By 6 October 2014, many laboratories in the United States must begin honoring new individual data access rights created by recent changes to federal privacy and laboratory regulations. These access rights are more expansive than has been widely understood and pose complex challenges for genomic testing laboratories. This article analyzes regulatory texts and guidances to explore which laboratories are affected. It offers the first published analysis of which parts of the vast trove of data generated during next-generation sequencing will be accessible to patients and research subjects. Persons tested at affected laboratories seemingly will have access, upon request, to uninterpreted gene variant information contained in their stored variant call format, binary alignment/map, and FASTQ files. A defect in the regulations will subject some non-CLIA-regulated research laboratories to these new access requirements unless the Department of Health and Human Services takes swift action to avert this apparently unintended consequence. More broadly, all affected laboratories face a long list of daunting operational, business, compliance, and bioethical issues as they adapt to this change and to the Food and Drug Administration’s recently announced plan to publish draft guidance outlining a new oversight framework for lab-developed tests.
access rights; CLIA; FDA; HIPAA; return of results
National Institutes of Health data-sharing policies aim to maximize public benefit derived from genetic studies by increasing research efficiency and the use of a pooled data resource for future studies. While broad access to data may lead to benefits for populations underrepresented in genetic studies, such as indigenous groups, tribes have ownership interest in their data. The Northwest-Alaska Pharmacogenetic Research Network, a partnership involving tribal organizations and universities conducting basic and translational pharmacogenetic research, convened a meeting to discuss the collection, management, and secondary use of research data, and of the processes surrounding access to data stored in federal repositories. This article reports on tribal perspectives that emerged from the dialogue and discusses the implications of tribal government sovereign status on research agreements and data-sharing negotiations. There is strong tribal support for efficient research processes that expedite the benefits from collaborative research, but there is also a need for data sharing procedures that take into account tribal sovereignty and appropriate oversight of research ¬ such as tribally-based research review processes and review of draft manuscripts. We also note specific ways in which accountability could be encouraged by National Institutes of Health as part of the research process.
genetics; tribal; indigenous; data-sharing; ethics
Whole exome and whole genome sequencing are applications of next generation sequencing transforming clinical care, but there is little evidence whether these tests improve patient outcomes or if they are cost effective compared to current standard of care. These gaps in knowledge can be addressed by comparative effectiveness and patient-centered outcomes research. We designed a randomized controlled trial that incorporates these research methods to evaluate whole exome sequencing compared to usual care in patients being evaluated for hereditary colorectal cancer and polyposis syndromes. Approximately 220 patients will be randomized and followed for 12 months after return of genomic findings. Patients will receive findings associated with colorectal cancer in a first return of result visit, and findings not associated with colorectal cancer (incidental findings) during a second return of result visit. The primary outcome is efficacy to detect mutations associated with these syndromes; secondary outcomes include psychosocial impact, cost-effectiveness and comparative costs. The secondary outcomes will be obtained via surveys before and after each return visit. The expected challenges in conducting this randomized controlled trial include the relatively low prevalence of genetic disease, difficult interpretation of some genetic variants, and uncertainty about which incidental findings should be returned to patients. The approaches utilized in this study may help guide other investigators in clinical genomics to identify useful outcome measures and strategies to address comparative effectiveness questions about the clinical implementation of genomic sequencing in clinical care.
Comparative effectiveness research; Genomics; Next generation sequencing; Randomized clinical trial; Outcomes research; Whole exome sequencing
Examination of families represents an important priority in health research. In this paper we report on individual and family-level factors associated with enrollment in a cancer prevention research project. We approached families affected by melanoma for possible participation in a randomized controlled trial of a web-based communication and support intervention.
We recruited three family members per family for assessment – the melanoma case, a first-degree relative (FDR), and a relative who is a parent of a child age 18 or younger. Recruitment involved three steps: requesting the physician’s consent to approach the melanoma case, approaching the case to request their participation and family contact information, and they approaching the FDRs and parents.
