The Human Pangenome Project: a global resource to map genomic diversity.

The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.

Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.

Genome sequencing is enabling precision medicine-tailoring treatment to the unique constellation of variants in an individual's genome. The impact of recurrent pathogenic variants is often understood, however there is a long tail of rare genetic variants that are uncharacterized. The problem of uncharacterized rare variation is especially acute when it occurs in genes of known clinical importance with functionally consequential variants and associated mechanisms. Variants of uncertain significance (VUSs) in these genes are discovered at a rate that outpaces current ability to classify them with databases of previous cases, experimental evaluation, and computational predictors. Clinicians are thus left without guidance about the significance of variants that may have actionable consequences. Computational prediction of the impact of rare genetic variation is increasingly becoming an important capability. In this paper, we review the technical and ethical challenges of interpreting the function of rare variants in two settings: inborn errors of metabolism in newborns and pharmacogenomics. We propose a framework for a genomic learning healthcare system with an initial focus on early-onset treatable disease in newborns and actionable pharmacogenomics. We argue that (1) a genomic learning healthcare system must allow for continuous collection and assessment of rare variants, (2) emerging machine learning methods will enable algorithms to predict the clinical impact of rare variants on protein function, and (3) ethical considerations must inform the construction and deployment of all rare-variation triage strategies, particularly with respect to health disparities arising from unbalanced ancestry representation.

Clinical Genetics Lacks Standard Definitions and Protocols for the Collection and Use of Diversity Measures.

Genetics researchers and clinical professionals rely on diversity measures such as race, ethnicity, and ancestry (REA) to stratify study participants and patients for a variety of applications in research and precision medicine. However, there are no comprehensive, widely accepted standards or guidelines for collecting and using such data in clinical genetics practice. Two NIH-funded research consortia, the Clinical Genome Resource (ClinGen) and Clinical Sequencing Evidence-generating Research (CSER), have partnered to address this issue and report how REA are currently collected, conceptualized, and used. Surveying clinical genetics professionals and researchers (n = 448), we found heterogeneity in the way REA are perceived, defined, and measured, with variation in the perceived importance of REA in both clinical and research settings. The majority of respondents (>55%) felt that REA are at least somewhat important for clinical variant interpretation, ordering genetic tests, and communicating results to patients. However, there was no consensus on the relevance of REA, including how each of these measures should be used in different scenarios and what information they can convey in the context of human genetics. A lack of common definitions and applications of REA across the precision medicine pipeline may contribute to inconsistencies in data collection, missing or inaccurate classifications, and misleading or inconclusive results. Thus, our findings support the need for standardization and harmonization of REA data collection and use in clinical genetics and precision health research.

The Genomic Medicine Integrative Research Framework: A Conceptual Framework for Conducting Genomic Medicine Research.

Conceptual frameworks are useful in research because they can highlight priority research domains, inform decisions about interventions, identify outcomes and factors to measure, and display how factors might relate to each other to generate and test hypotheses. Discovery, translational, and implementation research are all critical to the overall mission of genomic medicine and prevention, but they have yet to be organized into a unified conceptual framework. To fill this gap, our diverse team collaborated to develop the Genomic Medicine Integrative Research (GMIR) Framework, a simple but comprehensive tool to aid the genomics community in developing research questions, strategies, and measures and in integrating genomic medicine and prevention into clinical practice. Here we present the GMIR Framework and its development, along with examples of its use for research development, demonstrating how we applied it to select and harmonize measures for use across diverse genomic medicine implementation projects. Researchers can utilize the GMIR Framework for their own research, collaborative investigations, and clinical implementation efforts; clinicians can use it to establish and evaluate programs; and all stakeholders can use it to help allocate resources and make sure that the full complexity of etiology is included in research and program design, development, and evaluation.

The difficulties of broad data sharing in genomic medicine: Empirical evidence from diverse participants in prenatal and pediatric clinical genomics research.

