Fundamental behaviors emerge from simulations of a living minimal cell.

We present a whole-cell fully dynamical kinetic model (WCM) of JCVI-syn3A, a minimal cell with a reduced genome of 493 genes that has retained few regulatory proteins or small RNAs. Cryo-electron tomograms provide the cell geometry and ribosome distributions. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations over a cell cycle reveal how the cell balances demands of its metabolism, genetic information processes, and growth, and offer insight into the principles of life for this minimal cell. The energy economy of each process including active transport of amino acids, nucleosides, and ions is analyzed. WCM reveals how emergent imbalances lead to slowdowns in the rates of transcription and translation. Integration of experimental data is critical in building a kinetic model from which emerges a genome-wide distribution of mRNA half-lives, multiple DNA replication events that can be compared to qPCR results, and the experimentally observed doubling behavior.

Generation of de novo miRNAs from template switching during DNA replication.

The mechanisms generating novel genes and genetic information are poorly known, even for microRNA (miRNA) genes with an extremely constrained design. All miRNA primary transcripts need to fold into a stem-loop structure to yield short gene products ([Formula: see text]22 nt) that bind and repress their mRNA targets. While a substantial number of miRNA genes are ancient and highly conserved, short secondary structures coding for entirely novel miRNA genes have been shown to emerge in a lineage-specific manner. Template switching is a DNA-replication-related mutation mechanism that can introduce complex changes and generate perfect base pairing for entire hairpin structures in a single event. Here, we show that the template-switching mutations (TSMs) have participated in the emergence of over 6,000 suitable hairpin structures in the primate lineage to yield at least 18 new human miRNA genes, that is 26% of the miRNAs inferred to have arisen since the origin of primates. While the mechanism appears random, the TSM-generated miRNAs are enriched in introns where they can be expressed with their host genes. The high frequency of TSM events provides raw material for evolution. Being orders of magnitude faster than other mechanisms proposed for de novo creation of genes, TSM-generated miRNAs enable near-instant rewiring of genetic information and rapid adaptation to changing environments.

Revealing misattributed parentage through the integration of genetic information into the electronic health record.

The integration of genetic information (GI) into the electronic health record (EHR) seems inevitable as the mainstreaming of genomics continues. Such newly provided accessibility to GI could be beneficial for improving health care, as well as for supporting clinical decision-making and health management. Notwithstanding these promising benefits, the automatic integration of GI into the EHR, allowing unrestricted access to one's GI through patient portals, carries various knowledge-related risks for patients. This article is focused on the potential case of inadvertently revealing misattributed parentage through such practice. The article aims to identify key clinical and ethical implications of such revelation for adult patients. Clinical implications include, for example, altering the physician-patient interaction and the need to enhance physician's genetic literacy to improve genetic-information-specific communication skills. Ethical implications yield arguments supporting disclosure of MP, such as autonomy, individuals' right to know medical information pertaining to them, and the right to know one's genetic origins. Arguments opposing disclosure of MP centre on the right not to know GI and concerns for post-disclosure family relationships. Following the clinical and ethical analyses of these respective implications, we consider how such integration of GI into the EHR ought to be carried out, ethically. We therefore suggest a solution, featuring an autonomy-based approach, built around EHR users' right not to know. Our solution of nuanced consent options (including a 'genetic ignorance option') is designed to enable patients' informed exposure to GI through the EHR, allowing them some control over their self- and familial narrative.

Family Information Management in the Context of Inherited Conditions: An Integrative Review.

This review aimed to develop a framework to understand the process of information management in families with inherited conditions. Electronic databases were searched for relevant peer-reviewed articles. Articles were included if they were original research on families affected by any confirmed inherited condition, described how a family accesses, interprets, conveys, and/or uses information about the disease, included the recruitment of more than one family member, and used family as the unit of analysis. Data were analyzed through directed content analysis. Thirty-four articles from 27 studies were analyzed. We propose a framework for family information management consisting of the following domains: contextual influences, family information management behaviors, and family information management outcomes. This proposed framework expands the understanding of how families manage their genetic information in making health care decisions for their affected and at-risk relatives.

Looking Beyond GINA: Policy Approaches to Address Genetic Discrimination.

