Understanding variations in secondary findings reporting practices across U.S. genome sequencing laboratories

Genetic Testing: practical dos and don'ts for cats

PRACTICAL RELEVANCE

A significant number of genetic variants are known for domestic cats and their breeds. Several DNA variants are causal for inherited diseases and most of the variants for phenotypic traits have been discovered. Genetic testing for these variants can support breeding decisions for both health and aesthetics. Genetic testing can also be used to monitor for the health of, or provide targeted therapy for, an individual cat and, more widely, can progress scientific discovery. Technological improvements have led to the development of large panel genetic testing, which can provide many DNA results for a low cost.

CLINICAL CHALLENGES

With the development of large panel genetic testing has come companies that can carry out this service, but which company is best to use may not always be clear - more tests are not necessarily better. Usage and interpretation of genetic data and how the results are presented by commercial laboratories may also be confusing for veterinary practitioners and owners, leading to misinterpretations for healthcare, improper genetic counseling, and poor breed and population management.

EVIDENCE BASE

The information provided in this review draws on scientific articles reporting the discovery, and discussing the meaning and implications, of DNA variants, as well as information from the Online Mendelian Inheritance in Animals (OMIA) website, which documents all the DNA variant discoveries. The author also provides suggestions and recommendations based on her personal experience and expertise in feline genetics.

AUDIENCE

This review is aimed at general practitioners and discusses the genetic tests that can be performed, what to consider when choosing a testing laboratory and provides genetic testing counseling advice. Practitioners with a high proportion of cat breeder clientele will especially benefit from this review and all veterinarians should realize that genetic testing and genomic medicine should be part of diagnostic plans and healthcare for their cat clients.

Implementing evidence-based assertions of clinical actionability in the context of secondary findings: Updates from the ClinGen Actionability Working Group

PURPOSE

The ClinGen Actionability Working Group (AWG) developed an evidence-based framework to generate actionability reports and scores of gene-condition pairs in the context of secondary findings from genome sequencing. Here we describe the expansion of the framework to include actionability assertions.

METHODS

Initial development of the actionability rubric was based on previously scored adult gene-condition pairs and individual expert evaluation. Rubric refinement was iterative and based on evaluation, feedback, and discussion. The final rubric was pragmatically evaluated via integration into actionability assessments for 27 gene-condition pairs.

RESULTS

The resulting rubric has a 4-point scale (limited, moderate, strong, and definitive) and uses the highest-scoring outcome-intervention pair of each gene-condition pair to generate a preliminary assertion. During AWG discussions, predefined criteria and factors guide discussion to produce a consensus assertion for a gene-condition pair, which may differ from the preliminary assertion. The AWG has retrospectively generated assertions for all previously scored gene-condition pairs and are prospectively asserting on gene-condition pairs under assessment, having completed over 170 adult and 188 pediatric gene-condition pairs.

CONCLUSION

The AWG expanded its framework to provide actionability assertions to enhance the clinical value of their resources and increase their utility as decision aids regarding return of secondary findings.

A framework for the evaluation and reporting of incidental findings in clinical genomic testing

Currently, there are no widely accepted recommendations in the genomics field guiding the return of incidental findings (IFs), defined here as unexpected results that are unrelated to the indication for testing. Consequently, reporting policies for IFs among laboratories offering genomic testing are variable and may lack transparency. Herein we describe a framework developed to guide the evaluation and return of IFs encountered in probands undergoing clinical genome sequencing (cGS). The framework prioritizes clinical significance and actionability of IFs and follows a stepwise approach with stopping points at which IFs may be recommended for return or not. Over 18 months, implementation of the framework in a clinical laboratory facilitated the return of actionable IFs in 37 of 720 (5.1%) individuals referred for cGS, which is reduced to 3.1% if glucose-6-phosphate dehydrogenase (G6PD) deficiency is excluded. This framework can serve as a model to standardize reporting of IFs identified during genomic testing.

Avoiding Liability and Other Legal Land Mines in the Evolving Genomics Landscape

This article reviews evolving legal implications for clinicians and researchers as genomics is used more widely in both the clinic and in translational research, reflecting rapid changes in scientific knowledge as well as the surrounding cultural and political environment. Professionals will face new and changing duties to make or act upon a genetic diagnosis, address direct-to-consumer genetic testing in patient care, consider the health implications of results for patients' family members, and recontact patients when test results change over time. Professional duties in reproductive genetic testing will need to be recalibrated in response to disruptive changes to reproductive rights in the United States. We also review the debate over who controls the flow of genetic information and who is responsible for its protection, considering the globally influential European Union General Data Protection Regulation and the rapidly evolving data privacy law landscape of the United States.

ORCA, a values-based decision aid for selecting additional findings from genomic sequencing in adults: Efficacy results from a randomized trial

PURPOSE

Individuals having genomic sequencing can choose to be notified about pathogenic variants in genes unrelated to the testing indication. A decision aid can facilitate weighing one's values before making a choice about these additional results.

METHODS

We conducted a randomized trial (N = 231) comparing informed values-choice congruence among adults at risk for a hereditary cancer syndrome who viewed either the Optional Results Choice Aid (ORCA) or web-based additional findings information alone. ORCA is values-focused with a low-literacy design.