PURPOSE: This study aimed to understand broad data sharing decisions among predominantly underserved families participating in genomic research. METHODS: Drawing on clinic observations, semistructured interviews, and survey data from prenatal and pediatric families enrolled in a genomic medicine study focused on historically underserved and underrepresented populations, this paper expands empirical evidence regarding genomic data sharing communication and decision-making. RESULTS: One-third of parents declined to share family data, and pediatric participants were significantly more likely to decline than prenatal participants. The pediatric population was significantly more socioeconomically disadvantaged and more likely to require interpreters. Opt-in was tied to altruism and participants' perception that data sharing was inherent to research participation. Opt-out was associated with privacy concerns and influenced by clinical staff's presentation of data handling procedures. The ability of participants to make informed choices during enrollment about data sharing was weakened by suboptimal circumstances, which was revealed by poor understanding of data sharing in follow-up interviews as well as discrepancies between expressed participant desires and official recorded choices. CONCLUSION: These empirical data suggest that the context within which informed consent process is conducted in clinical genomics may be inadequate for respecting participants' values and preferences and does not support informed decision-making processes.

Perspectives and preferences regarding genomic secondary findings in underrepresented prenatal and pediatric populations: A mixed-methods approach.

PURPOSE: Patients undergoing clinical exome sequencing (ES) are routinely offered the option to receive secondary findings (SF). However, little is known about the views of individuals from underrepresented minority pediatric or prenatal populations regarding SF. METHODS: We explored the preferences for receiving hypothetical categories of SF (H-SF) and reasons for accepting or declining actual SF through surveying (n = 149) and/or interviewing (n = 47) 190 families undergoing pediatric or prenatal ES. RESULTS: Underrepresented minorities made up 75% of the probands. In total, 150 families (79%) accepted SF as part of their child/fetus's ES. Most families (63%) wanted all categories of H-SF. Those who declined SF as part of ES were less likely to want H-SF across all categories. Interview findings indicate that some families did not recall their SF decision. Preparing for the future was a major motivator for accepting SF, and concerns about privacy, discrimination, and psychological effect drove decliners. CONCLUSION: A notable subset of families (37%) did not want at least 1 category of H-SF, suggesting more hesitancy about receiving all available results than previously reported. The lack of recollection of SF decisions suggests a need for alternative communication approaches. Results highlight the importance of the inclusion of diverse populations in genomic research.

Preference for secondary findings in prenatal and pediatric exome sequencing.

OBJECTIVE: We aimed to determine the frequency of accepting secondary findings in families undergoing exome sequencing in prenatal and pediatric settings. METHODS: This was a secondary analysis of prospectively enrolled patients undergoing trio exome sequencing for congenital anomalies or developmental disorders in prenatal and pediatric settings, in which families were offered receiving secondary findings (initially assessed in the proband and, if identified, then in the parents). The primary outcome was frequency of accepting secondary findings. Secondary outcomes included frequency of acceptance in prenatal versus pediatric settings, and sociodemographic differences between those who accepted versus declined secondary findings. RESULTS: There were 682 families included in the cohort (289 prenatal and 393 pediatric). Overall, 84% (576/682) of families accepted secondary findings: 86.2% (249/289) of families undergoing prenatal versus 83.2% (327/393) pediatric (p = 0.30) testing. Secondary findings were identified in 2.6% (15/576) of cases, with no difference between prenatal and pediatric settings. There were no differences in sociodemographics between families that accepted versus declined secondary findings. CONCLUSION: The majority of families undergoing exome sequencing accepted secondary findings; this did not differ in prenatal versus pediatric settings. This highlights the need for guidance surrounding the offer of secondary findings in the prenatal setting.

The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations.

The Clinical Sequencing Evidence-Generating Research (CSER) consortium, now in its second funding cycle, is investigating the effectiveness of integrating genomic (exome or genome) sequencing into the clinical care of diverse and medically underserved individuals in a variety of healthcare settings and disease states. The consortium comprises a coordinating center, six funded extramural clinical projects, and an ongoing National Human Genome Research Institute (NHGRI) intramural project. Collectively, these projects aim to enroll and sequence over 6,100 participants in four years. At least 60% of participants will be of non-European ancestry or from underserved settings, with the goal of diversifying the populations that are providing an evidence base for genomic medicine. Five of the six clinical projects are enrolling pediatric patients with various phenotypes. One of these five projects is also enrolling couples whose fetus has a structural anomaly, and the sixth project is enrolling adults at risk for hereditary cancer. The ongoing NHGRI intramural project has enrolled primarily healthy adults. Goals of the consortium include assessing the clinical utility of genomic sequencing, exploring medical follow up and cascade testing of relatives, and evaluating patient-provider-laboratory level interactions that influence the use of this technology. The findings from the CSER consortium will offer patients, healthcare systems, and policymakers a clearer understanding of the opportunities and challenges of providing genomic medicine in diverse populations and settings, and contribute evidence toward developing best practices for the delivery of clinically useful and cost-effective genomic sequencing in diverse healthcare settings.