Of the 1380 families approached, 313 were enrolled, 263 were excluded because we could not find or contact a family member (FDR or parent), 331 did not have eligible family members, and 473 refused. The most frequently noted reason for refusal was being too busy or having no time. The primary predictors of participation for cases, FDRs, and parents included higher educational attainment (OR’s=1.5–2.15); FDRs were more likely to enroll if they were female (OR=1.77), parents were more likely to enroll if the case had been diagnosed more recently(OR=3.3), if the parent was partnered (OR=4.37), and if the parent lived in the same city as the case(2.88).
The results can provide information on the potential generalizability of family recruitment.
Recruitment; Family; Response rates; Behavioral intervention; Melanoma
Inadequate access to oral health care places children at risk for caries. Disease severity and inability to cooperate often result in treatment with general anesthesia (GA). Sedation is increasingly popular and viewed as lower risk than GA in community settings. Currently, few data are available to quantify pediatric morbidity and mortality related to dental anesthesia.
Summarize dental anesthesia-related pediatric deaths described in media reports.
Review of media reports in the Lexis-Nexis Academic database and a private foundation website.
Dental offices, ambulatory surgery centers, and hospitals.
U.S.-based children (≤ 21 y.o.) who died subsequent to receiving anesthesia for a dental procedure between 1980–2011.
Most deaths occurred among 2 –5 year-olds (n=21/44); in an office setting (n=21/44), and with a general/pediatric dentist (n=25/44) as the anesthesia provider. In this latter group, 17/25 deaths were linked with a sedation anesthetic.
This series of media reports likely represent only a fraction of the overall morbidity and mortality related to dental anesthesia. These data may indicate an association between mortality and pediatric dental procedures under sedation, particularly in office settings. However, these relationships are difficult to test in the absence of a database that could provide an estimate of incidence and prevalence of morbidity and mortality. With growing numbers of children receiving anesthesia for dental procedures from providers with variable training, it is imperative to be able to track anesthesia-related adverse outcomes. Creating a national database of adverse outcomes will enable future research to advance patient safety and quality.
Anesthesia; Patient safety; Child; Conscious Sedation/adverse effects; Dental Anxiety/drug therapy; Treatment Outcome
The return of individual results to research participants has been vigorously debated. Consensus statements indicate that researchers and bioethicists consider the return of research results most appropriate when the findings are clinically relevant. Even when clinical utility is the motivator, however, the return of individual research results is not equivalent to clinical care. There are important differences in the domains of research and medical care, both from a legal standpoint and in terms of the ethical responsibilities of clinicians and researchers. As a corollary, researchers risk promoting a therapeutic misconception if they create quasi-clinical settings for return of clinically relevant research results. Rather, efforts should be focused on clarity in the provision of research results, appropriate caveats and, most important, appropriate referrals when the results may be helpful to consider in medical care.
Genetic research results; medical practice; CLIA; HIPAA
The field of genomic medicine is moving beyond the domain of medical specialties into general care. As a result, primary care practitioners (PCPs) will be faced with questions regarding the interpretation, use, and application of genetic and genomic testing. Several studies have demonstrated the variable knowledge of PCPs, but few have assessed PCPs access to genetic specialists and how that may influence test use. As part of a survey of PCPs on pharmacogenetic testing, we assessed PCP access to genetic specialists and its association with referrals and test ordering.
We conducted an online/mail survey of a national sample of PCPs in the U.S.
Survey data indicate that PCP access to genetic specialists is limited, particularly to those practicing outside of academic medical centers, negatively impacting test ordering practices.
Given the small number of clinical genetic specialists, collaborative approaches are needed to develop educational and clinical resources to prepare and guide the safe and appropriate use of testing by future and current general practitioners, respectively.
Primary Care Physicians; Genetic Specialists; Access; Genomic Medicine
Pharmacogenetic research and clinical testing raise important concerns for individuals and communities, especially where past medical research and practice has perpetrated harm and cultivated distrust of health care systems and clinicians. We investigated perceptions of pharmacogenetics among Alaska Native (AN) people.
We held four focus groups for 32 ANs in south central Alaska to elicit views about pharmacogenetics in general and for treatment of cardiovascular disease, breast cancer, depression, and nicotine addiction. We analyzed data for perceived risks and rewards of pharmacogenetics.
