The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases.

Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.

Research participants' preferences for receiving genetic risk information: a discrete choice experiment.

PURPOSE: This study aims to determine research participants' preferences for receiving genetic risk information when participating in a scientific study that uses genome sequencing. METHODS: A discrete choice experiment questionnaire was sent to 650 research participants (response rate 60.5%). Four attributes were selected for the questionnaire: type of disease, disease penetrance probability, preventive opportunity, and effectiveness of the preventive measure. Panel mixed logit models were used to determine attribute level estimates and the heterogeneity in preferences. Relative importance of the attribute and the predicted uptake for different information scenarios were calculated from the estimates. In addition, this study estimates predicted uptake for receiving genetic risk information in different scenarios. RESULTS: All characteristics influenced research participants' willingness to receive genetic risk information. The most important characteristic was the effectiveness of the preventive opportunity. Predicted uptake ranged between 28% and 98% depending on what preventive opportunities and levels of effectiveness were presented. CONCLUSION: Information about an effective preventive measure was most important for participants. They valued that attribute twice as much as the other attributes. Therefore, when there is an effective preventive measure, risk communication can be less concerned with the magnitude of the probability of developing disease.

Values and value conflicts in implementation and use of preconception expanded carrier screening - an expert interview study.

BACKGROUND: Endeavors have been made to found and incorporate ethical values in most aspects of healthcare, including health technology assessment. Health technologies and their assessment are value-laden and could trigger problems with dissemination if they contradict societal norms. Per WHO definition, preconception expanded carrier screening is a new health technology that warrants assessment. It is a genetic test offered to couples who have no known risk of recessive genetic diseases and are interested pregnancy. A test may screen for carrier status of several autosomal recessive diseases and X-linked at one go. The technique has been piloted in the Netherlands and is discussed in other countries. The aim of the study was to examine values and value conflicts that healthcare experts recounted in relation to the discussion of implementation and use of preconception ECS in Sweden. METHODS: We interviewed ten experts, who were associated with influencing health policymaking in Sweden. We employed systematizing expert interviews, which endeavor to access experts' specialist knowledge. There were four female and six male informants, of which four were physicians, three bioethicists, one a legal expert, one a theologian and one a political party representative in the parliament. The participants functioned as members of two non-governmental bodies and three governmental organizations. We employed thematic analysis to identify themes, categories and subcategories. RESULTS: Two main themes surfaced: values and value conflicts. The main categories of Respect for persons, Solidarity, Human dignity, Do no harm, Health and Love formed the first theme, while values conflicting with autonomy and integrity respectively, constituted the second theme. Concepts relating to respect for persons were the most commonly mentioned among the participants, followed by notions alluding to solidarity. Furthermore, respondents discussed values conflicting with Swedish healthcare ones such as equality and solidarity. CONCLUSIONS: The experts highlighted values and concepts that are distinctive of welfare states such as Sweden and delineated how preconception ECS could challenge such values. Moreover, the analysis revealed that certain values were deemed more substantive than others, judging by the extent and detail of inference; for example, respect for persons and solidarity were on top of the list.

Freedom of Choice About Incidental Findings Can Frustrate Participants' True Preferences.

Ethicists, regulators and researchers have struggled with the question of whether incidental findings in genomics studies should be disclosed to participants. In the ethical debate, a general consensus is that disclosed information should benefit participants. However, there is no agreement that genetic information will benefit participants, rather it may cause problems such as anxiety. One could get past this disagreement about disclosure of incidental findings by letting participants express their preferences in the consent form. We argue that this freedom of choice is problematic. In transferring the decision to participants, it is assumed that participants will understand what they decide about and that they will express what they truly want. However, psychological findings about people's reaction to probabilities and risk have been shown to involve both cognitive and emotional challenges. People change their attitude to risk depending on what is at stake. Their mood affects judgments and choices, and they over- and underestimate probabilities depending on whether they are low or high. Moreover, different framing of the options can steer people to a specific choice. Although it seems attractive to let participants express their preferences to incidental findings in the consent form, it is uncertain if this choice enables people to express what they truly prefer. In order to better understand the participants' preferences, we argue that future empirical work needs to confront the participant with the complexity of the uncertainty and the trade-offs that are connected with the uncertain predictive value of genetic risk information.

Ethics rounds: An appreciated form of ethics support.

