Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience

Ethical, legal, and social implications (ELSI) and challenges in the design of a randomized controlled trial to test the online return of cancer genetic research results to U.S. Black women

BACKGROUND

A central challenge to precision medicine research efforts is the return of genetic research results in a manner that is effective, ethical, and efficient. Formal tests of alternate modalities are needed, particularly for racially marginalized populations that have historically been underserved in this context.

METHODS

We are conducting a randomized controlled trial (RCT) to test scalable modalities for results return and to examine the clinical utility of returning genetic research results to a research cohort of Black women. The primary aim is to compare the efficacy of two communication modalities for results return: 1) a conventional modality that entails telephone disclosure by a Board-certified genetic counselor, and 2) an online self-guided modality that entails results return directly to participants, with optional genetic counselor follow-up via telephone. The trial is being conducted among participants in the Black Women's Health Study (BWHS), where targeted sequencing of 4000 participants was previously completed.

RESULTS

Several ethical, legal, and social implications (ELSI) and challenges presented, which necessitated substantial revision of the original study protocol. Challenges included chain of custody, re-testing of research results in a CLIA lab, exclusion of VUS results, and digital literacy. Bioethical principles of autonomy, justice, non-maleficence, and beneficence were considered in the design of the study protocol.

CONCLUSION

This study is uniquely situated to provide critical evidence on the effectiveness of alternative models for genetic results return and provide further insight into the factors influencing access and uptake of genetic information among U.S. Black women.

CLINICALTRIALS

gov: NCT04407611.

Factors That Impact Hospital-Specific Enrollment Rates for a Neonatal Clinical Trial: An Analysis of the HEAL Study

Inconsistent enrollment among hospitals for neonatal clinical trials may lead to study populations that are not representative of the patient population in the neonatal intensive care unit. The High-Dose Erythropoietin for Asphyxia and Encephalopathy (HEAL) trial was a multisite randomized clinical trial investigating erythropoietin as a neuroprotective treatment for term infants (those born between 37 and 42 complete weeks) with hypoxic ischemic encephalopathy. Substantial variability was noted in enrollment rate by hospital. We developed survey questions across five conceptual domains to understand systems-level issues that might contribute to variation in enrollment rate by hospital. Our study found that hospitals varied in their responses across these five domains. We propose three potential reasons that we found a lack of identifiable hospital-level factors that correlated with enrollment rates: sample-size limitations, methodological concerns, and confounding factors. Future studies with a larger sample size should be considered to evaluate contributors to hospital-level variability. This will lead to more robust recruitment strategies, improved enrollment, and decreases in the waste of research resources.

Challenges for the implementation of next generation sequencing-based expanded carrier screening: Lessons learned from the ciliopathies

Next generation sequencing (NGS) can detect carrier status for rare recessive disorders, informing couples about their reproductive risk. The recent ACMG recommendations support offering NGS-based carrier screening (NGS-CS) in an ethnic and population-neutral manner for all genes that have a carrier frequency >1/200 (based on GnomAD). To evaluate current challenges for NGS-CS, we focused on the ciliopathies, a well-studied group of rare recessive disorders. We analyzed 118 ciliopathy genes by whole exome sequencing in ~400 healthy local individuals and ~1000 individuals from the UK1958-birth cohort. We found 20% of healthy individuals (1% of couples) to be carriers of reportable variants in a ciliopathy gene, while 50% (4% of couples) carry variants of uncertain significance (VUS). This large proportion of VUS is partly explained by the limited utility of the ACMG/AMP variant-interpretation criteria in healthy individuals, where phenotypic match or segregation criteria cannot be used. Most missense variants are thus classified as VUS and not reported, which reduces the negative predictive value of the screening test. We show how gene-specific variation patterns and structural protein information can help prioritize variants most likely to be disease-causing, for (future) functional assays. Even when considering only strictly pathogenic variants, the observed carrier frequency is substantially higher than expected based on estimated disease prevalence, challenging the 1/200 carrier frequency cut-off proposed for choice of genes to screen. Given the challenges linked to variant interpretation in healthy individuals and the uncertainties about true carrier frequencies, genetic counseling must clearly disclose these limitations of NGS-CS.

