Contributions from the 2019 Literature on Bioinformatics and Translational Informatics

OBJECTIVES

Summarize recent research and select the best papers published in 2019 in the field of Bioinformatics and Translational Informatics (BTI) for the corresponding section of the International Medical Informatics Association Yearbook.

METHODS

A literature review was performed for retrieving from PubMed papers indexed with keywords and free terms related to BTI. Independent review allowed the section editors to select a list of 15 candidate best papers which were subsequently peer-reviewed. A final consensus meeting gathering the whole Yearbook editorial committee was organized to finally decide on the selection of the best papers.

RESULTS

Among the 931 retrieved papers covering the various subareas of BTI, the review process selected four best papers. The first paper presents a logical modeling of cancer pathways. Using their tools, the authors are able to identify two known behaviours of tumors. The second paper describes a deep-learning approach to predicting resistance to antibiotics in Mycobacterium tuberculosis. The authors of the third paper introduce a Genomic Global Positioning System (GPS) enabling comparison of genomic data with other individuals or genomics databases while preserving privacy. The fourth paper presents a multi-omics and temporal sequence-based approach to provide a better understanding of the sequence of events leading to Alzheimer's Disease.

CONCLUSIONS

Thanks to the normalization of open data and open science practices, research in BTI continues to develop and mature. Noteworthy achievements are sophisticated applications of leading edge machine-learning methods dedicated to personalized medicine.

Genome privacy: challenges, technical approaches to mitigate risk, and ethical considerations in the United States

Accessing and integrating human genomic data with phenotypes are important for biomedical research. Making genomic data accessible for research purposes, however, must be handled carefully to avoid leakage of sensitive individual information to unauthorized parties and improper use of data. In this article, we focus on data sharing within the scope of data accessibility for research. Current common practices to gain biomedical data access are strictly rule based, without a clear and quantitative measurement of the risk of privacy breaches. In addition, several types of studies require privacy-preserving linkage of genotype and phenotype information across different locations (e.g., genotypes stored in a sequencing facility and phenotypes stored in an electronic health record) to accelerate discoveries. The computer science community has developed a spectrum of techniques for data privacy and confidentiality protection, many of which have yet to be tested on real-world problems. In this article, we discuss clinical, technical, and ethical aspects of genome data privacy and confidentiality in the United States, as well as potential solutions for privacy-preserving genotype-phenotype linkage in biomedical research.

[Bioinformatics: a key role in oncology]

Bioinformatics is essential in clinical oncology and research. Combining biology, computer science and mathematics, bioinformatics aims to derive useful information from clinical and biological data, often poorly structured, at a large scale. Bioinformatics approaches have reclassified certain cancers based on their molecular and biological presentation, improving treatment selection. Many molecular signatures have been developed and, after validation, some are now usable in clinical practice. Other applications could facilitate daily practice, reduce the risk of error and increase the precision of medical decision-making. Bioinformatics must evolve in accordance with ethical considerations and requires multidisciplinary collaboration. Its application depends on a sound technical foundation that meets strict quality requirements.

Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014

This Pulmonary Perspective summarizes the content and main conclusions of an international workshop on personalized respiratory medicine coorganized by the Barcelona Respiratory Network ( www.brn.cat ) and the AJRCCM in June 2014. It discusses (1) its definition and historical, social, legal, and ethical aspects; (2) the view from different disciplines, including basic science, epidemiology, bioinformatics, and network/systems medicine; (3) the bottlenecks and opportunities identified by some currently ongoing projects; and (4) the implications for the individual, the healthcare system and the pharmaceutical industry. The authors hope that, although it is not a systematic review on the subject, this document can be a useful reference for researchers, clinicians, healthcare managers, policy-makers, and industry parties interested in personalized respiratory medicine.