Concerns about genetic discrimination (GD) often surface when discussing research and innovation in genetics. Over recent decades, countries around the world have attempted to address GD using various policy measures. In this article, we survey these approaches and provide a critical commentary on their advantages and disadvantages. Our examination begins with regions featuring extensive policy-making activities (North America and Europe), followed by regions with moderate policy-making activities (Australia, Asia, and South America) and regions with minimal policy-making activities (the Middle East and Africa). Our analysis then turns to emerging issues regarding genetic testing and GD, including the expansion of multiomics sciences and direct-to-consumer genetic tests outside the health context. We additionally survey the shortcomings of current normative approaches addressing GD. Finally, we conclude by highlighting the evolving nature of GD and the need for more innovative policy-making in this area.

Revisiting informed consent in forensic genomics in light of current technologies and the times.

Informed consent is based on basic ethical principles that should be considered when conducting biomedical and behavioral research involving human subjects. These principles-respect, beneficence, and justice-form the foundations of informed consent which in itself is grounded on three fundamental elements: information, comprehension, and voluntary participation. While informed consent has focused on human subjects and research, the practice has been adopted willingly in the forensic science arena primarily to acquire reference samples from family members to assist in identifying missing persons. With advances in molecular biology technologies, data mining, and access to metadata, it is important to assess whether the past informed consent process and in particular associated risks are concomitant with these increased capabilities. Given the state-of-the-art, areas in which informed consent may need to be modified and augmented are as follows: reference samples from family members in missing persons or unidentified human remains cases; targeted analysis of an individual(s) during forensic genetic genealogy cases to reduce an investigative burden; donors who provide their samples for validation studies (to include population studies and entry into databases that would be applied to forensic statistical calculations) to support implementation of procedures and operations of the forensic laboratory; family members that may contribute samples or obtain genetic information from a molecular autopsy; and use of medical and other acquired samples that could be informative for identification purposes. The informed consent process should cover (1) purpose for collection of samples; (2) process to analyze the samples (to include type of data); (3) benefits (to donor, target, family, community, etc. as applicable); (4) risks (to donor, target, family, community, etc. as applicable); (5) access to data/reports by the donor; (6) sample disposition; (7) removal of data process (i.e., expungement); (8) process to ask questions/assessment of comprehension; (9) follow-up processes; and (10) voluntary, signed, and dated consent. Issues surrounding these topics are discussed with an emphasis on addressing risk factors. Addressing informed consent will allow human subjects to make decisions voluntarily and with autonomy as well as secure the use of samples for intended use.

Detection of cutaneous malignant melanoma by tape stripping of pigmented skin lesions - A systematic review.

BACKGROUND: Cutaneous malignant melanoma (MM) is potentially aggressive, and numerous clinically suspicious pigmented skin lesions are excised, causing unnecessary mutilation for patients at high healthcare costs, but without histopathological evidence of MM. The high number of excisions may be lowered by using more accurate diagnostics. Tape stripping (TS) of clinically suspicious lesions is a non-invasive diagnostic test of MM that can potentially lower the number needed to biopsy/excise. MATERIALS AND METHODS: The aim is to determine the diagnostic accuracy of TS in detecting MM in clinically suspicious pigmented skin lesions. This systematic review following PRISMA guidelines searched PubMed, Web of Science, and Embase (September 2022) using melanoma combined with tape stripping, adhesive patch(es), pigmented lesion assay, or epidermal genetic information retrieval. RESULTS: Ten studies were included. Sensitivity ranged from 68.8% (95% confidence interval [CI] 51.5, 82.1) to 100% (95% CI 91.0, 100). Specificity ranged from 69.1% (95% CI 63.8, 74.0) to 100% (95% CI 78.5, 100). A pooled analysis of five studies testing the RNA markers LINC00518 and PRAME found a sensitivity of 86.9% (95% CI 81.7, 90.8) and a specificity of 82.4% (95% CI 80.8, 83.9). CONCLUSION: Overall quality of studies was low, and the reliability of sensitivity and specificity is questionable. However, TS may supplement well-established diagnostic methods as pooled analysis of five studies indicates a moderate sensitivity. Future studies are needed to obtain more reliable data as independent studies with no conflict of interest.

Relatives' Right to Know Genetic Information in Aotearoa New Zealand.

