Epigenome data release: a participant-centered approach to privacy protection

Assessing Privacy Vulnerabilities in Genetic Data Sets: Scoping Review

BACKGROUND

Genetic data are widely considered inherently identifiable. However, genetic data sets come in many shapes and sizes, and the feasibility of privacy attacks depends on their specific content. Assessing the reidentification risk of genetic data is complex, yet there is a lack of guidelines or recommendations that support data processors in performing such an evaluation.

OBJECTIVE

This study aims to gain a comprehensive understanding of the privacy vulnerabilities of genetic data and create a summary that can guide data processors in assessing the privacy risk of genetic data sets.

METHODS

We conducted a 2-step search, in which we first identified 21 reviews published between 2017 and 2023 on the topic of genomic privacy and then analyzed all references cited in the reviews (n=1645) to identify 42 unique original research studies that demonstrate a privacy attack on genetic data. We then evaluated the type and components of genetic data exploited for these attacks as well as the effort and resources needed for their implementation and their probability of success.

RESULTS

From our literature review, we derived 9 nonmutually exclusive features of genetic data that are both inherent to any genetic data set and informative about privacy risk: biological modality, experimental assay, data format or level of processing, germline versus somatic variation content, content of single nucleotide polymorphisms, short tandem repeats, aggregated sample measures, structural variants, and rare single nucleotide variants.

CONCLUSIONS

On the basis of our literature review, the evaluation of these 9 features covers the great majority of privacy-critical aspects of genetic data and thus provides a foundation and guidance for assessing genetic data risk.

Researcher perspectives on ethics considerations in epigenetics: an international survey

Over the past decade, bioethicists, legal scholars and social scientists have started to investigate the potential implications of epigenetic research and technologies on medicine and society. There is growing literature discussing the most promising opportunities, as well as arising ethical, legal and social issues (ELSI). This paper explores the views of epigenetic researchers about some of these discussions. From January to March 2020, we conducted an online survey of 189 epigenetic researchers working in 31 countries. We questioned them about the scope of their field, opportunities in different areas of specialization, and ELSI in the conduct of research and knowledge translation. We also assessed their level of concern regarding four emerging non-medical applications of epigenetic testing—i.e., in life insurance, forensics, immigration and direct-to-consumer testing. Although there was strong agreement on DNA methylation, histone modifications, 3D structure of chromatin and nucleosomes being integral elements of the field, there was considerable disagreement on transcription factors, RNA interference, RNA splicing and prions. The most prevalent ELSI experienced or witnessed by respondents were in obtaining timely access to epigenetic data in existing databases, and in the communication of epigenetic findings by the media. They expressed high levels of concern regarding non-medical applications of epigenetics, echoing cautionary appraisals in the social sciences and humanities literature.

Ethical implications of epigenetics in the era of personalized medicine

Given the increasing research activity on epigenetics to monitor human diseases and its connection with lifestyle and environmental expositions, the field of epigenetics has attracted a great deal of interest also at the ethical and societal level. In this review, we will identify and discuss current ethical, legal and social issues of epigenetics research in the context of personalized medicine. The review covers ethical aspects such as how epigenetic information should impact patient autonomy and the ability to generate an intentional and voluntary decision, the measures of data protection related to privacy and confidentiality derived from epigenome studies (e.g., risk of discrimination, patient re-identification and unexpected findings) or the debate in the distribution of responsibilities for health (i.e., personal versus public responsibilities). We pay special attention to the risk of social discrimination and stigmatization as a consequence of inferring information related to lifestyle and environmental exposures potentially contained in epigenetic data. Furthermore, as exposures to the environment and individual habits do not affect all populations equally, the violation of the principle of distributive justice in the access to the benefits of clinical epigenetics is discussed. In this regard, epigenetics represents a great opportunity for the integration of public policy measures aimed to create healthier living environments. Whether these public policies will coexist or, in contrast, compete with strategies reinforcing the personalized medicine interventions needs to be considered. The review ends with a reflection on the main challenges in epigenetic research, some of them in a technical dimension (e.g., assessing causality or establishing reference epigenomes) but also in the ethical and social sphere (e.g., risk to add an epigenetic determinism on top of the current genetic one). In sum, integration into life science investigation of social experiences such as exposure to risk, nutritional habits, prejudice and stigma, is imperative to understand epigenetic variation in disease. This pragmatic approach is required to locate clinical epigenetics out of the experimental laboratories and facilitate its implementation into society.

Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic

COVID-19 was declared to be a pandemic in March 2020 by the World Health Organization. Timely sharing of viral genomic sequencing data accompanied by a minimal set of contextual data is essential for informing regional, national, and international public health responses. Such contextual data is also necessary for developing, and improving clinical therapies and vaccines, and enhancing the scientific community’s understanding of the SARS-CoV-2 virus. The Canadian COVID-19 Genomics Network (CanCOGeN) was launched in April 2020 to coordinate and upscale existing genomics-based COVID-19 research and surveillance efforts. CanCOGeN is performing large-scale sequencing of both the genomes of SARS-CoV-2 virus samples (VirusSeq) and affected Canadians (HostSeq). This paper addresses the privacy concerns associated with sharing the viral sequence data with a pre-defined set of contextual data describing the sample source and case attribute of the sequence data in the Canadian context. Currently, the viral genome sequences are shared by provincial public health laboratories and their healthcare and academic partners, with the Canadian National Microbiology Laboratory and with publicly accessible databases. However, data sharing delays and the provision of incomplete contextual data often occur because publicly releasing such data triggers privacy and data governance concerns. The CanCOGeN Ethics and Governance Expert Working Group thus has investigated several privacy issues cited by CanCOGeN data providers/stewards. This paper addresses these privacy concerns and offers insights primarily in the Canadian context, although similar privacy considerations also exist in other jurisdictions. We maintain that sharing viral sequencing data and its limited associated contextual data in the public domain generally does not pose insurmountable privacy challenges. However, privacy risks associated with reidentification should be actively monitored due to advancements in reidentification methods and the evolving pandemic landscape. We also argue that during a global health emergency such as COVID-19, privacy should not be used as a blanket measure to prevent such genomic data sharing due to the significant benefits it provides towards public health responses and ongoing research activities.

Exploring the Ethics of Implementation of Epigenomics Technologies in Cancer Screening: A Focus Group Study

New epigenomics technologies are being developed and used for the detection and prediction of various types of cancer. By allowing for timely intervention or preventive measures, epigenomics technologies show promise for public health, notably in population screening. In order to assess whether implementation of epigenomics technologies in population screening may be morally acceptable, it is important to understand – in an early stage of development – ethical and societal issues that may arise. We held 3 focus groups with experts in science and technology studies (STS) (n = 13) in the Netherlands, on 3 potential future applications of epigenomic technologies in screening programmes of increasing scope: cervical cancer, female cancers and ‘global’ cancer. On the basis of these discussions, this paper identifies ethical issues pertinent to epigenomics-based population screening, such as risk communication, trust and public acceptance; personal responsibility, stigmatisation and societal pressure, and data protection and data governance. It also points out how features of epigenomics (eg, modifiability) and changing concepts (eg, of cancer) may challenge the existing evaluative framework for screening programmes. This paper aims to anticipate and prepare for future ethical challenges when epigenomics technologies can be tested and introduced in public health settings.

Toward a Framework for Assessing Privacy Risks in Multi-Omic Research and Databases

While the accumulation and increased circulation of genomic data have captured much attention over the past decade, privacy risks raised by the diversification and integration of omics have been largely overlooked. In this paper, we propose the outline of a framework for assessing privacy risks in multi-omic research and databases. Following a comparison of privacy risks associated with genomic and epigenomic data, we dissect ten privacy risk-impacting omic data properties that affect either the risk of re-identification of research participants, or the sensitivity of the information potentially conveyed by biological data. We then propose a three-step approach for the assessment of privacy risks in the multi-omic era. Thus, we lay grounds for a data property-based, 'pan-omic' approach that moves away from genetic exceptionalism. We conclude by inviting our peers to refine these theoretical foundations, put them to the test in their respective fields, and translate our approach into practical guidance.

