A semiquantitative metric for evaluating clinical actionability of incidental or secondary findings from genome-scale sequencing.

PURPOSE: As genome-scale sequencing is increasingly applied in clinical scenarios, a wide variety of genomic findings will be discovered as secondary or incidental findings, and there is debate about how they should be handled. The clinical actionability of such findings varies, necessitating standardized frameworks for a priori decision making about their analysis. METHODS: We established a semiquantitative metric to assess five elements of actionability: severity and likelihood of the disease outcome, efficacy and burden of intervention, and knowledge base, with a total score from 0 to 15. RESULTS: The semiquantitative metric was applied to a list of putative actionable conditions, the list of genes recommended by the American College of Medical Genetics and Genomics (ACMG) for return when deleterious variants are discovered as secondary/incidental findings, and a random sample of 1,000 genes. Scores from the list of putative actionable conditions (median = 12) and the ACMG list (median = 11) were both statistically different than the randomly selected genes (median = 7) (P < 0.0001, two-tailed Mann-Whitney test). CONCLUSION: Gene-disease pairs having a score of 11 or higher represent the top quintile of actionability. The semiquantitative metric effectively assesses clinical actionability, promotes transparency, and may facilitate assessments of clinical actionability by various groups and in diverse contexts.Genet Med 18 5, 467-475.

Obtaining consent from both parents for pediatric research: what does "reasonably available" mean?

OBJECTIVE: Circumstances surrounding parental availability and decision-making were examined in the setting of a research protocol involving newborn screening (NBS) for fragile X syndrome, in which the institutional review board (IRB) had determined that consent (permission) was required from both parents. METHODS: A survey was conducted with 3001 families who were approached to participate in optional NBS. In addition to basic demographics, observational notes detailed the reasons why fathers were not present or deemed "not reasonably available" (per IRB regulations), and content analysis identified the factors for this lack of availability. Logistic regression models estimated the likelihood that both parents would agree to enroll their infant in the screening project. RESULTS: Fathers were not present in 589 cases, including 158 in which fathers were ultimately determined to be not reasonably available. Primary reasons for father's unavailability were deployment with the military, incarceration, living out of state, or not involved in the mother's life. In cases in which both parents were available, 64% agreed to enroll in the NBS study. Criteria to guide researchers in making required determinations were developed from consultations with IRB officials and legal counsel. CONCLUSIONS: In a large-scale population-based study, 19.6% of fathers were absent for the consent process. Scenarios encountered underscore the complexity of parental relations and their implications for obtaining consent for research involving children. The algorithm developed may serve as a useful tool for others in applying the regulatory requirements for dual parental permission.

Recommendations for ethical approaches to genotype-driven research recruitment.

Recruiting research participants based on genetic information generated about them in a prior study is a potentially powerful way to study the functional significance of human genetic variation. However, it also presents significant ethical challenges that, to date, have received only minimal consideration. We convened a multi-disciplinary workshop to discuss key issues relevant to the conduct and oversight of genotype-driven recruitment and to translate those considerations into practical policy recommendations. Workshop participants were invited from around the US, and included genomic researchers and study coordinators, research participants, clinicians, bioethics scholars, experts in human research protections, and government representatives. Discussion was directed by experienced facilitators and informed by empirical data collected in a national survey of IRB chairs and in-depth interviews with research participants in studies where genotype-driven recontact occurred. A high degree of consensus was attained on the resulting seven recommendations, which cover informed consent disclosures and choices, the process for how and by whom participants are recontacted, the disclosure of individual genetic research results, and the importance of tailoring approaches based on specific contextual factors. These recommendations are intended to represent a balanced approach-protecting research participants, yet avoiding overly restrictive policies that hinder advancement on important scientific questions.

Research participants' perspectives on genotype-driven research recruitment.

Genotype-driven recruitment is a potentially powerful approach for studying human genetic variation but presents ethical challenges. We conducted in-depth interviews with research participants in six studies where such recruitment occurred. Nearly all responded favorably to the acceptability of recontact for research recruitment, and genotype-driven recruitment was viewed as a positive sign of scientific advancement. Reactions to questions about the disclosure of individual genetic research results varied. Common themes included explaining the purpose of recontact, informing decisions about further participation, reciprocity, "information is valuable," and the possibility of benefit, as well as concerns about undue distress and misunderstanding. Our findings suggest contact about additional research may be least concerning if it involves a known element (e.g., trusted researchers). Also, for genotype-driven recruitment, it may be appropriate to set a lower bar for disclosure of individual results than the clinical utility threshold recommended more generally.

Getting from A to IRB: developing an institutional review board at a historically black university.

Shaw University, the oldest historically black college or university in the southern USA, recently partnered with the University of North Carolina at Chapel Hill, a major research institution in North Carolina, to further develop Shaw's research infrastructure. One aim of the partnership involved establishing a human research ethics committee and an accompanying administrative structure and research ethics education program. This paper describes the process of developing an entire human research protection program de novo through collaboration with and mentoring by the members of the human research protection program at a nearby major research institution. This paper provides a detailed description of the aims, procedures, accomplishments, and challenges involved in such a project, which may serve as a useful model for other primarily teaching institutions wishing to develop research infrastructure and ethical capacity.

Applying research ethics guidelines: the view from a sub-saharan research ethics committee.