Potential risks of pharmacogenetics included health care rationing, misuse of information, and stigma to individuals and the AN community. Potential rewards included decreased care costs, improved outcomes, and community development. Participants also discussed 8 contingent conditions that could mitigate risks and increase pharmacogenetic acceptability.
Alaska Natives perceive pharmacogenetics as potentially benefitting and harming individuals, communities, and health systems, depending on methods and oversight. Researchers, clinicians, and administrators, especially in community-based clinic and health care systems serving minority populations, must address this “double-edged sword” to effectively conduct pharmacogenetics.
Little is known about factors that influence patients’ preferences for the return of incidental findings from genome sequencing. This study identified attributes of incidental findings that were important to patients and developed a discrete choice experiment (DCE) instrument to quantify patient preferences.
An initial set of key attributes and attribute levels was developed from a literature review and in consultation with experts. The attributes’ salience and communication were refined using focus group methodology (N=12) and cognitive interviews (N=6) with patients who had received conventional genetic testing for familial colorectal cancer or polyposis syndromes. The attributes and levels used in the hypothetical choices presented to participants were identified using validated experimental design techniques.
The final DCE instrument incorporates the following attributes and levels: lifetime risk of disease (5%, 40%, 70%); disease treatability (medical, lifestyle, none); disease severity (mild, moderate, severe); carrier status (yes, no); drug response likelihood (high, moderate, none), and test cost ($250, $425, $1000, $1900).
Patient preferences for incidental genomic findings are likely influenced by a complex set of diverse attributes. Quantification of patient preferences can inform patient-provider communication by highlighting the attributes of incidental findings that matter most to patients and warrant further discussion.
The American College of Medical Genetics and Genomics recently issued recommendations for reporting incidental findings from clinical whole-genome sequencing and whole-exome sequencing. The recommendations call for evaluating a specific set of genes as part of all whole-genome sequencing/whole-exome sequencing and reporting all pathogenic variants irrespective of patient age. The genes are associated with highly penetrant disorders for which treatment or prevention is available. The effort to generate a list of genes with actionable findings is commendable, but the recommendations raise several concerns. They constitute a call for opportunistic screening, through intentional effort to identify pathogenic variants in specified genes unrelated to the clinical concern that prompted testing. Yet for most of the genes, we lack evidence about the predictive value of testing, genotype penetrance, spectrum of phenotypes, and efficacy of interventions in unselected populations. Furthermore, the recommendations do not allow patients to decline the additional findings, a position inconsistent with established norms. Finally, the recommendation to return adult-onset disease findings when children are tested is inconsistent with current professional consensus, including other policy statements of the American College of Medical Genetics and Genomics. Instead of premature practice recommendations, we call for robust dialogue among stakeholders to define a pathway to normatively sound, evidence-based guidelines.
Genome sequencing technology provides new and promising tests for clinical practice, including whole genome sequencing, which measures an individual’s complete DNA sequence, and whole exome sequencing, which measures the DNA for all genes coding for proteins. These technologies make it possible to test for multiple genes in a single test, which increases the efficiency of genetic testing. However, they can also produce large amounts of information that cannot be interpreted or is of limited clinical utility. This additional information could be distracting for patients and clinicians, and contribute to unnecessary healthcare costs. The potential for genomic sequencing to improve care will be context-dependent, varying for different patients and clinical settings. This Article argues that a disciplined approach is needed, incorporating research to assess when and how genomic information can improve clinical outcomes, practice guidelines that direct optimal uses of genomic sequencing, and efforts to limit the production of genomic information unrelated to the clinical needs of the patient. Without this approach, genomic testing could add to current unsustainable healthcare costs and prove unaffordable in the long run.
Higher education has long made efforts to increase underrepresented minority participation in biomedical research and health fields. However, relatively few minority trainees complete advanced degrees or proceed to independent research careers, a loss referred to as the “leaky pipeline.” Minority trainees may take alternate pathways to climbing the academic ladder, exiting to pursue multiple disciplinary or community-serving roles.