Once someone is diagnosed with a genetic abnormality or disorder, that information can be extremely valuable to their biological relatives. It may allow them to access preventive treatment or make informed decisions, such as whether to have a biological child or not. However, when the original family member refuses to disclose that information to at-risk relatives, a conflict arises between their right to patient confidentiality and their relatives' right to know. Aotearoa New Zealand lacks a specific, workable mechanism for disclosing genetic information to at-risk relatives. This article traverses the theoretical and practical issues involved in non-consensual disclosure of genetic information to suggest a new path for Aotearoa. It argues that the current, Western attitude of autonomy as an individual right free from obligations to others is no longer an appropriate justification for confidentiality over genetic information. Instead, patients diagnosed with a genetic abnormality or disorder should only be entitled to confidentiality where they have a reasonable expectation of privacy - determined by weighing the objective interests for and against disclosure. This approach recognises that we ought to consider our close relationships with others when we exercise autonomy over what is ultimately shared family information.

From proband to provider: is there an obligation to inform genetic relatives of actionable risks discovered through direct-to-consumer genetic testing?

Direct-to-consumer genetic testing is a growing phenomenon, fuelled by the notion that knowledge equals control. One ethical question that arises concerns the proband's duty to share information indicating genetic risks in their relatives. However, such duties are unenforceable and may result in the realisation of anticipated harm to relatives. We argue for a shift in responsibility from proband to provider, placing a duty on test providers in the event of identified actionable risks to relatives. Starting from Parker and Lucassen's (2004) 'joint account model', we adapt Kilbride's (2018) application of the rule of rescue and balance it against the relative's right not to know, placing responsibility on the providers of direct-to-consumer genetic testing. Where the risk of disease to a relative is actionable, we argue providers ought to share results even in the face of the proband's objections. Confidentiality issues are navigated by a pre-emptive consent model, whereby consumers agree to the sharing of certain information with their relatives ahead of testing and as a condition of testing. When a relative is informed, the proband's privacy is protected by maximal deidentification, and the rights of the relative are met by a stepwise approach to informing that allows them to decide how much information they receive.

The goldilocks conundrum: Disclosing discrimination risks in informed consent.

Informed consent is a foundational ethical and legal principle in human subjects research and clinical care. Yet, there is extensive debate over how much information must be disclosed to meet ethical goals and legal requirements, especially about non-medical risks. In this online, survey-based experiment of a diverse sample of the US general population, we explored one aspect of this debate by testing whether the level of detail included in informed consent regarding genetic anti-discrimination protections alters individuals' willingness to participate in a hypothetical research study and their concerns regarding genetic discrimination. Participants were randomized to receive sample informed consent language with one of three levels of disclosure regarding the protections and limitations of the Genetic Information Nondiscrimination Act (GINA). Our sample (n = 1,195) had a mean age of 45.9 (SD = 17.9) years and 40% with ≤high school education. Participants were 51.3% female and 36.7% non-Hispanic White. On average, those who received consent language with none of GINA's limitations highlighted were more willing to participate than those who were warned about various gaps in GINA. They also had significantly lower perceived risk of discrimination than those presented with the most information about limitations. Our study found that providing more comprehensive information about GINA notably lessened willingness to participate in the hypothetical studies, highlighting the need for clinicians and researchers to thoughtfully consider how to disclose anti-discrimination risks in informed consent.

Commercial DNA tests and police investigations: a broad bioethical perspective.

Over 30 million people worldwide have taken a commercial at-home DNA test, because they were interested in their genetic ancestry, disease predisposition or inherited traits. Yet, these consumer DNA data are also increasingly used for a very different purpose: to identify suspects in criminal investigations. By matching a suspect's DNA with DNA from a suspect's distant relatives who have taken a commercial at-home DNA test, law enforcement can zero in on a perpetrator. Such forensic use of consumer DNA data has been performed in over 200 criminal investigations. However, this practice of so-called investigative genetic genealogy (IGG) raises ethical concerns. In this paper, we aim to broaden the bioethical analysis on IGG by showing the limitations of an individual-based model. We discuss two concerns central in the debate: privacy and informed consent. However, we argue that IGG raises pressing ethical concerns that extend beyond these individual-focused issues. The very nature of the genetic information entails that relatives may also be affected by the individual customer's choices. In this respect, we explore to what extent the ethical approach in the biomedical genetic context on consent and consequences for relatives can be helpful for the debate on IGG. We argue that an individual-based model has significant limitations in an IGG context. The ethical debate is further complicated by the international, transgenerational and commercial nature of IGG. We conclude that IGG should not only be approached as an individual but also-and perhaps primarily-as a collective issue.