Privacy considerations for sharing genomics data

An increasing amount of attention has been geared towards understanding the privacy risks that arise from sharing genomic data of human origin. Most of these efforts have focused on issues in the context of genomic sequence data, but the popularity of techniques for collecting other types of genome-related data has prompted researchers to investigate privacy concerns in a broader genomic context. In this review, we give an overview of different types of genome-associated data, their individual ways of revealing sensitive information, the motivation to share them as well as established and upcoming methods to minimize information leakage. We further discuss the concise threats that are being posed, who is at risk, and how the risk level compares to potential benefits, all while addressing the topic in the context of modern technology, methodology, and information sharing culture. Additionally, we will discuss the current legal situation regarding the sharing of genomic data in a selection of countries, evaluating the scope of their applicability as well as their limitations. We will finalize this review by evaluating the development that is required in the scientific field in the near future in order to improve and develop privacy-preserving data sharing techniques for the genomic context.

Conducting epigenetics research with refugees and asylum seekers: attending to the ethical challenges

An increase in global violence has forced the displacement of more than 70 million people, including 26 million refugees and 3.5 asylum seekers. Refugees and asylum seekers face serious socioeconomic and healthcare barriers and are therefore particularly vulnerable to physical and mental health risks, which are sometimes exacerbated by immigration policies and local social discriminations. Calls for a strong evidence base for humanitarian action have encouraged conducting research to address the barriers and needs of refugees and asylum seekers. Given the role of epigenetics factors to mediate the effect of psychological and environmental exposures, epigenetic modifications have been used as biomarkers for life adversity and disease states. Therefore, epigenetic research can be potentially beneficial to address some of the issues associated with refugees and asylum seekers. Here, we review the value of previous and ongoing epigenetic studies with traumatized populations, explore some of the ethical challenges associated with epigenetic research with refugees and asylees and offer suggestions to address or mitigate some of these challenges. Researchers have an ethical responsibility to implement strategies to minimize the harms and maximize the short and long-term benefits to refugee and asylee participants.

Ethical Issues in Research and Development of Epigenome-wide Technologies

To date, few scholarly discussions on ethical implications of epigenetics and epigenomics technologies have focused on the current phase of research and development, in which researchers are confronted with real and practical ethical dilemmas. In this article, a responsible research and innovation approach, using interviews and an expert meeting, is applied to a case of epigenomic test development for cervical cancer screening. This article provides an overview of ethical issues presently facing epigenomics researchers and test developers, and discusses 3 sets of issues in depth: (1) informed consent; (2) communication with donors and/or research participants, and (3) privacy and publication of data and research results. Although these issues are familiar to research ethics, some aspects are new and most require reinterpretation in the context of epigenomics technologies. With this article, we aim to start a discussion of the practical ethical issues rising in research and development of epigenomic technologies and to offer guidance for researchers working in the field of epigenetic and epigenomic technology.

Ethical dilemmas posed by mobile health and machine learning in psychiatry research

The application of digital technology to psychiatry research is rapidly leading to new discoveries and capabilities in the field of mobile health. However, the increase in opportunities to passively collect vast amounts of detailed information on study participants coupled with advances in statistical techniques that enable machine learning models to process such information has raised novel ethical dilemmas regarding researchers' duties to: (i) monitor adverse events and intervene accordingly; (ii) obtain fully informed, voluntary consent; (iii) protect the privacy of participants; and (iv) increase the transparency of powerful, machine learning models to ensure they can be applied ethically and fairly in psychiatric care. This review highlights emerging ethical challenges and unresolved ethical questions in mobile health research and provides recommendations on how mobile health researchers can address these issues in practice. Ultimately, the hope is that this review will facilitate continued discussion on how to achieve best practice in mobile health research within psychiatry.

DNA methylation aging clocks: challenges and recommendations

Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.