The authors propose a model for understanding minority departures from the education pipeline as a basis for nurturing careers that support community goals for health.
Concepts of the traditional pipeline training model are compared with a model that aligns with CBPR principles and practices. The article describes an irrigation model that incorporates informal learning from academic and community knowledge bases to prepare trainees for CBPR and interdisciplinary research. Students serve as agents that foster individual, institutional and social change needed to address health problems while attending to root causes of disparities.
Viewing minority students as agents for community engagement allows institutions to reassess the role training can play in diversifying participation in higher education and research. An irrigation model supports development of an infrastructure that optimizes success at all post-secondary levels, and enhances CBPR capacity wherever trainees live, work, and learn. Linking formal education to informal learning in context of community-based participatory research experiences can also reduce community mistrust of research while nurturing productive research partnerships with communities to address health disparities.
As genomic and exomic testing expands in both the research and clinical arenas, determining whether, how, and which incidental findings to return to the ordering clinician and patient becomes increasingly important. Although opinion is varied on what should be returned to consenting patients or research participants, most experts agree that return of medically actionable results should be considered. There is insufficient evidence to fully inform evidence-based clinical practice guidelines regarding return of results from genome-scale sequencing, and thus generation of such evidence is imperative, given the rapidity with which genome-scale diagnostic tests are being incorporated into clinical care. We present an overview of the approaches to incidental findings by members of the Clinical Sequencing Exploratory Research network, funded by the National Human Genome Research Institute, to generate discussion of these approaches by the clinical genomics community. We also report specific lists of “medically actionable” genes that have been generated by a subset of investigators in order to explore what types of findings have been included or excluded in various contexts. A discussion of the general principles regarding reporting of novel variants, challenging cases (genes for which consensus was difficult to achieve across Clinical Sequencing Exploratory Research network sites), solicitation of preferences from participants regarding return of incidental findings, and the timing and context of return of incidental findings are provided.
actionability; actionable genes; clinical sequencing; genomic medicine; incidental findings
Clinical whole exome and whole genome sequencing will result in a broad range of incidental findings (IFs), but clinicians’ obligations to identify and disclose such findings are a matter of debate. We sought legal cases that could offer insights into clinicians’ legal liability.
We searched for cases in which IFs were related to the cause of action, using the search engines WestLaw, WestLaw Next, Lexis, and Lexis Advance.
We found no case law related to IFs from genetic testing, but identified eight cases involving IFs in medical imaging. These cases suggest that clinicians may face liability for failing to disclose IFs that would have offered an opportunity for interventions to improve health outcome, if (1) under the applicable standard of care, they fail to identify or appreciate the significance of the IF; or 2) they negligently fail to notify other clinicians and/or the patient of the identified IF. Other cases support liability for failure to refer appropriately to a clinician with greater expertise.
Clinicians may face liability if they fail to disclose incidental information that could inform interventions to improve health outcome; information lacking clinical actionability is likely to have less import.
The objectives of this study were to study maternal preferences for the return of their child’s genetic results and to describe the experiences, perceptions, attitudes and values that are brought to bear when individuals from different racial and cultural backgrounds consider participating in genetic research. We recruited women with diverse sociodemographic profiles to participate in seven focus groups. Twenty-eight percent of participants self-identified as Hispanic; 49% as White, Non-Hispanic; and 21% as Asian or Asian American. Focus groups were conducted in English or Spanish and were audio-recorded and transcribed verbatim. Transcripts were analyzed using qualitative thematic methods. Results indicated that preferences and decisions regarding the return of results may depend on both research and individual contextual factors. Participants understood the return of results as a complex issue, where individual and cultural differences in preferences are certain to arise. Another key finding was that participants desired an interpersonal, dynamic, flexible process that accommodated individual preferences and contextual differences for returning results. Our findings indicate a need to have well-developed systems for allowing participants to make and change over time their choices regarding the return of their child’s genetic results.
genomic; genetic; research participation; return of results; context
It is anticipated that as the range of drugs for which pharmacogenetic testing becomes available expands, primary care physicians (PCPs) will become major users of these tests. To assess their training, familiarity, and attitudes toward pharmacogenetic testing in order to identify barriers to uptake that may be addressed at this early stage of test use, we conducted a national survey of a sample of PCPs. Respondents were mostly white (79%), based primarily in community-based primary care (81%) and almost evenly divided between family medicine and internal medicine. The majority of respondents had heard of PGx testing and anticipated that these tests are or would soon become a valuable tool to inform drug response. However, only a minority of respondents (13%) indicated they felt comfortable ordering PGx tests and almost a quarter reported not having any education about pharmacogenetics.