Ethical, Legal, and Social Implications of Fetal Gene Therapy.

As fetal gene therapies move from experimental animal models to human in utero phase I clinical trials, there is a need to consider the ethical, legal, and social implications. While fetal gene therapies are attracting more regulatory oversight than previous fetal interventions such as fetal surgery, old sociological questions should be applied to this new context. As health care pathways around fetal therapy are shaped by the ways in which a pregnant person and the fetus are constituted, and as risks and benefits are evaluated, we cannot afford to lose sight of long-term consequences, especially those pertaining to social inclusion.

Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.

A Multicenter Comparison of Complementary and Alternative Medicine (CAM) Discussions in Oncology Care: The Role of Time, Patient-Centeredness, and Practice Context.

BACKGROUND: Little is known about how complementary and alternative medicine (CAM) is discussed in cancer care across varied settings in the U.S. METHODS: In two practices affiliated with one academic medical center in southern California (SoCal), and one in the upper Midwest (UM), we audio-recorded patient-clinician interactions in medical oncology outpatient practices. We counted the frequency and duration of CAM-related conversations. We coded recordings using the Roter Interaction Analysis System. We used chi-square tests for bivariate analysis of categorical variables and generalized linear models for continuous variables to examine associations between dialogue characteristics, practice setting, and population characteristics with the occurrence of CAM discussion in each setting followed by multivariate models adjusting for clinician clustering. RESULTS: Sixty-one clinicians and 529 patients participated. Sixty-two of 529 (12%) interactions included CAM discussions, with significantly more observed in the SoCal university practice than in the other settings. Visits that included CAM were on average 6 minutes longer, with CAM content lasting an average of 78 seconds. In bivariate tests of association, conversations containing CAM included more psychosocial statements from both clinicians and patients, higher patient-centeredness, more positive patient and clinician affect, and greater patient engagement. In a multivariable model including significant bivariate terms, conversations containing CAM were independently associated with higher patient-centeredness, slightly longer visits, and being at the SoCal university site. CONCLUSION: The frequency of CAM-related discussion in oncology varied substantially across sites. Visits that included CAM discussion were longer and more patient centered. IMPLICATIONS FOR PRACTICE: The Institute of Medicine and the American Society of Clinical Oncology have called for more open discussions of complementary and alternative medicine (CAM). But little is known about the role population characteristics and care contexts may play in the frequency and nature of those discussions. The present data characterizing actual conversations in practice complements a much larger literature based on patient and clinician self-report about CAM disclosure and use. It was found that CAM discussions in academic oncology visits varied significantly by practice context, that the majority were initiated by the patient, and that they may occur more when visit time exists for lifestyle, self-care, and psychosocial concerns.

Rethinking the "open future" argument against predictive genetic testing of children.

Professional consensus has traditionally discouraged predictive genetic testing when no childhood interventions can reduce future morbidity or mortality. However, advances in genome sequencing and accumulating evidence that children and families cope adequately with predictive genetic information have weakened this consensus. The primary argument remaining against testing appeals to children's "right to an open future." It claims that the autonomy of the future adult is violated when others make an irreversible choice to obtain or disclose predictive genetic information during childhood. We evaluate this argument and conclude that children's interest in an open future should not be understood as a right. Rather an open future is one significant interest to weigh against other important interests when evaluating decisions. Thus, predictive genetic testing is ethically permissible in principle, as long as the interests promoted outweigh potential harms. We conclude by offering an expanded model of children's interests that might be considered in such circumstances, and present two case analyses to illustrate how this framework better guides decisions about predictive genetic testing in pediatrics.

