Pragmatic and Ethical Challenges of Incorporating the Genome into the Electronic Medical Record

Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes

The repurposing of biomedical data is inhibited by its fragmented and multi-formatted nature that requires redundant investment of time and resources by data scientists. This is particularly true for Type 1 Diabetes (T1D), one of the most intensely studied common childhood diseases. Intense investigation of the contribution of pancreatic β-islet and T-lymphocytes in T1D has been made. However, genetic contributions from B-lymphocytes, which are known to play a role in a subset of T1D patients, remain relatively understudied. We have addressed this issue through the creation of Biomedical Data Commons (BMDC), a knowledge graph that integrates data from multiple sources into a single queryable format. This increases the speed of analysis by multiple orders of magnitude. We develop a pipeline using B-lymphocyte multi-dimensional epigenome and connectome data and deploy BMDC to assess genetic variants in the context of Type 1 Diabetes (T1D). Pipeline-identified variants are primarily common, non-coding, poorly conserved, and are of unknown clinical significance. While variants and their chromatin connectivity are cell-type specific, they are associated with well-studied disease genes in T-lymphocytes. Candidates include established variants in the HLA-DQB1 and HLA-DRB1 and IL2RA loci that have previously been demonstrated to protect against T1D in humans and mice providing validation for this method. Others are included in the well-established T1D GRS2 genetic risk scoring method. More intriguingly, other prioritized variants are completely novel and form the basis for future mechanistic and clinical validation studies The BMDC community-based platform can be expanded and repurposed to increase the accessibility, reproducibility, and productivity of biomedical information for diverse applications including the prioritization of cell type-specific disease alleles from complex phenotypes.

The anatomy of electronic patient record ethics: a framework to guide design, development, implementation, and use

BACKGROUND

This manuscript presents a framework to guide the identification and assessment of ethical opportunities and challenges associated with electronic patient records (EPR). The framework is intended to support designers, software engineers, health service managers, and end-users to realise a responsible, robust and reliable EPR-enabled healthcare system that delivers safe, quality assured, value conscious care.

METHODS

Development of the EPR applied ethics framework was preceded by a scoping review which mapped the literature related to the ethics of EPR technology. The underlying assumption behind the framework presented in this manuscript is that ethical values can inform all stages of the EPR-lifecycle from design, through development, implementation, and practical application.

RESULTS

The framework is divided into two parts: context and core functions. The first part 'context' entails clarifying: the purpose(s) within which the EPR exists or will exist; the interested parties and their relationships; and the regulatory, codes of professional conduct and organisational policy frame of reference. Understanding the context is required before addressing the second part of the framework which focuses on EPR 'core functions' of data collection, data access, and digitally-enabled healthcare.

CONCLUSIONS

The primary objective of the EPR Applied Ethics Framework is to help identify and create value and benefits rather than to merely prevent risks. It should therefore be used to steer an EPR project to success rather than be seen as a set of inhibitory rules. The framework is adaptable to a wide range of EPR categories and can cater for new and evolving EPR-enabled healthcare priorities. It is therefore an iterative tool that should be revisited as new EPR-related state-of-affairs, capabilities or activities emerge.

Examination and diagnosis of electronic patient records and their associated ethics: a scoping literature review

Background

Electronic patient record (EPR) technology is a key enabler for improvements to healthcare service and management. To ensure these improvements and the means to achieve them are socially and ethically desirable, careful consideration of the ethical implications of EPRs is indicated. The purpose of this scoping review was to map the literature related to the ethics of EPR technology. The literature review was conducted to catalogue the prevalent ethical terms, to describe the associated ethical challenges and opportunities, and to identify the actors involved. By doing so, it aimed to support the future development of ethics guidance in the EPR domain.

Methods

To identify journal articles debating the ethics of EPRs, Scopus, Web of Science, and PubMed academic databases were queried and yielded 123 eligible articles. The following inclusion criteria were applied: articles need to be in the English language; present normative arguments and not solely empirical research; include an abstract for software analysis; and discuss EPR technology.