BACKGROUND: Ethics rounds are one way to support healthcare personnel in handling ethically difficult situations. A previous study in the present project showed that ethics rounds did not result in significant changes in perceptions of how ethical issues were handled, that is, in the ethical climate. However, there was anecdotal evidence that the ethics rounds were viewed as a positive experience and that they stimulated ethical reflection. AIM: The aim of this study was to gain a deeper understanding of how the ethics rounds were experienced and why the intervention in the form of ethics rounds did not succeed in improving the ethical climate for the staff. RESEARCH DESIGN: An exploratory and descriptive design with a qualitative approach was adopted, using individual interviews. PARTICIPANTS AND RESEARCH CONTEXT: A total of 11 healthcare personnel, working in two different psychiatry outpatient clinics and with experience of participating in ethics rounds, were interviewed. ETHICAL CONSIDERATIONS: The study was based on informed consent and was approved by one of the Swedish Regional Ethical Review Boards. FINDINGS: The participants were generally positive about the ethics rounds. They had experienced changes by participating in the ethics rounds in the form of being able to see things from different perspectives as well as by gaining insight into ethical issues. However, these changes had not affected daily work. DISCUSSION: A crucial question is whether or not increased reflection ability among the participants is a good enough outcome of ethics rounds and whether this result could have been measured in patient-related outcomes. Ethics rounds might foster cooperation among the staff and this, in turn, could influence patient care. CONCLUSION: By listening to others during ethics rounds, a person can learn to see things from a new angle. Participation in ethics rounds can also lead to better insight concerning ethical issues.

Broad Consent for Research With Biological Samples: Workshop Conclusions.

Different types of consent are used to obtain human biospecimens for future research. This variation has resulted in confusion regarding what research is permitted, inadvertent constraints on future research, and research proceeding without consent. The National Institutes of Health (NIH) Clinical Center's Department of Bioethics held a workshop to consider the ethical acceptability of addressing these concerns by using broad consent for future research on stored biospecimens. Multiple bioethics scholars, who have written on these issues, discussed the reasons for consent, the range of consent strategies, and gaps in our understanding, and concluded with a proposal for broad initial consent coupled with oversight and, when feasible, ongoing provision of information to donors. This article describes areas of agreement and areas that need more research and dialogue. Given recent proposed changes to the Common Rule, and new guidance regarding storing and sharing data and samples, this is an important and timely topic.

Ethics rounds do not improve the handling of ethical issues by psychiatric staff.

BACKGROUND: One way to support healthcare staff in handling ethically difficult situations is through ethics rounds that consist of discussions based on clinical cases and are moderated by an ethicist. Previous research indicates that the handling of ethically difficult situations in the workplace might have changed after ethics rounds. This, in turn, would mean that the "ethical climate", i.e. perceptions of how ethical issues are handled, would have changed. AIM: To investigate whether ethics rounds could improve the ethical climate perceived by staff working in psychiatry outpatient clinics. METHODS: In this quasi-experimental study, six inter-professional ethics rounds led by a philosopher/ethicist were conducted at two psychiatry outpatient clinics. Changes in ethical climate were measured at these clinics as well as at two control clinics at baseline and after the intervention period using the instrument Hospital Ethical Climate Survey. RESULTS: Within-groups comparisons of median sum scores of ethical climate showed that no statistically significant differences were found in the intervention group before or after the intervention period. The median sum scores for ethical climate were significantly higher, both at baseline and after the intervention period (P ≤ 0.001; P = 0.046), in the intervention group. CONCLUSIONS: Ethics rounds in psychiatric outpatient clinics did not result in significant changes in ethical climate. Outcomes of ethics rounds might, to a higher degree, be directed towards patient-related outcomes rather than towards the staff's working environment, as the questions brought up for discussion during the ethics rounds concerned patient-related issues.

RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research.

Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets. Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest. Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights. Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases.

Why participating in (certain) scientific research is a moral duty.

Our starting point in this article is the debate between John Harris and Iain Brassington on whether or not there is a duty to take part in scientific research. We consider the arguments that have been put forward based on fairness and a duty to rescue, and suggest an alternative justification grounded in a hypothetical agreement: that is, because effective healthcare cannot be taken for granted, but requires continuous medical research, and nobody knows what kind of healthcare they will need, participating in research should be viewed from the perspective of a social contract, based on our mutual need for medical advances.