Our results indicate that primary care practitioners envision a major role for themselves in the delivery of PGx testing but recognize their lack of adequate knowledge and experience about these tests. Development of effective tools for guiding PCPs in the use of PGx tests should be a high priority.
Return of individual genetic results to research participants, including participants in archives and biorepositories, is receiving increased attention. However, few groups have deliberated on specific results or weighed deliberations against relevant local contextual factors.
The Electronic Medical Records and GEnomics (eMERGE) network, which includes five biorepositories conducting genome-wide association studies, convened a Return of Results Oversight Committee (RROC) to identify potentially returnable results. Network-wide deliberations were then brought to local constituencies for final decision-making.
Defining results that should be considered for return required input from clinicians with relevant expertise and much deliberation. The RROC identified two sex chromosomal anomalies, Klinefelter Syndrome and Turner Syndrome, as well as homozygosity for Factor V Leiden, as findings that could warrant reporting. Views about returning HFE gene mutations associated with hemochromatosis were mixed due to low penetrance. Review of EMRs suggested that most participants with detected abnormalities were unaware of these findings. Local considerations relevant to return varied and, to date, four sites have elected not to return findings (return was not possible at one site).
The eMERGE experience reveals the complexity of return of results decision-making and provides a potential deliberative model for adoption in other collaborative contexts.
Result return; biorepository; electronic medical records; deliberation; context
To promote effective genome-scale research, genomic and clinical data for large population samples must be collected, stored, and shared.
We conducted focus groups with 45 members of a Seattle-based integrated healthcare delivery system to learn about their views and expectations for informed consent in genome-scale studies.
Participants viewed information about study purpose, aims, and how and by whom study data could be used to be at least as important as information about risks and possible harms. They generally supported a tiered consent approach for specific issues, including research purpose, data sharing, and access to individual research results. Participants expressed a continuum of opinions with respect to the acceptability of broad consent, ranging from completely acceptable to completely unacceptable. Older participants were more likely to view the consent process in relational – rather than contractual – terms, compared with younger participants. The majority of participants endorsed seeking study subjects’ permission regarding material changes in study purpose and data sharing.
Although this study sample was limited in terms of racial and socioeconomic diversity, our results suggest a strong positive interest in genomic research on the part of at least some prospective participants and indicate a need for increased public engagement, as well as strategies for ongoing communication with study participants.
Informed consent; participant views; genomic research; biobank; research ethics
Although issues involved in offering individual results to participants in genomic research have received considerable attention, communication of aggregate results has been the subject of relatively little ethical analysis. Offering participants aggregate results is typically assumed to be a good thing, and studies have found that a significant majority of biobank research participants, when asked about their interest in aggregate results, say that access to such information would be important. Even so, return of aggregate results remains a relatively uncommon practice.
In this paper, we explore the opportunities involved in communicating aggregate results to participants in genomic research, including affirming the value of research participation, informing participants about research being conducted based on broad consent for future unspecified research, educating participants and the public about the research process, and building trust in the research enterprise. We also explore some of the challenges, including the complex intersection between individual and aggregate results, as well as practical hurdles. We conclude by offering our preliminary recommendations concerning the provision of aggregate results and an agenda for much-needed future research.