Genetic information, insurance and a pluralistic approach to justice.

The use of genetic testing has prompted the question of whether insurance companies should be able to use predictive genetic test results (GTRs) in their risk classification of clients. While some jurisdictions have passed legislation to prohibit this practice, the UK has instead adopted a voluntary code of practice that merely restricts the ways in which insurance companies may use GTRs. Critics have invoked various theories of justice to argue that this approach is unfair. However, as well as sometimes relying on somewhat idealised assumptions, these analyses have tended to invoke theories that have wide-ranging and highly revisionary implications for insurance. Moreover, they fail to adequately engage with a conception of justice that plausibly undergirds the status quo approach to insurance in the UK. I argue that it is a mistake to simply invoke a single contestable theory in seeking to develop sound policy on the use of GTRs in insurance. To that end, in this paper, I outline three plausible principles of justice that policy on this issue ought to balance: A principle of equity, a principle of equal access and a principle of need. In doing so, I shall offer a pluralist justice-based argument in support of the spirit, if not the precise letter, of the UK approach.

Ethics of genomic passports: should the genetically resistant be exempted from lockdowns and quarantines?

Lockdowns and quarantines have been implemented widely in response to the COVID-19 pandemic. This has been accompanied by a rise in interest in the ethics of 'passport' systems that allow low-risk individuals greater freedoms during lockdowns and exemptions to quarantines. Immunity and vaccination passports have been suggested to facilitate the greater movement of those with acquired immunity and who have been vaccinated. Another group of individuals who pose a low risk to others during pandemics are those with genetically mediated resistances to pathogens. In this paper, we introduce the concept of genomic passports, which so far have not been explored in the bioethics literature. Using COVID-19 as an illustrative example, we explore the ethical issues raised by genomic passports and highlight differences and similarities to immunity passports. We conclude that, although there remain significant practical and ethical challenges to the implementation of genomic passports, there will be ways to ethically use them in the future.

Using a biomarker acutely to identify babies at risk of serious adverse effects from antibiotics: where is the 'Terrible Moral and Medical Dilemma'?

We thank Parker and Wright for engaging in this roundtable debate in such a spirited way. The 'Pharmacogenetic [test] to Avoid Loss of Hearing' (PALOH) Trial is the first time a genetic point of care test has been applied in the acute neonatal setting; therefore, it is not surprising that questions have been raised which require debate, discussion and clarification. Parker and Wright misattribute several assumptions to the roundtable authors, which we would like to clarify here. Since they raise wider questions about the PALOH trial itself, several of the roundtable discussants have made a joint response.

Social media usage in family communication about genetic information: 'I no longer speak with my sister but she needed to know'.

The use of social media has become a ubiquitous form of communication. Little is known about whether social media is used in families to assist with the communication of genetic information. This study aimed to understand if and why individuals use social media to communicate genetic information to at-risk relatives. Individuals with either a pathogenic variant in a cancer-predisposing gene or a heterozygous pathogenic variant in an autosomal or X-linked recessive gene were surveyed about communicating genetic information to their at-risk relatives and their use of social media to assist this process. Surveys were sent to 323 individuals from a reproductive carrier screening program and 250 individuals from a familial cancer center. The 128 responses (response rate 25.2%) showed that while most participants (79.0%) did not use social media to communicate genetic information, those that did use social media (21.0%) found it to be helpful as it was easy, accessible and allowed individuals to overcome communication barriers. Genetic professionals should be aware that social media is being used by individuals to assist family communication about genetic information and should discuss this method of communication with individuals who are faced with communicating genetic information with their family.

Genetic counselors, patients', and carers' views on an Australian clinical genetics service information system.