CONSIDERABLE VARIATION HAS BEEN demonstrated in applying regulations across research ethics committees (RECs) in the U.S., U.K., and European nations. With the rise of international research collaborations, RECs in developing countries apply a variety of international regulations. We conducted a qualitative descriptive pilot study with members of the national REC in Malawi to determine criteria they use to review research, and their views on international collaborations. Qualitative content analysis demonstrated that international guidelines are interpreted in light of local African conditions such that emphasis is placed on examining benefit to the community and ensuring the informed consent process translates concepts in locally-meaningful ways. Members suggest that RECs often must comply with regulations that do not fit local conditions. Recommendations are provided for improving such international collaborations.

Therapeutic misconception in early phase gene transfer trials.

Many subjects in early phase clinical trials expect to benefit in some way from the research intervention. It is understandable that people hope for improvement in their condition, no matter what the evidence. Yet unreasonable expectation of medical benefit may reflect problems with informed consent: Investigators may not disclose clearly that direct medical benefit from an early phase experimental intervention is unlikely or impossible, or subjects may not appreciate the differences between treatment and research. This paper presents findings from recent interviews with researchers and subjects and analysis of consent forms in early phase gene transfer research, a cutting-edge technology often called 'gene therapy'. We use three variables to construct a composite measure of therapeutic misconception TM, tapping misconceptions about the purposes of early phase research and the potential for direct medical benefit in these trials. Our multivariate model demonstrates the importance of both subject- and study-level factors as predictors of this TM index: education, disease type, and communication by study personnel about the likelihood of benefit. We hope that this work will deepen the discussion of how to define and measure TM, and refine the specification of factors that are related to subjects' TM.

Common (mis)perceptions about IRB review of human subjects research.

Every researcher who conducts research involving human subjects for their data has experiences with one or more institutional review boards. Some view their institutional review board experiences as helpful; others view them as painful and obstructive. However, there are many misperceptions about institutional review boards and their operation. Some common misperceptions are presented and discussed in an effort to correct false views held by researchers.

Preliminary evaluation of whole-blood gamma interferon release for clinical assessment of cellular immunity in patients with active coccidioidomycosis.

Assessment of the cellular immune response in coccidioidomycosis has epidemiologic and prognostic importance. Measurement of delayed-type hypersensitivity to skin testing has been used in the past to determine cellular immunity in coccidioidomycosis. However, no skin tests are currently available in the United States. Assay of gamma interferon (IFN-gamma) release in whole blood in response to incubation with antigen has been used to assess cellular immunity in tuberculosis. We used a similar assay using the coccidioidal antigen preparation T27K to measure the in vitro cellular immune responses among a cohort of 69 subjects with active coccidioidomycosis. IFN-gamma release was bimodal, with concentrations above and below 5 IU/ml. Using multivariate logistic regression, underlying disease and disseminated or chronic pulmonary coccidioidomycosis was significantly associated with the release of IFN-gamma at a concentration of <5 IU/ml (P = 0.02 or 0.05, respectively). In addition, the release IFN-gamma concentration was <5 IU/ml in all subjects with a clinical severity score of > or =6 (P = 0.02). The release IFN-gamma concentration correlated with expression of CD69 on T lymphocytes in an in vitro assay using T27K as the antigen (Spearman's rho = 0.59; P < 0.01). These results suggest that the IFN-gamma release assay with T27K as the antigen may be a useful clinical test for assessing cellular immunity in patients with active coccidioidomycosis.

The mannose receptor mediates the cellular immune response in human coccidioidomycosis.

Mannose is the predominant monosaccharide in the coccidioidal antigen preparation T27K. Mannan and anti-CD206 antibody significantly decreased the surface expression of mannose receptor (MR) on adherent peripheral blood mononuclear cells and reduced the interleukin-2 (IL-2) release induced by T27K. These data suggest that MR mediates IL-2 release by T27K.

Uncertain benefit: investigators' views and communications in early phase gene transfer trials.

We report on a study of potential sources of therapeutic misconception in early phase gene transfer research, examining how investigators and their consent forms represent the prospect for direct benefit. Our analysis demonstrates that even though half of PIs said they expected direct medical benefit for their subjects, they did not necessarily convey this to their subjects. What they reported telling subjects resembled what was written in their consent form, which suggests that, far from being irrelevant, the consent form is an influential component of the consent process. We also demonstrate that the language used to describe direct benefit in consent forms and PIs' discussions was mostly vague, ambiguous, and indeterminate about benefit, rather than clearly negative. This was especially true for cancer and vascular disease trials. Our respondents found the problem of balancing hopes and expectations, for themselves and for their subjects, extraordinarily challenging. In the current era, investigators face such challenges without consistent normative guidance or agreed-upon standards for how to talk about scientific promise and uncertainty in early phase trials. This dilemma cannot be effectively addressed by individual investigators alone, but must be acknowledged and openly discussed by the scientific community at large.

The cost of operating institutional review boards (IRBs).

PURPOSE: Recent reports have claimed that institutional review boards (IRBs) are underfunded, yet little is known about the costs of operating IRBs. This study estimated the costs for operating high-volume and low-volume IRBs. METHOD: IRB costs were calculated from published summary data. Costs were standardized to reflect 2001 dollars. RESULTS: Total estimated costs for operating high-volume and low-volume IRBs were $770,674 and $76,626, respectively. The average cost per action, a measure of economic efficiency, was lower for high-volume IRBs ($277 per action) than it was for low-volume IRBs ($799 per action). CONCLUSIONS: Although high-volume IRBs are more expensive than are low-volume IRBs in absolute terms, they are more economically efficient. Policy debates should consider the potential savings from large IRBs, perhaps by encouraging small IRBs to merge, although this may result in less local review, control, and oversight.