Transition to noncurative end-of-life care in paediatric oncology--a nationwide follow-up in Sweden.

AIM: To estimate whether and when children dying from a malignancy are recognized as being beyond cure and to study patterns of care the last weeks of life. METHODS: A nationwide retrospective medical record review was conducted. Medical records of 95 children (60% of eligible children) who died from a malignancy 2007-2009 in Sweden were studied. RESULTS: Eighty-three children (87%) were treated without curative intent at the time of death. Children with haematological malignancies were less likely to be recognized as being beyond cure than children with brain tumours [relative risks (RR) 0.7; 95% confidence interval (CI) 0.6-0.9] or solid tumours (RR 0.8; 0.6-1.0). The transition to noncurative care varied from the last day of life to over four years prior to death (median 60 days). Children with haematological malignancies were treated with a curative intent closer to death and were also given chemotherapy (RR 5.5; 1.3-22.9), transfusions (RR 2.0; 1.0-4.0) and antibiotics (RR 5.3; 1.8-15.5) more frequently than children with brain tumours the last weeks of life. CONCLUSION: The majority of children dying from a malignancy were treated with noncurative intent at the time of death. The timing of a transition in care varied with the diagnoses, being closer to death in children with haematological malignancies.

Adequate trust avails, mistaken trust matters: on the moral responsibility of doctors as proxies for patients' trust in biobank research.

In Sweden, most patients are recruited into biobank research by non-researcher doctors. Patients' trust in doctors may therefore be important to their willingness to participate. We suggest a model of trust that makes sense of such transitions of trust between domains and distinguishes adequate trust from mistaken trust. The unique position of doctors implies, we argue, a Kantian imperfect duty to compensate for patients' mistaken trust. There are at least three kinds of mistaken trust, each of which requires a different set of countermeasures. First, trust is mistaken when necessary competence is lacking; the competence must be developed or the illusion dispelled. Second, trust is irrational whenever the patient is mistaken about his actual reasons for trusting. Care must therefore be taken to support the patient's reasoning and moral agency. Third, some patients inappropriately trust doctors to recommend only research that will benefit them directly. Such trust should be counteracted by nurturing a culture where patients expect to be asked occasionally to contribute to the common good.

Does being exposed to an educational tool influence patient preferences? The influence of an educational tool on patient preferences assessed by a discrete choice experiment.

OBJECTIVES: There is an increased interest in patient preferences informing the development and authorisation of medical products. A requirement for robust and meaningful results of such studies is that patients adequately understand the risks and benefits associated with treatments for which their preferences are elicited. This study aims to determine the influence of an educational tool, compared with traditional written information on patient preferences elicited in a discrete choice experiment (DCE). METHODS: Treatment preferences of Swedish patients with rheumatoid arthritis (RA) were assessed using a DCE. Patients were recruited via clinics, a research panel, and the Swedish Rheumatism Association. Respondents received training materials either as plain written text or as an online educational tool. The educational tool was designed to enhance understanding of the written text by using graphics, pictograms, icon arrays, spoken text, and click-on functions. Data were analysed using random parameter logit models. RESULTS: 675 patients with RA were included in the analysis. The patients received either a written information (n = 358) or information via an educational tool (n = 317). Respondents receiving the educational tool placed relatively more importance on all included side effects in their decision making, compared to respondents receiving the written text, who placed greater importance on treatment effectiveness and administration methods. CONCLUSION: Compared to the respondents receiving the written text, the decisions of respondents receiving the educational tool were more influenced by medication side effects. Further research is needed to provide guidance on how and when to use educational tools to inform and elicit patients' preferences. PRACTICE IMPLICATIONS: The ways in which attributes are presented to patients significantly impacts preferences measured in a DCE.

Changing defaults in biobank research could save lives too.

In an effort to increase the amount of organs available for transplantation, many countries have implemented presumed consent for organ donation. Presuming a wish to contribute to medical advances through biobank research on previously taken tissue samples could similarly improve health and wellbeing. In this article we analyze common arguments for and against presumed consent for organ donation and assess their relevance in the context of biobank research. In spite of obvious differences between biobank research and organ transplantation the cases for implementing presumption of a positive attitude appear quite analogous. It has repeatedly been shown that a majority of the general population supports these projects and selecting informed consent as the default position decreases the amount of organs and samples available and thus reduces the prospect of promoting health. We conclude that instead of presuming that individuals do not wish to contribute to the advancement of healthcare through biobank research on previously taken samples, ethics committees should presume that they do.