Epigenetics, ethics, law and society: A multidisciplinary review of descriptive, instrumental, dialectical and reflexive analyses

Epigenetics, defined as 'the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence', has emerged as a promissory yet controversial field of scientific inquiry over the past decade. Scholars from many disciplines have formulated both optimistic and cautionary claims regarding its potential normative implications. This article provides a comprehensive review of the nascent literature at the crossroads of epigenetics, ethics, law and society. It describes nine emerging areas of discussion, relating to (1) the impact of epigenetics on the nature versus nurture dualism, (2) the potential resulting biologization of the social, (3) the meaning of epigenetics for public health, its potential influence on (4) reproduction and parenting, (5) political theory and (6) legal proceedings, and concerns regarding (7) stigmatization and discrimination, (8) privacy protection and (9) knowledge translation. While there is some degree of similarity between the nature and content of these areas and the abundant literature on ethical, legal and social issues in genetics, the potential implications of epigenetics ought not be conflated with the latter. Critical studies on epigenetics are emerging within a separate space of bioethical and biopolitical investigations and claims, with scholars from various epistemological standpoints utilizing distinct yet complementary analytical approaches.

Twin Registries Moving Forward and Meeting the Future: A Review

Twin registries have developed as a valuable resource for the study of many aspects of disease and society over the years in many different countries. A number of these registries include large numbers of twins with data collected at varying information levels for twin cohorts over the past several decades. More recent expansion of twin datasets has allowed for the collection of genetic data, together with many other levels of 'omic' information along with multiple demographic, physiological, health outcomes and other measures typically used in epidemiologic research. Other twin data sources outside these registries reflect research interests in particular aspects of disease or specific phenotypic assessment. Twin registries have the potential to play a key role in many aspects of the artificial intelligence/machine learning-driven projects of the future and will continue to keep adapting to the changing research landscape.

Points-to-consider on the return of results in epigenetic research

As epigenetic studies become more common and lead to new insights into health and disease, the return of individual epigenetic results to research participants, in particular in large-scale epigenomic studies, will be of growing importance. Members of the International Human Epigenome Consortium (IHEC) Bioethics Workgroup considered the potential ethical, legal, and social issues (ELSI) involved in returning epigenetic research results and incidental findings in order to produce a set of 'Points-to-consider' (P-t-C) for the epigenetics research community. These P-t-C draw on existing guidance on the return of genetic research results, while also integrating the IHEC Bioethics Workgroup's ELSI research on and discussion of the issues associated with epigenetic data as well as the experience of a return of results pilot study by the Personal Genome Project UK (PGP-UK). Major challenges include how to determine the clinical validity and actionability of epigenetic results, and considerations related to environmental exposures and epigenetic marks, including circumstances warranting the sharing of results with family members and third parties. Interdisciplinary collaboration and good public communication regarding epigenetic risk will be important to advance the return of results framework for epigenetic science.

Epigenetics: ethics, politics, biosociality

BACKGROUND

Epigenetics is a burgeoning field of contemporary biosciences, which has attracted a lot of interest both in biomedical and in social sciences.

SOURCES OF DATA

Unsystematic literature analysis and retrospective mapping of highly cited work (source: Web of Science core collection) in the social sciences and humanities engaging with epigenetics.

AREAS OF AGREEMENT

Epigenetics poses no new ethical issue over and above those discussed in relation to genetics.

AREAS OF CONTROVERSY

However, it encourages a different framing and reflexivity on some of the commonly held categories in the moral uptake of scientific discoveries.

GROWING POINTS

Epigenetics presents us with normative questions that touch upon privacy, responsibility for individual health and for the well-being of future generations, as well as matters of health justice and equality of opportunities.

AREAS TIMELY FOR DEVELOPING RESEARCH

Epigenetic thinking could help us adjust and refine the problem frames and categories that inform our ethical and political questions with a complex biosocial description of situations, of persons or actions.

Opportunities for community awareness platforms in personal genomics and bioinformatics education

Precision and personalized medicine will be increasingly based on the integration of various type of information, particularly electronic health records and genome sequences. The availability of cheap genome sequencing services and the information interoperability will increase the role of online bioinformatics analysis. Being on the Internet poses constant threats to security and privacy. While we are connected and we share information, websites and internet services collect various types of personal data with or without the user consent. It is likely that genomics will merge with the internet culture of connectivity. This process will increase incidental findings, exposure and vulnerability. Here we discuss the social vulnerability owing to the genome and Internet combined security and privacy weaknesses. This urges more efforts in education and social awareness on how biomedical data are analysed and transferred through the internet and how inferential methods could integrate information from different sources. We propose that digital social platforms, used for raising collective awareness in different fields, could be developed for collaborative and bottom-up efforts in education. In this context, bioinformaticians could play a meaningful role in mitigating the future risk of digital-genomic divide.