Interest in Cancer Predisposition Testing and Carrier Screening Offered as Part of Routine Healthcare Among an Ethnically Diverse Sample of Young Women

Sequencing technologies can inform individuals’ risks for multiple conditions, supporting population-level screening approaches. Prior research examining interest in genetic testing has not generally examined the context of population-based approaches offered in routine healthcare or among ethnically diverse populations. Cancer predisposition testing and carrier screening could be offered broadly to women of reproductive age. This study therefore examined interest in these tests when offered as part of routine care, and predictors of interest, among an ethnically diverse sample of women aged 20–35. We conducted an online English-language survey of 450 women; 39% identified as Latina. We examined predictors of interest for two outcomes, interest in testing in the next year and level of interest, in multivariable logistic regression models and stratified analyses by Latina ethnicity. More than half of respondents reported being interested in cancer predisposition testing (55%) and carrier screening (56%) in the next year; this did not differ by ethnicity. About 26% reported being very interested in cancer predisposition testing and 27% in carrier screening. Latina respondents (32%) were more likely to be very interested in cancer predisposition testing than non-Latina respondents (22%; p < 0.03). In multivariable models, having higher worry about genetic risks, higher genetic knowledge, and higher perceived importance of genetic information were associated with higher interest across multiple models. Predictors of interest were generally similar by ethnicity. Our findings show substantial interest in both cancer predisposition testing and carrier screening among young women as part of routine healthcare with similar interest between Latina and non-Latina women. Efforts to broadly offer such testing could be important in improving access to genetic information. It will be critical to develop tools to help healthcare providers communicate about genetic testing and to address the needs of those who have less prior knowledge about genetics to support informed decision making.

Moving Genomics to Routine Care

Background:

Whole-genome sequencing (WGS) costs are falling, yet, outside oncology, this information is seldom used in adult clinics. We piloted a rapid WGS (rWGS) workflow, focusing initially on estimating power for a feasibility study of introducing genome information into acute cardiovascular care.

Methods:

A prospective implementation study was conducted to test the feasibility and clinical utility of rWGS in acute cardiovascular care. rWGS was performed on 50 adult patients with acute cardiovascular events and cardiac arrest survivors, testing for primary and secondary disease-causing variants, cardiovascular-related pharmacogenomics, and carrier status for recessive diseases. The impact of returning rWGS results on short-term clinical care of participants was investigated. The utility of polygenic risk scores to stratify coronary artery disease was also assessed.

Results:

Pathogenic variants, typically secondary findings, were identified in 20% (95% CI, 11.7–34.3). About 60% (95% CI, 46.2–72.4) of participants were carriers for one or more recessive traits, most commonly inHFEandSERPINA1genes. Although 64% (95% CI, 50.1–75.9) of participants carried at least one pharmacogenetic variant of cardiovascular relevance, these were actionable in only 14% (95% CI, 7–26.2). Coronary artery disease prevalence among participants at the 95th percentile of polygenic risk score was 88.2% (95% CI, 71.8–95.7).

Conclusions:

We demonstrated the feasibility of rWGS integration into the inpatient management of adults with acute cardiovascular events. Our pilot identified pathogenic variants in one out of 5 acute vascular patients. Integrating rWGS in clinical care will progressively increase actionability.

Genomic Sequencing for Newborn Screening: Results of the NC NEXUS Project

Newborn screening (NBS) was established as a public health program in the 1960s and is crucial for facilitating detection of certain medical conditions in which early intervention can prevent serious, life-threatening health problems. Genomic sequencing can potentially expand the screening for rare hereditary disorders, but many questions surround its possible use for this purpose. We examined the use of exome sequencing (ES) for NBS in the North Carolina Newborn Exome Sequencing for Universal Screening (NC NEXUS) project, comparing the yield from ES used in a screening versus a diagnostic context. We enrolled healthy newborns and children with metabolic diseases or hearing loss (106 participants total). ES confirmed the participant's underlying diagnosis in 15 out of 17 (88%) children with metabolic disorders and in 5 out of 28 (∼18%) children with hearing loss. We discovered actionable findings in four participants that would not have been detected by standard NBS. A subset of parents was eligible to receive additional information for their child about childhood-onset conditions with low or no clinical actionability, clinically actionable adult-onset conditions, and carrier status for autosomal-recessive conditions. We found pathogenic variants associated with hereditary breast and/or ovarian cancer in two children, a likely pathogenic variant in the gene associated with Lowe syndrome in one child, and an average of 1.8 reportable variants per child for carrier results. These results highlight the benefits and limitations of using genomic sequencing for NBS and the challenges of using such technology in future precision medicine approaches.