The case for open science: rare diseases.

The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community. Research into RDs has been limited by insufficient patient data and resources, a paucity of trained disease experts, and lack of therapeutics, leading to long delays in diagnosis and treatment. These issues can be ameliorated by following the principles and practices of sharing that are intrinsic to Open Science. Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine. We also present recommendations that can advance Open Science more globally.

Practical matters, rather than lack of trust, motivate non-participation in a long-term cohort trial.

OBJECTIVE: The objective of this study was to investigate the importance of trust in researchers and other reasons that participating parents, former participants, and non-participants had for participating, or not participating, in a longitudinal cohort study on prediction and development of diabetes in children. STUDY DESIGN: A questionnaire addressing each of these groups, where respondents graded the importance of a set of listed reasons for participating/not participating, was randomly distributed to 2500 families in the All Babies in Southeast Sweden (ABIS) study region with children born between 1997 and 1999. RESULTS: Lack of trust was not a central factor to a great majority of respondents who decided not to participate in the ABIS study or who later decided to opt out. Practical matters, like blood sampling and lack of time, were important factors to many more. Yet, four fifths of those who still participate in the ABIS study stated trust in the researchers to be an important factor to their initial decision to participate. CONCLUSIONS: Trust in researchers may be a necessary prerequisite in order for people to be willing to participate in research, but practical matters such as time that has to be spent or pain involved in collecting blood were more important factors than lack of trust in explaining opt out in relation to the ABIS study.

Pregnant women are satisfied with the information they receive about prenatal diagnosis, but are their decisions well informed?

OBJECTIVE. To survey the information about prenatal diagnosis that midwives give to pregnant women and to find out how the women experience the information. Furthermore, to evaluate the midwives' opinion about their knowledge and personal need for education. DESIGN. Descriptive cross-sectional study. SETTING. The southeast healthcare region of Sweden. METHODS. One hundred and fifty-seven midwives and 150 pregnant women were invited to reply to a confidential questionnaire in 2008. RESULTS. The reply rate was 78% for the midwives and 53% for the women. Ninety-six percentage of the midwives used < or =10 minutes to inform women about prenatal diagnosis. Seventy-two percentage always informed about the advantages and 41% about the choice to continue or terminate the pregnancy if a serious abnormality was detected. In addition, 41% considered that they had sufficient knowledge to inform about prenatal diagnosis, while 84% wanted additional education. Seventy-six percentage of the women took the decision to have prenatal diagnosis as soon as they found out that they were pregnant. A majority considered that they had been given enough time for questions and reflections. CONCLUSIONS. There was discrepancy between the amount of information, which midwives gave to pregnant women about prenatal diagnosis compared to what would be needed for a complete understanding of the relevant medical facts and the risks involved, but even so the women were satisfied with the information.

Concern for privacy in relation to age during physical examination of children: an exploratory study.

OBJECTIVES: To explore whether physicians behave differently regarding ethics and respect for privacy depending on children's age. We explored whether physician behaviours contributed to child uneasiness. STUDY DESIGN: Observational study of 21 children (0-12 years; 18 boys; mean age 3.2) undergoing evaluation for inguinal hernia. Specific physician-initiated verbal and nonverbal behaviours were coded from digital video discs of the consultations. RESULTS: Physician intrusiveness (i.e. approaching the child suddenly or in an uninvited way) during the physical examination was related to concurrent child uneasiness (r = 0.42, p < 0.06) and lasted through the postexamination phase of the consultation (r = 0.52, p < 0.01). Child mood during the examination strongly predicted postexamination mood (r = 0.69, p < 0.0001). Neither the total number of physician-initiated positive behaviours or privacy-related behaviours was associated with child age. Negative physician behaviours were strongly related to negative mood in the child (r = 0.72, p < 0.0001) at the close of the consultation. CONCLUSION: Although physicians were more likely to provide information to older than younger children, their behaviours regarding privacy did not differ by child age. We found that intrusiveness was rather common and related to child uneasiness that has implications for the ethical practice and a child's willingness to be examined.