Results

The medical specialty, type of information captured and stored in EPRs, their use and functionality varied widely across the included articles. Ethical terms extracted were categorised into clusters ‘privacy’, ‘autonomy’, ‘risk/benefit’, ‘human relationships’, and ‘responsibility’. The literature shows that EPR-related ethical concerns can have both positive and negative implications, and that a wide variety of actors with rights and/or responsibilities regarding the safe and ethical adoption of the technology are involved.

Conclusions

While there is considerable consensus in the literature regarding EPR-related ethical principles, some of the associated challenges and opportunities remain underdiscussed. For example, much of the debate is presented in a manner more in keeping with a traditional model of healthcare and fails to take account of the multidimensional ensemble of factors at play in the EPR era and the consequent need to redefine/modify ethical norms to align with a digitally-enabled health service. Similarly, the academic discussion focuses predominantly on bioethical values. However, approaches from digital ethics may also be helpful to identify and deliberate about current and emerging EPR-related ethical concerns.

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.

Evaluation of prescriber responses to pharmacogenomics clinical decision support for thiopurine S-methyltransferase testing

PURPOSE

Results of a study of prescribers' responses to a pharmacogenomics-based clinical decision support (CDS) alert designed to prompt thiopurine S-methyltransferase (TPMT) status testing are reported.

METHODS

A single-center, retrospective, chart review-based study was conducted to evaluate prescriber compliance with a pretest CDS alert that warned of potential thiopurine drug toxicity resulting from deficient TPMT activity due to TPMT gene polymorphism. The CDS alert was triggered when prescribers ordered thiopurine drugs for patients whose records did not indicate TPMT status or when historical thiopurine use was documented in the electronic health record. The alert pop-up also provided a link to online educational resources to guide thiopurine dosing calculations.

RESULTS

During the 9-month study period, 500 CDS alerts were generated: in 101 cases (20%), TPMT phenotyping or TPMT genotyping was ordered; in 399 cases (80%), testing was not ordered. Multivariable regression analysis indicated that documentation of historical thiopurine use was the only independent predictor of test ordering. Among the 99 patients tested subsequent to CDS alerts, 70 (71%) had normal TPMT activity, 29 (29%) had intermediate activity, and none had deficient activity. The online resources provided thiopurine dosing recommendations applicable to 24 patients, but only 3 were prescribed guideline-supported doses after CDS alerts.

CONCLUSION

The pretest CDS rule resulted in a large proportion of neglected alerts due to poor alerting accuracy and consequent alert fatigue. Prescriber usage of online thiopurine dosing resources was low.

Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design

Background

With the goal of realizing genome-based personalized healthcare, we have developed a biobank that integrates personal health, genome, and omics data along with biospecimens donated by volunteers of 150,000. Such a large-scale of data integration involves obvious risks of privacy violation. The research use of personal genome and health information is a topic of global discussion with regard to the protection of privacy while promoting scientific advancement. The present paper reports on our plans, current attempts, and accomplishments in addressing security problems involved in data sharing to ensure donor privacy while promoting scientific advancement.

Methods

Biospecimens and data have been collected in prospective cohort studies with the comprehensive agreement. The sample size of 150,000 participants was required for multiple researches including genome-wide screening of gene by environment interactions, haplotype phasing, and parametric linkage analysis.

Results

We established the TohokuMedicalMegabank (TMM) data sharing policy: a privacy protection rule that requires physical, personnel, and technological safeguards against privacy violation regarding the use and sharing of data. The proposed policy refers to that of NCBI and that of the Sanger Institute. The proposed policy classifies shared data according to the strength of re-identification risks. Local committees organized by TMM evaluate re-identification risk and assign a security category to a dataset. Every dataset is stored in an assigned segment of a supercomputer in accordance with its security category. A security manager should be designated to handle all security problems at individual data use locations. The proposed policy requires closed networks and IP-VPN remote connections.

Conclusion

The mission of the biobank is to distribute biological resources most productively. This mission motivated us to collect biospecimens and health data and simultaneously analyze genome/omics data in-house. The biobank also has the mission of improving the quality and quantity of the contents of the biobank. This motivated us to request users to share the results of their research as feedback to the biobank. The TMM data sharing policy has tackled every security problem originating with the missions. We believe our current implementation to be the best way to protect privacy in data sharing.

Electronic supplementary material

The online version of this article (doi:10.1186/s12911-017-0494-5) contains supplementary material, which is available to authorized users.