Participant choices for return of genomic results in the eMERGE Network

PURPOSE

Secondary findings are typically offered in an all or none fashion when sequencing is used for clinical purposes. This study aims to describe the process of offering categorical and granular choices for results in a large research consortium.

METHODS

Within the third phase of the electronic MEdical Records and GEnomics (eMERGE) Network, several sites implemented studies that allowed participants to choose the type of results they wanted to receive from a multigene sequencing panel. Sites were surveyed to capture the details of the implementation protocols and results of these choices.

RESULTS

Across the ten eMERGE sites, 4664 participants including adolescents and adults were offered some type of choice. Categories of choices offered and methods for selecting categories varied. Most participants (94.5%) chose to learn all genetic results, while 5.5% chose subsets of results. Several sites allowed participants to change their choices at various time points, and 0.5% of participants made changes.

CONCLUSION

Offering choices that include learning some results is important and should be a dynamic process to allow for changes in scientific knowledge, participant age group, and individual preference.

Experience of parents receiving results from a quality-of-life study in pediatric advanced cancer: A report from the PediQUEST study

Little is known about the experience of parents receiving results of quality-of-life research in pediatric advanced cancer. The PediQUEST study participants who indicated interest in results during enrollment were mailed summarized findings and the Disseminating Quality-of-Life Research Questionnaire. Respondents (86%,12/14) reported feeling more than "a little" recognized, grateful, or satisfied to receive results. Concurrently, 43% (6/14) endorsed feeling more than "a little" sad, confused, or anxious. Nonetheless, 81% (13/16) prefer to be informed in the future. Although parents experience a spectrum of strong emotions, our findings suggest quality-of-life study results should be shared.

Integrating Genomics into Healthcare: A Global Responsibility

Genomic sequencing is rapidly transitioning into clinical practice, and implementation into healthcare systems has been supported by substantial government investment, totaling over US$4 billion, in at least 14 countries. These national genomic-medicine initiatives are driving transformative change under real-life conditions while simultaneously addressing barriers to implementation and gathering evidence for wider adoption. We review the diversity of approaches and current progress made by national genomic-medicine initiatives in the UK, France, Australia, and US and provide a roadmap for sharing strategies, standards, and data internationally to accelerate implementation.

Approaches to carrier testing and results disclosure in translational genomics research: The clinical sequencing exploratory research consortium experience

BACKGROUND

Clinical genome and exome sequencing (CGES) is primarily used to address specific clinical concerns by detecting risk of future disease, clarifying diagnosis, or directing treatment. Additionally, CGES makes possible the disclosure of autosomal recessive and X-linked carrier results as additional secondary findings, and research about the impact of carrier results disclosure in this context is needed.

METHODS

Representatives from 11 projects in the clinical sequencing exploratory research (CSER) consortium collected data from their projects using a structured survey. The survey focused on project characteristics, which variants were offered and/or disclosed to participants as carrier results, methods for carrier results disclosure, and project-specific outcomes. We recorded quantitative responses and report descriptive statistics with the aim of describing the variability in approaches to disclosing carrier results in translational genomics research projects.

RESULTS

The proportion of participants with carrier results was related to the number of genes included, ranging from 3% (three genes) to 92% (4,600 genes). Between one and seven results were disclosed to those participants who received any positive result. Most projects offered participants choices about whether to receive some or all of the carrier results. There were a range of approaches to communicate results, and many projects used separate approaches for disclosing positive and negative results.

CONCLUSION

Future translational genomics research projects will need to make decisions regarding whether and how to disclose carrier results. The CSER consortium experience identifies approaches that balance potential participant interest while limiting impact on project resources.