubMed Central
PubMed
Google Scholar
Data Levels and Data Types. The Cancer Genome Atlas Data Portal. https://tcga-data.nci.nih.gov/tcga/tcgaDataType.jsp. Accessed 1 July 2015.
Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, et al. Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science. 2013;342:744–7.
Article
CAS
PubMed
Google Scholar
Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, et al. DNase I sensitivity QTLs are a major determinant of human expression variation. Nature. 2012;482:390–4.
Article
CAS
PubMed Central
PubMed
Google Scholar
McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, et al. Identification of genetic variants that affect histone modifications in human cells. Science. 2013;342:747–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lin X, Sun D, Rodriguez B, Zhao Q, Sun H, Zhang Y, et al. BSeQC: quality control of bisulfite sequencing experiments. Bioinformatics. 2013;29:3227–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012;13:R83.
Article
PubMed Central
PubMed
Google Scholar
Jin SG, Kadam S, Pfeifer GP. Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids Res. 2010;38:e125.
Article
PubMed Central
PubMed
Google Scholar
Guo JU, Su Y, Zhong C, Ming GL, Song H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell. 2011;145:423–34.
Article
CAS
PubMed Central
PubMed
Google Scholar
Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012;13:R61.
Article
CAS
PubMed Central
PubMed
Google Scholar
Barturen G, Rueda A, Oliver JL, Hackenberg M. MethylExtract: high-quality methylation maps and SNV calling from whole genome bisulfite sequencing data. F1000Res. 2013;2:217.
PubMed Central
PubMed
Google Scholar
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al. The NIH roadmap epigenomics mapping consortium. Nat Biotechnol. 2010;28:1045–8.
Article
CAS
PubMed Central
PubMed
Google Scholar
McGill Epigenomics Mapping Centre Portal. http://epigenomesportal.ca. Accessed 1 July 2015.
Allum F, Shao X, Guénard F, Simon MM, Busche S, Caron M, et al. Characterization of functional methylomes by next-generation capture sequencing identifies novel disease associated variants. Nat Commun. 2015;6:7211.
Article
PubMed
Google Scholar
Busche S, Ge B, Vidal R, Spinella JF, Saillour V, Richer C, et al. Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia. Cancer Res. 2013;73:4323–36.
Article
CAS
PubMed
Google Scholar
Grundberg E, Small KS, Hedman AK, Nica AC, Buil A, Keildson S, et al. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet. 2012;44:1084–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Malin B, Sweeney L. Re-identification of DNA through an automated linkage process. Proc AMIA Symp. 2001:423–7.
Sobrido MJ, Coppola G, Oliveira J, Hopfer S, Geschwind DH. Primary familial brain calcification. In: Pagon RA, Adam MP, Ardinger HH, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington; 1993–2015.
Consumer Partnership for eHealth. Protecting sensitive health information in the context of health information technology. June 2010. http://www.nationalpartnership.org/research-library/health-care/HIT/protecting-sensitive-health.pdf. Accessed 1 July 2015.
Kaback MM, Desnick RJ. Hexosaminidase A Deficiency. In: Pagon RA, Adam MP, Ardinger HH, editors. GeneReviews® [Internet]. Seattle (WA): University of Washington; 1993–2015.
Laberge AM, Michaud J, Richter A, Lemyre E, Lambert M, Brais B, et al. Population history and its impact on medical genetics in Quebec. Clin Genet. 2005;68:287–301.
Article
PubMed
Google Scholar
Weidner CI, Lin Q, Koch CM, Eisele L, Beier F, Ziegler P, et al. Aging of blood can be tracked by DNA methylation changes at just three CpG sites. Genome Biol. 2014;15:R24.
Article
PubMed Central
PubMed
Google Scholar
Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, et al. Extensive variation in chromatin states across humans. Science. 2013;342:750–2.
Article
CAS
PubMed Central
PubMed
Google Scholar
Benitez K, Malin B. Evaluating re-identification risks with respect to the HIPAA privacy rule. J Am Med Inform Assoc. 2010;17:169–77.
Article
PubMed Central
PubMed
Google Scholar
Sankar P, Cho MK. Genetics. Toward a new vocabulary of human genetic variation. Science. 2002;298:1337–8.
Article
CAS
PubMed Central
PubMed
Google Scholar
Caulfield T, Fullerton SM, Ali-Khan SE, Arbour L, Burchard EG, Cooper RS, et al. Race and ancestry in biomedical research: exploring the challenges. Genome Med. 2009;1:8.
Article
PubMed Central
PubMed
Google Scholar
National Institutes of Health. NIH policy and guidelines on the inclusion of women and minorities as subjects in clinical research; 2001. http://grants.nih.gov/grants/guide/notice-files/NOT-OD-02-001.html. Accessed 1 July 2015.
International HapMap Consortium. Integrating ethics and science in the International HapMap Project. Nat Rev Genet. 2004;5:467–75.
Article
Google Scholar
Smart A, Tutton R, Martin P, Ellison GT, Ashcroft R. The standardization of race and ethnicity in biomedical science editorials and UK biobanks. Soc Stud Sci. 2008;38:407–23.
Article
PubMed
Google Scholar
Gitschier J. Inferential genotyping of Y chromosomes in Latter-Day Saints founders and comparison to Utah samples in the HapMap project. Am J Hum Genet. 2009;84:251–8.