Toward Reproducible Computational Research: An Empirical Analysis of Data and Code Policy Adoption by Journals

Journal policy on research data and code availability is an important part of the ongoing shift toward publishing reproducible computational science. This article extends the literature by studying journal data sharing policies by year (for both 2011 and 2012) for a referent set of 170 journals. We make a further contribution by evaluating code sharing policies, supplemental materials policies, and open access status for these 170 journals for each of 2011 and 2012. We build a predictive model of open data and code policy adoption as a function of impact factor and publisher and find higher impact journals more likely to have open data and code policies and scientific societies more likely to have open data and code policies than commercial publishers. We also find open data policies tend to lead open code policies, and we find no relationship between open data and code policies and either supplemental material policies or open access journal status. Of the journals in this study, 38% had a data policy, 22% had a code policy, and 66% had a supplemental materials policy as of June 2012. This reflects a striking one year increase of 16% in the number of data policies, a 30% increase in code policies, and a 7% increase in the number of supplemental materials policies. We introduce a new dataset to the community that categorizes data and code sharing, supplemental materials, and open access policies in 2011 and 2012 for these 170 journals.

From patients to partners: participant-centric initiatives in biomedical research

Advances in computing technology and bioinformatics mean that medical research is increasingly characterized by large international consortia of researchers that are reliant on large data sets and biobanks. These trends raise a number of challenges for obtaining consent, protecting participant privacy concerns and maintaining public trust. Participant-centred initiatives (PCIs) use social media technologies to address these immediate concerns, but they also provide the basis for long-term interactive partnerships. Here, we give an overview of this rapidly moving field by providing an analysis of the different PCI approaches, as well as the benefits and challenges of implementing PCIs.

Translational bioinformatics and healthcare informatics: computational and ethical challenges

Exponentially growing biological and bioinformatics data sets present a challenge and an opportunity for researchers to contribute to the understanding of the genetic basis of phenotypes. Due to breakthroughs in microarray technology, it is possible to simultaneously monitor the expressions of thousands of genes, and it is imperative that researchers have access to the clinical data to understand the genetics and proteomics of the diseased tissue. This technology could be a landmark in personalized medicine, which will provide storage for clinical and genetic data in electronic health records (EHRs). In this paper, we explore the computational and ethical challenges that emanate from the intersection of bioinformatics and healthcare informatics research. We describe the current situation of the EHR and its capabilities to store clinical and genetic data and then discuss the Genetic Information Nondiscrimination Act. Finally, we posit that the synergy obtained from the collaborative efforts between the genomics, clinical, and healthcare disciplines has potential to enhance and promote faster and more advanced breakthroughs in healthcare.

Privacy, the individual and genetic information: a Buddhist perspective

Bioinformatics is a new field of study whose ethical implications involve a combination of bioethics, computer ethics and information ethics. This paper is an attempt to view some of these implications from the perspective of Buddhism. Privacy is a central concern in both computer/information ethics and bioethics, and with information technology being increasingly utilized to process biological and genetic data, the issue has become even more pronounced. Traditionally, privacy presupposes the individual self but as Buddhism does away with the ultimate conception of an individual self, it has to find a way to analyse and justify privacy that does not presuppose such a self. It does this through a pragmatic conception that does not depend on a positing of the substantial self, which is then found to be unnecessary for an effective protection of privacy. As it may be possible one day to link genetic data to individuals, the Buddhist conception perhaps offers a more flexible approach, as what is considered to be integral to an individual person is not fixed in objectivity but depends on convention.

Bioinformatics: The philosophical and ethical issues at stake in a new modality of research practices

This article deals with the integration of ethical reflection into the research practices of the project at the Lille Nord-Pas-de-Calais genopole: "Multifactorial genetic pathologies and therapeutic innovations". The general hypothesis of this text is that changes in research practices in biology (mainly through the use of bioinformatics) imply changes in medical practices, which require critical reflection. This hypothesis could be broken down into three sub-hypotheses: (1) Research in biology is undergoing a complete transformation; (2) Research in biology is a cultural practice, which cannot be reduced to a simple cognitive action; (3) Research in biology is a techno-scientific practice. As for the method, the aim of our research at the Medical Ethics Centre is to elucidate the philosophical and ethical range of biomedical practices. This work entails a double task for reflection. On the one hand, from the revelation of ethical tensions present in these practices, we have to think about what is at stake in these practices, and more broadly in society. On the other hand, we have to analyse the conditions enabling the actors to assume the significance of ethical reflection in their practices. The method set up to undertake this double task could be qualified as "narrative hermeneutics", as its aim is to attempt to interpret the stakes in practices from proximity with these practices and from what their actors have to say about them. The text then goes on to analyse more specifically the emergence and place of bioinformatics in present-day biomedical research.

