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Informed consent for next-generation nucleotide sequencing studies: Aiding communication between participants and investigators.

ABSTRACT: Obtaining informed consent from prospective participants for research studies that include next-generation nucleotide sequencing (NGS) presents significant challenges because of the need to explain all the potential implications of participating, including the possible return of "incidental" findings, in easy-to-understand language.After reviewing the consent processes at other institutions, we decided to supplement the protocol-specific informed consent form with the following: (1) a short pamphlet for the prospective participant that includes a series of questions that she or he is encouraged to ask the investigator, and (2) a more detailed companion guide for investigators to help them develop simple-language answers to the questions. Both documents are available to use or modify.We propose an approach to obtaining informed consent for NGS studies that encourages discussion of key issues without creating a complex, comprehensive document for participants; it also maximizes investigator flexibility. We also suggest mechanisms to return restricted information to participants.

SUBMITTER: Kost RG

PROVIDER: S-EPMC5471895 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

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Informed consent for next-generation nucleotide sequencing studies: Aiding communication between participants and investigators.

Kost Rhonda G RG Poppel Stephen M SM Coller Barry S BS

Journal of clinical and translational science 20170207 2

<h4>Introduction</h4>Obtaining informed consent from prospective participants for research studies that include next-generation nucleotide sequencing (NGS) presents significant challenges because of the need to explain all the potential implications of participating, including the possible return of "incidental" findings, in easy-to-understand language.<h4>Methods and results</h4>After reviewing the consent processes at other institutions, we decided to supplement the protocol-specific informed ...[more]

PMID: 28649453

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Project description:A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores. Others, such as SeqEM, estimate error rates from the read data without using any quality scores. It is also a common quality control procedure to filter out reads with low phred scores. However, choosing an appropriate phred score threshold is problematic as a too high threshold may lose data, while a too low threshold may introduce errors. We propose a new likelihood-based genotype-calling approach that exploits all reads and estimates the per-base error rates by incorporating phred scores through a logistic regression model. The approach, which we call PhredEM, uses the expectation-maximization (EM) algorithm to obtain consistent estimates of genotype frequencies and logistic regression parameters. It also includes a simple, computationally efficient screening algorithm to identify loci that are estimated to be monomorphic, so that only loci estimated to be nonmonomorphic require application of the EM algorithm. Like GATK, PhredEM can be used together with a linkage-disequilibrium-based method such as Beagle, which can further improve genotype calling as a refinement step. We evaluate the performance of PhredEM using both simulated data and real sequencing data from the UK10K project and the 1000 Genomes project. The results demonstrate that PhredEM performs better than either GATK or SeqEM, and that PhredEM is an improved, robust, and widely applicable genotype-calling approach for NGS studies. The relevant software is freely available.

Project description:Cognitive impairment is a characteristic of schizophrenia. This impairment may affect the retention of information required for ongoing knowledgeable participation in clinical trials. This study monitored retention of study-related knowledge-including assessment of therapeutic misconception-in people with stable, DSM-IV schizophrenia during participation in placebo-controlled clinical trials of adjunctive agents. Stability was defined as being on an antipsychotic with no change in medication or dose over the previous 4 weeks.This longitudinal study assessed retention of clinical trial-related consent information. Individuals enrolling in 1 of 8 clinical trials were approached for participation. Participants came from research clinics and community mental health centers. At baseline, clinical trial consent forms were reviewed and study knowledge assessed. Participants were randomized to follow-up assessments at weeks 1, 4, and 8; weeks 4 and 8; or at week 8 only. Clinical trial consent forms were not rereviewed at any follow-up visit.Fifty-nine participants were enrolled; analysis included 52 participants with at least 1 follow-up visit. Study knowledge did not decrease meaningfully in any group. Therapeutic misconception was not observed in participants during the study. The group assessed most frequently demonstrated significant improvement over baseline (t44 = 3.43, P = .001). Retention of study knowledge was not related to symptoms but had a weak correlation with cognitive capacity (R = 0.28, P = .07). Performance did not differ between participants from research clinics and those from community mental health centers.Clinically stable people with schizophrenia enrolling in a placebo-controlled adjunctive medication study, once determined to have capacity to consent to a clinical trial, retained appropriate study knowledge for at least 8 weeks. In the absence of a specific reason to suspect a loss of decisional capacity, there appears to be no need to routinely reevaluate participants during this type of clinical trial.