Article
CAS
PubMed Central
PubMed
Google Scholar
Schadt EE, Woo S, Hao K. Bayesian method to predict individual SNP genotypes from gene expression data. Nat Genet. 2012;44:603–8.
Article
CAS
PubMed
Google Scholar
Miura F, Enomoto Y, Dairiki R, Ito T. Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging. Nucleic Acids Res. 2012;40:e136.
Article
CAS
PubMed Central
PubMed
Google Scholar
Byun HM, Siegmund KD, Pan F, Weisenberger DJ, Kanel G, Laird PW, et al. Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet. 2009;18:4808–17.
Article
CAS
PubMed Central
PubMed
Google Scholar
Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013;8:203–9.
Article
CAS
PubMed Central
PubMed
Google Scholar
US-EU Safe Harbor Framework Documents. http://www.export.gov/safeharbor/eu/. Accessed 3 July 2015.
Milius D, Dove ES, Chalmers D, Dyke SO, Kato K, Nicolas P, et al. The International Cancer Genome Consortium’s evolving data-protection policies. Nat Biotechnol. 2014;32:519–23.
Article
CAS
PubMed
Google Scholar
Joly Y, Ngueng Feze I, Simard J. Genetic discrimination and life insurance: a systematic review of the evidence. BMC Med. 2013;11:25.
Article
PubMed Central
PubMed
Google Scholar
Caulfield T, Evans J, McGuire A, McCabe C, Bubela T, Cook-Deegan R, et al. Reflections on the cost of ‘low-cost’ whole genome sequencing: framing the health policy debate. PLoS Biol. 2013;11:e1001699.
Article
PubMed Central
PubMed
Google Scholar
Godard B, Pratte A, Dumont M, Simard-Lebrun A, Simard J. Factors associated with an individual’s decision to withdraw from genetic testing for breast and ovarian cancer susceptibility: implications for counseling. Genet Test. 2007;11:45–54.
Article
PubMed
Google Scholar
Phoenix Strategic Perspectives Inc. Survey of Canadians on privacy-related issues. Office of the Privacy Commissioner of Canada Ottawa, Canada. 2013. https://www.priv.gc.ca/information/por-rop/2013/por_2013_01_e.asp. Accessed 1 July 2015.
Keogh LA, van Vliet CM, Studdert DM, Maskiell JA, Macrae FA, St John DJ, et al. Is uptake of genetic testing for colorectal cancer influenced by knowledge of insurance implications? Med J Aust. 2009;191:255–8.
PubMed
Google Scholar
Geelen E, Horstman K, Marcelis CL, Doevendans PA, Van Hoyweghen I. Unravelling fears of genetic discrimination: an exploratory study of Dutch HCM families in an era of genetic non-discrimination acts. Eur J Hum Genet. 2012;20:1018–23.
Article
PubMed Central
PubMed
Google Scholar
Church GM. The personal genome project. Mol Syst Biol. 2005;1:2005.0030.
CAS
PubMed Central
PubMed
Google Scholar
Lunshof JE, Chadwick R, Vorhaus DB, Church GM. Science and society - from genetic privacy to open consent. Nat Rev Genet. 2008;9:406–11.
Article
CAS
PubMed
Google Scholar
Ball MP, Bobe JR, Chou MF, Clegg T, Estep PW, Lunshof JE, et al. Harvard Personal Genome Project: lessons from participatory public research. Genome Med. 2014;6:10.
Article
PubMed Central
PubMed
Google Scholar
Joly Y, Burton H, Knoppers BM, Feze IN, Dent T, Pashayan N, et al. Life insurance: genomic stratification and risk classification. Eur J Hum Genet. 2014;22:575–9.
Article
PubMed Central
PubMed
Google Scholar
Rothstein MA, Cai Y, Marchant GE. The ghost in our genes: legal and ethical implications of epigenetics. Health Matrix Clevel. 2009;19:1–62.
PubMed Central
PubMed
Google Scholar
Rothstein MA. Epigenetic exceptionalism. J Law Med Ethics. 2013;41:733–6.
PubMed
Google Scholar
U.S. Equal Employment Opportunity Commission. The Genetic Information Nondiscrimination Act (GINA) of 2008. Section 201(7). http://www.eeoc.gov/laws/statutes/gina.cfm. Accessed 1 July 2015.
Joly Y, Dove ES, Knoppers BM, Bobrow M, Chalmers D. Data sharing in the post-genomic world: the experience of the International Cancer Genome Consortium (ICGC) Data Access Compliance Office (DACO). PLoS Comput Biol. 2012;8:e1002549.
Article
CAS
PubMed Central
PubMed
Google Scholar
Philibert RA, Terry N, Erwin C, Philibert WJ, Beach SRH, Brody GH. Methylation array data can simultaneously identify individuals and convey protected health information: an unrecognized ethical concern. Clin Epigenet. 2014;6:28.
Article
Google Scholar
NIH Roadmap Epigenomics Project GEO Repository. ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/roadmapepigenomics/by_experiment/Bisulfite-Seq/. Accessed 1 July 2015.
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315–22.
Article
CAS
PubMed Central
PubMed
Google Scholar
Johnson MD, Mueller M, Game L, Aitman TJ. Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing. Curr Protoc Mol Biol. 2012;Chapter 21:Unit21.23.
PubMed
Google Scholar