Intellectual property strategy in bioinformatics and biochips

Intellectual property rights are essential in today's technology-driven age. A strong intellectual property protection strategy is crucial in the bioinformatics and biochips technology spaces as monetary and temporal resources are tremendous in finding a blockbuster drug or gene therapy, as well as in deploying advanced biosensor and other medical systems. Current problems and intellectual property practice in the genomic space are presented and analyzed. Various strategy and solutions are proposed to guide bioinformatic and biochip companies in forming an aggressive strategy to protect one's intellectual property and competitive positioning.

Regulating genomics in the 21st century: from logos to pathos?

There is currently an important change in the governance of genomics. In the past, much of the regulatory discussion about genomics has focused on issues of risk. Today, a new discussion is evolving that emphasizes the uncertainties involved in the development and diffusion of genomics into society. The increasing importance of emotional language and the focus on trust in the discussion about genomics reflects the attempt to substitute for the shortcomings of logos with ethos and pathos.

Human genetic research: emerging trends in ethics

Genetic research has moved from Mendelian genetics to sequence maps to the study of natural human genetic variation at the level of the genome. This past decade of discovery has been accompanied by a shift in emphasis towards the ethical principles of reciprocity, mutuality, solidarity, citizenry and universality.

Bioinformatics: perspectives for the future

I give here a very personal perspective of Bioinformatics and its future, starting by discussing the origin of the term (and area) of bioinformatics and proceeding by trying to foresee the development of related issues, including pattern recognition/data mining, the need to reintegrate biology, the potential of complex networks as a powerful and flexible framework for bioinformatics and the interplay between bio- and neuroinformatics. Human resource formation and market perspective are also addressed. Given the complexity and vastness of these issues and concepts, as well as the limited size of a scientific article and finite patience of the reader, these perspectives are surely incomplete and biased. However, it is expected that some of the questions and trends that are identified will motivate discussions during the IcoBiCoBi round table (with the same name as this article) and perhaps provide a more ample perspective among the participants of that conference and the readers of this text.

Systems Theory and the Ethics of Human Enhancement: A Framework for NBIC Convergence

Representatives from government and the private sector recommend a major, cooperative initiative directed toward using NBIC (nano-, bio-, info-, and cogno-) technologies for human enhancement. By appropriately seeding the convergence of NBIC domains, they believe that the rate of development can be both accelerated and simultaneously channeled to avoid adverse risk and advance human good. However, to accomplish these goals, leaders of the convergence efforts identified as a major intellectual barrier the "development of a hierarchical architecture for integrating science across many scales, disciplines, and data modalities." Such a holistic framework requires a radical rethinking of the nature of science and engineering, and, beyond this, is also necessary for addressing their normative ethical and societal implications. In the first part of this essay, I consider the claim that a new view of science and engineering is needed. After reviewing the central features of a classical view of science, I consider aspects of the nano-revolution, showing why the classical conception is inappropriate and how a systems-oriented perspective is responsive to the character of this new science. I then consider how both science and engineering are transformed, calling into question older dichotomies between pure and applied domains. With the reworking of this distinction comes opportunities for rethinking the relation between science and the humanities more generally, which is necessary if we are to more appropriately address normative ethical aspects of the convergence initiative. After providing this groundwork for the needed hierarchical architecture, I consider a useful example of how a systems perspective might guide NBIC convergence. In the 1960s-1990s George Engel advocated a systems-theoretic model as an alternative to a more reductionistic "biomedical model" in medicine, and he did it for the exact same reasons as those advocated by the leaders of the NBIC convergence; namely, it embodies a more appropriate notion of science and enables one to address ethical aspects of medicine that were insufficiently addressed in the older model. By reviewing Engel's "biopsychosocial model" we can learn important lessons for developing the needed NBIC framework. I close by extending Engel's model so that it addresses all areas of enhancement envisioned as a part of NBIC convergence, and then identify areas where future research is still needed.