Navigating the research-clinical interface in genomic medicine: analysis from the CSER Consortium.

PurposeThe Clinical Sequencing Exploratory Research (CSER) Consortium encompasses nine National Institutes of Health-funded U-award projects investigating translation of genomic sequencing into clinical care. Previous literature has distinguished norms and rules governing research versus clinical care. This is the first study to explore how genomics investigators describe and navigate the research-clinical interface.MethodsA CSER working group developed a 22-item survey. All nine U-award projects participated. Descriptive data were tabulated and qualitative analysis of text responses identified themes and characterizations of the research-clinical interface.ResultsSurvey responses described how studies approached the research-clinical interface, including in consent practices, recording results, and using a research versus clinical laboratory. Responses revealed four characterizations of the interface: clear separation between research and clinical care, interdigitation of the two with steps to maintain separation, a dynamic interface, and merging of the two. All survey respondents utilized at least two different characterizations. Although research has traditionally been differentiated from clinical care, respondents pointed to factors blurring the distinction and strategies to differentiate the domains.ConclusionThese results illustrate the difficulty in applying the traditional bifurcation of research versus clinical care to translational models of clinical research, including in genomics. Our results suggest new directions for ethics and oversight.

Physician Perception of Pay Fairness and its Association with Work Satisfaction, Intent to Leave Practice, and Personal Health.

BACKGROUND: Primary care physicians generally earn less than specialists. Studies of other occupations have identified perception of pay fairness as a predictor of work- and life-related outcomes. We evaluated whether physicians' pay fairness perceptions were associated with their work satisfaction, turnover intention, and personal health. METHODS: Three thousand five hundred eighty-nine physicians were surveyed. Agreement with "my total compensation is fair" was used to assess pay fairness perceptions. Total compensation was self-reported, and we used validated measures of work satisfaction, likelihood of leaving current practice, and health status. Hierarchical logistic regressions were used to assess the associations between pay fairness perceptions and work/life-related outcomes. RESULTS: A total of 2263 physicians completed surveys. Fifty-seven percent believed their compensation was fair; there was no difference between physicians in internal medicine and non-primary care specialties (P = 0.58). Eighty-three percent were satisfied at work, 70% reported low likelihood of leaving their practice, and 77% rated their health as very good or excellent. Higher compensation levels were associated with greater work satisfaction and lower turnover intention, but most associations became statistically non-significant after adjusting for pay fairness perceptions. Perceived pay fairness was associated with greater work satisfaction (OR, 4.90; 95% CI, 3.94-6.08; P < 0.001), lower turnover intention (OR, 2.46; 95% CI, 2.01-3.01; P < 0.001), and better health (OR, 1.33; 95% CI, 1.08-1.65; P < 0.01). DISCUSSION: Physicians who thought their pay was fair reported greater work satisfaction, lower likelihood of leaving their practice, and better overall health. Addressing pay fairness perceptions may be important for sustaining a satisfied and healthy physician workforce, which is necessary to deliver high-quality care.

How California Prepared for Implementation of Physician-Assisted Death: A Primer.

Physician-assisted death is now legal in California, and similar laws are being considered in many other states. The California law includes safeguards, yet health care providers will face practical and ethical issues while implementing physician-assisted death that are not addressed by the law. To help providers and health care facilities in California prepare to provide optimal care to patients who inquire about physician-assisted death, we brought together experts from California, Oregon, and Washington. We convened a conference of 112 stakeholders in December 2015, and herein present their recommendations. Themes of recommendations regarding implementation include (1) institutions should develop and revise physician-assisted death policies; (2) legal physician-assisted death will have implications for California's culturally and socioeconomically diverse population, and for patients from vulnerable groups; (3) conscientious objection and moral distress for health care providers must be considered; and (4) palliative care is essential to the response to the law. The expert conference participants' insights are a valuable guide, both for providers and health care facilities in California planning or revising their response, and for other jurisdictions where physician-assisted death laws are being considered or implemented.

If you build it, they will come: unintended future uses of organised health data collections.