Project description:BackgroundThe process of informed consent for enrolment to a clinical research study can be complex for both participants and research staff. Challenges include respecting the potential participant's autonomy and information needs while simultaneously providing adequate information to enable an informed decision. Qualitative research with small sample sizes has added to our understanding of these challenges. However, there is value in garnering the perspectives of research participants and staff across larger samples to explore the impact of contextual factors (time spent, the timing of the discussion and the setting), on the informed consent process.MethodsResearch staff and research participants from Ireland and the UK were invited to complete an anonymous survey by post or online (research participants) and online (research staff). The surveys aimed to quantify the perceptions of research participants and staff regarding some contextual factors about the process of informed consent. The survey, which contained 14 and 16 multiple choice questions for research participants and staff respectively, was analysed using descriptive statistics. Both surveys included one optional, open-ended question, which were analysed thematically.ResultsResearch participants (169) and research staff (115) completed the survey. Research participants were predominantly positive about the informed consent process but highlighted the importance of having sufficient time and the value of providing follow-up once the study concludes, e.g. providing results to participants. Most staff (74.4%) staff reported that they felt very confident or confident facilitating informed consent discussions, but 63% felt information leaflets were too long and/or complicated, 56% were concerned about whether participants had understood complex information and 40% felt that time constraints were a barrier. A dominant theme from the open-ended responses to the staff survey was the importance of adequate time and resources.ConclusionsResearch participants in this study were overwhelmingly positive about their experience of the informed consent process. However, research staff expressed concern about how much participants have understood and studies of patient comprehension of research study information would seem to confirm these fears. This study highlights the importance of allocating adequate time to informed consent discussions, and research staff could consider using Teach Back techniques.Trial registrationNot applicable.

Project description:BackgroundClinical trial participants are required to sign an informed consent form (ICF). However, information is lacking on the most effective methods to convey trial relevant information prior to inviting participants to sign the ICF, being particularly pertinent in low-income countries. A previous study on Pemba Island, Tanzania, found that a verbal information session (IS) was significantly better than providing an ICF alone. However, knowledge gaps remained. Building on these findings, we investigated the effect of adding a slideshow or a theater to the IS in the informed consent procedure of an anthelminthic clinical trial.Methodology/principal findingsA total of 604 caregivers were randomized into the control group that only received an ICF (n = 150) or an ICF plus one of three intervention strategies: (i) verbal IS (n = 135), (ii) verbal IS with a slideshow (n = 174) or (iii) verbal IS followed by a theater (n = 145). All modes of information covered the same key messages. Participants' understanding was assessed using a semi-structured questionnaire. The mean score of caregivers in the control group (ICF only) was 4.41 (standard deviation = 1.47). Caregivers attending the IS alone were more knowledgeable than those in the control group (estimated difference in mean scores: 2.40, 95% confidence interval (CI) 1.95 to 2.86, p < 0.01). However, there was no evidence of an improvement compared to the IS only when participants attended a slideshow (0.09, 95% CI -0.53 to 0.35, p = 0.68) or a theater (0.28, 95% CI -0.27 to 0.82, p = 0.32). Three out of 10 key messages remained largely misunderstood, regardless of the mode of information group.Conclusions/significanceOur study confirmed that, in this setting, an ICF alone was not sufficient to convey clinical trial-related information. An IS was beneficial, however, additional theater and slideshows did not further improve understanding. Future research should explore methods to improve communication between study teams and participants for different key messages, study types and settings.

Dataset Information

Informed consent for next-generation nucleotide sequencing studies: Aiding communication between participants and investigators.

Publications

Informed consent for next-generation nucleotide sequencing studies: Aiding communication between participants and investigators.

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