The Genetic Information System (GIS) is an Australian database of family genetic information. This health information technology system has been used by all 31 publicly operated clinical genetics services across New South Wales (NSW) and the Australian Capital Territory (ACT) for over a decade. As these services are separated geographically, the linkage engendered by the GIS facilitates the services to operate as a virtual state-wide service. This study aimed to explore the views of genetic counselors, patients, and carers on the use and storage of family genetic information in the GIS. Data were collected using audio-recorded semi-structured telephone interviews with genetic counselors experienced with using the GIS and focus groups with past patients/carers of the services. Using thematic analysis, four themes were identified from genetic counselor participant interviews (n = 12): (a) Shared information is valuable; (b) inconsistent data entry provides a challenge; (c) perceived need for the GIS to be current and integrated with other health systems; and (d) future challenges and strategies for the GIS. Three themes were identified following three focus groups with consumer participants (n = 14): (a) access to family genetic information provides a 'clearer picture'; (b) support, but caution, concerning use of information for relatives' health care; and (c) stewardship of family information. Genetic counselors and consumers identified similar advantages and privacy concerns regarding the sharing of family genetic information and all participants wanted patients/carers to be better informed about the GIS early in the genetic counseling process. Consumers were reassured by genetics health professionals' stewardship of their information, but surprised the GIS was not available nationally or for private geneticists or certain non-genetic specialists. These findings may inform further development of the GIS and other clinical genetic databases and lead to increased patient/carer knowledge through education and resource development.

The genetic informational network: how DNA conveys semantic information.

The question of whether "genetic information" is a merely causal factor in development or can be made sense of semantically, in a way analogous to a language or other type of representation, has generated a long debate in the philosophy of biology. It is intimately connected with another intense debate, concerning the limits of genetic determinism. In this paper I argue that widespread attempts to draw analogies between genetic information and information contained in books, blueprints or computer programs, are fundamentally inadequate. In development, gene exons are the central part of an intricate and densely ramified semantic Genetic Informational Network. DNA in the entire genome is in a state of continuous positive and negative feedback with itself and with its 'environment', and is 'read' and acted upon by the cell in various alternative and complementary ways. The linear combinatorial coding relation between codons and amino acids is but one aspect of semantic genetic information, which is, when considered in its entirety, a far wider and richer concept.

The 'Expiry Problem' of broad consent for biobank research - And why a meta consent model solves it.

In this response to Neil Manson's latest intervention in our debate about the best consent model for biobank research we show, contra Manson that the 'expiry problem' that affects broad consent models because of changes over time in methods, purposes, types of data used and governance structures is a real and significant problem. We further show that our preferred implementation of meta consent as a national consent platform solves this problem and is not subject to the cost and burden objections that Manson raises.

Healthcare professionals' responsibility for informing relatives at risk of hereditary disease.

Advances in genetic diagnostics lead to more patients being diagnosed with hereditary conditions. These findings are often relevant to patients' relatives. For example, the success of targeted cancer prevention is dependent on effective disclosure to relatives at risk. Without clear information, individuals cannot take advantage of predictive testing and preventive measures. Against this background, we argue that healthcare professionals have a duty to make actionable genetic information available to their patients' at-risk relatives. We do not try to settle the difficult question of how this duty should be balanced against other duties, such as the duty of confidentiality and a possible duty not to know one's genetic predisposition. Instead, we argue for the importance of recognising a general responsibility towards at-risk relatives, to be discharged as well as possible within the limits set by conflicting duties and practical considerations. According to a traditional and still dominant perspective, it is the patient's duty to inform his or her relatives, while healthcare professionals are only obliged to support their patients in discharging this duty. We argue that this perspective is a mistake and an anomaly. Healthcare professionals do not have a duty to ensure that their patients promote the health of third parties. It is often effective and desirable to engage patients in disseminating information to their relatives. However, healthcare professionals should not thereby deflect their own moral responsibility.

Accessing medical biobanks to solve crimes: ethical considerations.

Millions of human biological samples are stored worldwide for medical research or treatment purposes. These biospecimens are of enormous potential value to law enforcement as DNA profiles can be obtained from these samples. However, forensic use of such biospecimens raises a number of ethical questions. This article aims to explore ethical issues of using human bodily material in medical biobanks for crime investigation and prosecution purposes. Concerns about confidentiality, trust, autonomy and justice will be discussed. We explore how to balance these concerns against the importance of crime solving. Relevant case examples of forensic use of medical biobanks show that requests by law enforcement to access biobanks are handled in disparate ways. We identify some core ethical issues and conclude that further research on these issues is needed to provide ethical guidance.