Epigenetic Discrimination: Emerging Applications of Epigenetics Pointing to the Limitations of Policies Against Genetic Discrimination

Over more than two decades, various policies have been adopted worldwide to restrict the use of individual genetic information for non-medical reasons by third parties and prevent ‘genetic discrimination’. In this paper, we bring attention to the growing interest for individual epigenetic information by insurers and forensic scientists. We question whether such interest could lead to ‘epigenetic discrimination’ – the differential adverse treatment or abusive profiling of individuals or groups based on their actual or presumed epigenetic characteristics – and argue that we might already be facing the limitations of recently adopted normative approaches against genetic discrimination. First, we highlight some similarities and differences between genetic and epigenetic modifications, and stress potential challenges to regulating epigenetic discrimination. Second, we argue that most existing normative approaches against genetic discrimination fall short in providing oversight into the field of epigenetics. We conclude with a call for discussion on the issue, and the development of comprehensive and forward-looking preventive strategies against epigenetic discrimination.

Cancer epigenetics: Moving forward

Defects in chromatin modifiers and remodelers have been described both for hematological and solid malignancies, corroborating and strengthening the role of epigenetic aberrations in the etiology of cancer. Furthermore, epigenetic marks-DNA methylation, histone modifications, chromatin remodeling, and microRNA-can be considered potential markers of cancer development and progression. Here, we review whether altered epigenetic landscapes are merely a consequence of chromatin modifier/remodeler aberrations or a hallmark of cancer etiology. We critically evaluate current knowledge on causal epigenetic aberrations and examine to what extent the prioritization of (epi)genetic deregulations can be assessed in cancer as some type of genetic lesion characterizing solid cancer progression. We also discuss the multiple challenges in developing compounds targeting epigenetic enzymes (named epidrugs) for epigenetic-based therapies. The implementation of acquired knowledge of epigenetic biomarkers for patient stratification, together with the development of next-generation epidrugs and predictive models, will take our understanding and use of cancer epigenetics in diagnosis, prognosis, and treatment of cancer patients to a new level.

A catalog of potential putative functional variants in psoriasis genome-wide association regions

Psoriasis is a common inflammatory skin disease, with considerable genetic contribution. Genome-wide association studies have successfully identified a number of genomic regions for the risk of psoriasis. However, it is challenging to pinpoint the functional causal variants and then further decipher the genetic mechanisms underlying each region. In order to prioritize potential functional causal variants within psoriasis susceptibility regions, we integrated the genetic association findings and functional genomic data publicly available, i.e. histone modifications in relevant immune cells. We characterized a pervasive enrichment pattern of psoriasis variants in five core histone marks across immune cells/tissues. We discovered that genetic alleles within psoriasis association regions might influence gene expression levels through significantly affecting the binding affinities of 17 transcription factors. We established a catalog of 654 potential functional causal variants for psoriasis and suggested that they significantly overlapped with causal variants for autoimmune diseases. We identified potential causal variant rs79824801 overlay with the peaks of five histone marks in primary CD4+ T cells. Its alternative allele affected the binding affinity of transcription factor IKZF1. This study highlights the complex genetic architecture and complicated mechanisms for psoriasis. The findings will inform the functional experiment design for psoriasis.

Person-oriented research ethics: integrating relational and everyday ethics in research

Research ethics is often understood by researchers primarily through the regulatory framework reflected in the research ethics review process. This regulatory understanding does not encompass the range of ethical considerations in research, notably those associated with the relational and everyday aspects of human subject research. In order to support researchers in their effort to adopt a broader lens, this article presents a "person-oriented research ethics" approach. Five practical guideposts of person-oriented research ethics are identified, as follows: (1) respect for holistic personhood; (2) acknowledgement of lived world; (3) individualization; (4) focus on researcher-participant relationships; and (5) empowerment in decision-making. These guideposts are defined and illustrated with respect to different aspects of the research process (e.g., research design, recruitment, data collection). The person-oriented research ethics approach provides a toolkit to individual researchers, research groups, and research institutions in both biomedical and social science research wishing to expand their commitment to ethics in research.