Research results; aggregate results; research participants; trust; education; informed consent
We examined the experiences, perceptions, and values that are brought to bear when individuals from different ethnic and cultural backgrounds consider participating in health research. Fifty-three women from Latino, Asian American, Middle Eastern, or Non-Latino, White backgrounds participated in seven English or Spanish focus groups facilitated by trained investigators using a standard protocol. Investigators described the National Children’s Study (NCS) and then asked questions to elicit potential concerns, expectations, and informational needs. Group sessions were audio-recorded, transcribed verbatim, and analyzed using qualitative thematic methods. A major theme that emerged during focus groups was participant self-identification as a member of a cultural group or community when raising issues that would influence their decision to participate in research. A related theme was the belief by some that communities may differ in the ease of participation in the NCS. Identified themes related to the informed consent process included perceived risks, anticipated burden, perceived benefits, informational needs, and decision-making strategies. Although themes were shared across groups, there were cultural differences within themes. Findings indicated that individuals from diverse backgrounds may have different perspectives on and expectations for the research process. To effectively recruit representative samples, it will be important to address a range of issues relevant for informed consent and to consider the impact of participation on both individuals and communities.
Informed consent; Research participation; Diversity; Culture; Recruitment; National Children’s Study
Genetic research involving human participants can pose challenging questions related to ethical and regulatory standards for research oversight. However, few empirical studies describe how genetic researchers and institutional review board (IRB) professionals conceptualize ethical issues in genetic research or where common ground might exist.
Parallel online surveys collected information from human genetic researchers (n = 351) and IRB professionals (n = 208) regarding their views about human participant oversight for genetic protocols.
A range of opinions were observed within groups on most issues. In both groups, a minority thought it likely that people would be harmed by participation in genetic research or identified from coded genetic data. A majority of both groups agreed that reconsent should be required for four of the six scenarios presented. Statistically significant differences were observed between groups on some issues, with more genetic researcher respondents trusting the confidentiality of coded data, fewer expecting harms from reidentification, and fewer considering reconsent necessary in certain scenarios.
The range of views observed within and between IRB and genetic researcher groups highlights the complexity and unsettled nature of many ethical issues in genome research. Our findings also identify areas where researcher and IRB views diverge and areas of common ground.
comparison; genetics; human genomics; identifiability; institutional review board; reconsent; survey
Genetic research can produce information that is beyond the aims of the research study yet may be of clinical or personal interest to study participants. We conducted semi-structured interviews with 44 researchers who were asked to describe how they would respond to a hypothetical vignette regarding the disclosure of findings with unanticipated clinical significance to research study participants. Interviews were transcribed and analyzed using content and thematic analyses. Researchers’ decision-making processes about whether to disclose incidental findings were governed by potentially conflicting duties in three primary domains: information quality, adherence to rules, and participant welfare. There are several actions researchers can take to prepare for incidental findings, including: adding specific language in informed consent documents to state clearly how investigators will handle disclosure; exploring how prepared participants might be during the consent process to make decisions about how they would like to be approached in the event of incidental findings; developing procedures for appropriately communicating individual results and providing follow-up support based on participant preferences; and, in genetic research, having an awareness of the range of traits expressed by the genes under study.
incidental findings; genetic studies; decision-making processes; communication of results; disclosure; qualitative research; vignette study
Current approaches to genetic screening include newborn screening to identify infants who would benefit from early treatment, reproductive genetic screening to assist reproductive decision making, and family history assessment to identify individuals who would benefit from additional prevention measures. Although the traditional goal of screening is to identify early disease or risk in order to implement preventive therapy, genetic screening has always included an atypical element—information relevant to reproductive decisions. New technologies offer increasingly comprehensive identification of genetic conditions and susceptibilities. Tests based on these technologies are generating a different approach to screening that seeks to inform individuals about all of their genetic traits and susceptibilities for purposes that incorporate rapid diagnosis, family planning, and expediting of research, as well as the traditional screening goal of improving prevention. Use of these tests in population screening will increase the challenges already encountered in genetic screening programs, including false-positive and ambiguous test results, overdiagnosis, and incidental findings. Whether this approach is desirable requires further empiric research, but it also requires careful deliberation on the part of all concerned, including genomic researchers, clinicians, public health officials, health care payers, and especially those who will be the recipients of this novel screening approach.
genetic testing; genetics, medical; genomics; heterozygote detection; neonatal screening; prenatal diagnosis