BACKGROUND: Health research increasingly relies on organized collections of health data and biological samples. There are many types of sample and data collections that are used for health research, though these are collected for many purposes, not all of which are health-related. These collections exist under different jurisdictional and regulatory arrangements and include: 1) Population biobanks, cohort studies, and genome databases 2) Clinical and public health data 3) Direct-to-consumer genetic testing 4) Social media 5) Fitness trackers, health apps, and biometric data sensors Ethical, legal, and social challenges of such collections are well recognized, but there has been limited attention to the broader societal implications of the existence of these collections. DISCUSSION: Although health research conducted using these collections is broadly recognized as beneficent, secondary uses of these data and samples may be controversial. We examine both documented and hypothetical scenarios of secondary uses of health data and samples. In particular, we focus on the use of health data for purposes of: Forensic investigations Civil lawsuits Identification of victims of mass casualty events Denial of entry for border security and immigration Making health resource rationing decisions Facilitating human rights abuses in autocratic regimes CONCLUSIONS: Current safeguards relating to the use of health data and samples include research ethics oversight and privacy laws. These safeguards have a strong focus on informed consent and anonymization, which are aimed at the protection of the individual research subject. They are not intended to address broader societal implications of health data and sample collections. As such, existing arrangements are insufficient to protect against subversion of health databases for non-sanctioned secondary uses, or to provide guidance for reasonable but controversial secondary uses. We are concerned that existing debate in the scholarly literature and beyond has not sufficiently recognized the secondary data uses we outline in this paper. Our main purpose, therefore, is to raise awareness of the potential for unforeseen and unintended consequences, in particular negative consequences, of the increased availability and development of health data collections for research, by providing a comprehensive review of documented and hypothetical non-health research uses of such data.

Unwarranted optimism in media portrayals of genetic research on addiction overshadows critical ethical and social concerns.

The cost of addiction in the United States, in combination with a host of new tools and techniques, has fueled an explosion of genetic research on addiction. Because the media has the capacity to reflect and influence public perception, there is a need to examine how treatments and preventive approaches projected to emerge from addiction genetic research are presented to the public. The authors conducted a textual analysis of 145 news articles reporting on genetic research on addiction from popular print media in the United States and from popular news and medical internet sites. In articles that report on prevention, the media emphasize vaccine development and identifying individuals at genetic risk through population screening. Articles that emphasize treatment often promote current pharmaceutical solutions and highlight the possibility of tailoring treatments to specific genetic variants. The authors raise concerns about the tendency of this coverage to focus on the benefits of pharmaceutical treatments and genetic-based approaches to prevention while neglecting or downplaying potential risks and ethical issues. This analysis suggests a need for more balanced, evidence-based media reporting on the potential outcomes of genetic research.

Dying in the Hospital: Perspectives of family members.

BACKGROUND: Although most patients express a preference to die at home, many (over 30 percent) still die in hospital. This study's purpose was to explore the experience of hospital death from the perspective of patients' family members. METHODS: interviews were conducted with family members of patients who had died at hospitals affiliated with a large tertiary referral centre in the United States. Content analysis was used to analyze findings. FINDINGS: We interviewed 30 family members by phone. Themes were arranged by time frame: before death, time of death, and after death. CONCLUSION: Families do not interpret clinical cues leading up to death in the same way healthcare providers do; families need clear and direct explanations from providers. Clinicians should assess patient and family understandings of prognosis and communicate clearly and directly. Family members value being with their loved one at the time of death, and they value spending time with the body after death; this should be facilitated in clinical practice.

The media and behavioral genetics: Alternatives coexisting with addiction genetics.

To understand public discourse in the U.S. on genetic causation of behavioral disorders, we analyzed media representations of genetic research on addiction published between 1990 and 2010. We conclude first that the media simplistically represent biological bases of addiction and willpower as being mutually exclusive: behaviors are either genetically determined, or they are a choice. Second, most articles provide only cursory or no treatment of the environmental contribution. A media focus on genetics directs attention away from environmental factors. Rhetorically, media neglect the complexity underlying of the etiology of addiction and direct focus back toward individual causation and responsibility.