Are Data Sharing and Privacy Protection Mutually Exclusive?

We review emerging strategies to protect the privacy of research participants in international epigenome research: open consent, genome donation, registered access, automated procedures, and privacy-enhancing technologies.

Evolving data access policy: The Canadian context

In setting up a data access policy to share controlled access data from the McGill Epigenomics Mapping Centre (EMC), an International Human Epigenome Consortium (IHEC) partner project, we encountered ethical and legal challenges that are likely to be relevant to other researchers sharing data, especially from Canadian projects. We discuss our solutions to the following data-sharing challenges, based on comparative legal and policy analysis: (1) providing access to data to a growing number of researchers; (2) maintaining Canadian privacy standards while sharing controlled access data internationally; (3) freedom of information requests; and (4) providing more incentives for researchers to share pre-publication data.

Das Tumorepigenom – von der Genregulation über die Tumorklassifikation zum Therapietarget

Epigenetische Regulationsmechanismen sind essenziell für den koordinierten Ablauf zahlreicher zellulärer Prozesse wie die Differenzierung und Entwicklung oder auch die Anpassung der Genaktivität an die herrschenden Umweltbedingungen. Insbesondere Tumorerkrankungen gehen mit oftmals umfangreichen Alterationen im Epigenom einher. Diese Veränderungen sind dabei vielfach charakteristisch entweder für die Tumorentität, das Stadium der Erkrankung oder aber das klinische Ansprechen des Tumors auf eine Therapie und damit die individuelle Prognose des Patienten. Nach einer kurzen Darstellung epigenetischer Marker und ihrer Bedeutung bei malignen Erkrankungen werden in diesem Artikel Alterationen im Tumorepigenom und ihre Nutzbarkeit im Rahmen einer individualisierten Medizin exemplarisch vorgestellt.

Sharing health-related data: a privacy test?

Greater sharing of potentially sensitive data raises important ethical, legal and social issues (ELSI), which risk hindering and even preventing useful data sharing if not properly addressed. One such important issue is respecting the privacy-related interests of individuals whose data are used in genomic research and clinical care. As part of the Global Alliance for Genomics and Health (GA4GH), we examined the ELSI status of health-related data that are typically considered 'sensitive' in international policy and data protection laws. We propose that 'tiered protection' of such data could be implemented in contexts such as that of the GA4GH Beacon Project to facilitate responsible data sharing. To this end, we discuss a Data Sharing Privacy Test developed to distinguish degrees of sensitivity within categories of data recognised as 'sensitive'. Based on this, we propose guidance for determining the level of protection when sharing genomic and health-related data for the Beacon Project and in other international data sharing initiatives.

Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

BACKGROUND

CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution.

RESULTS

Purely invariable CpGs display a bimodal distribution with enrichment of unmethylated CpGs and depletion of fully methylated CpGs in promoter and enhancer regions. Population-variable CpGs account for approximately 15-20 % of total CpGs per tissue, are enriched in enhancer-associated regions and depleted in promoters, and single nucleotide polymorphisms at CpGs are a frequent confounder of extreme methylation variation. Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific. Tobacco smoking is associated with differential methylation in blood with no evidence of this exposure impacting cell counts. Opposite to non-genetic effects, genetic effects of CpG methylation are shared across tissues and thus limit inter-tissue epigenetic drift. CpH methylation is rare, and shows similar characteristics of variation patterns as CpGs.

CONCLUSIONS

Our study highlights the utility of low pass whole-genome bisulfite sequencing in identifying methylome variation beyond promoter regions, and suggests that targeting the population dynamic methylome of tissues requires assessment of understudied intergenic CpGs distal to gene promoters to reveal the full extent of inter-individual variation.