RESULTS

Individuals in both arms had informed values-choice congruence (75% and 73% in the decision aid and web-based groups, respectively; odds ratio [OR] = 1.10, 95% CI = 0.58-2.08). Most participants had adequate knowledge (79% and 76% in the decision aid and web-based groups, respectively; OR = 1.20, 95% CI = 0.61-2.34), with no significant difference between groups. Most had information-seeking values (97% and 98% in the decision aid and web-based groups, respectively; OR = 0.59, 95% CI = 0.10-3.61) and chose to receive additional findings.

CONCLUSION

The ORCA decision aid did not significantly improve informed values-choice congruence over web-based information in this cohort of adults deciding about genomic results. Both web-based approaches may be effective for adults to decide about receiving medically actionable additional results.

Best practices for the interpretation and reporting of clinical whole genome sequencing

Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.

How to deal with uncertainty in prenatal genomics: A systematic review of guidelines and policies

Exome sequencing (ES) enhanced the diagnostic yield of genetic testing, but has also increased the possibility of uncertain findings. Prenatal ES is increasingly being offered after a fetal abnormality is detected through ultrasound. It is important to know how to handle uncertainty in this particularly stressful period. This systematic review aimed to provide a comprehensive overview of guidelines available for addressing uncertainty related to prenatal chromosomal microarray (CMA) and ES. Ten uncertainty types associated with prenatal ES and CMA were identified and defined by an international multidisciplinary team. Medline (all) and Embase were systematically searched. Laboratory scientists, clinical geneticists, psychologists, and a fetal medicine specialist screened the papers and performed the data extraction. Nineteen papers were included. Recommendations generally emphasized the importance of trio analysis, clinical information, data sharing, validation and re-analysis, protocols, multidisciplinary teams, genetic counselling, whether to limit the possible scope of results, and when to report particular findings. This systematic review helps provide a vocabulary for uncertainties, and a compass to navigate uncertainties. Prenatal CMA and ES guidelines provide a strong starting point for determining how to handle uncertainty. Gaps in guidelines and recommendations were identified and discussed to provide direction for future research and policy making.

A decision aid for additional findings in genomic sequencing: Development and pilot testing

OBJECTIVE

To describe the development of a web-based, patient-facing decision aid to support patients and research participants to make an informed, values-based decision about whether to receive additional results from genomic sequencing.

METHODS

We developed the decision aid following the multi-step process described in the International Patient Decision Aids Standards. This utilized literature review, focus groups, and alpha testing with research participants undergoing clinical genomic sequencing.

RESULTS

The decision aid, the Optional Results Choice Aid (ORCA), includes a seven-question "values clarification exercise," illustrative patient quotes, and summative guidance for the user. The decision aid was found to be highly readable, acceptable and relevant in alpha testing.

CONCLUSION

We developed a decision aid to support informed, values-based decision making for patients and research participants considering whether to receive additional results from genomic sequencing. ORCA is being implemented in the NHGRI-funded Cancer Health Assessment Reaching Many (CHARM) study, where we are measuring informed values-choice congruence.

PRACTICE IMPLICATIONS

ORCA was designed to support patients and research participants to make an informed, values-based decision about whether to receive additional results from genomic sequencing.

Evaluating the resource implications of different service delivery models for offering additional genomic findings

PURPOSE

To evaluate the resource implications of different delivery models for the provision of additional findings (AF) in genomics from a health-care purchaser perspective.

METHODS

Data from the Additional Findings study were used to develop and validate a discrete event simulation model that represented the pathway of delivering AF. Resource implications were estimated by microcosting the consultations, sample verifications, bioinformatics, curation, and multidisciplinary case review meetings. A proof-of-concept model was used to generate costing, and then the simulation model was varied to assess the impact of an automated analysis pipeline, use of telehealth consultation, full automation with electronic decision support, and prioritizing case review for cases with pathogenic variants.

RESULTS

For the proof-of-concept delivery model, the average total cost to report AF was US$430 per patient irrespective of result pathogenicity (95% confidence interval [CI] US$375-US$489). However, the cost of per AF diagnosis was US$4349 (95% CI US$3794-US$4953). Alternative approaches to genetic counseling (telehealth, decision support materials) and to multidisciplinary case review (pathogenic AF cases only) lowered the total per patient cost of AF analysis and reporting by 41-51%.

CONCLUSION

Resources required to provide AF can be reduced substantially by implementing alternative approaches to counseling and multidisciplinary case review.

Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies

Harmonization of variant pathogenicity classification across laboratories is important for advancing clinical genomics. The two CLIA-accredited Electronic Medical Record and Genomics Network sequencing centers and the six CLIA-accredited laboratories and one research laboratory performing genome or exome sequencing in the Clinical Sequencing Evidence-Generating Research Consortium collaborated to explore current sources of discordance in classification. Eight laboratories each submitted 20 classified variants in the ACMG secondary finding v.2.0 genes. After removing duplicates, each of the 158 variants was annotated and independently classified by two additional laboratories using the ACMG-AMP guidelines. Overall concordance across three laboratories was assessed and discordant variants were reviewed via teleconference and email. The submitted variant set included 28 P/LP variants, 96 VUS, and 34 LB/B variants, mostly in cancer (40%) and cardiac (27%) risk genes. Eighty-six (54%) variants reached complete five-category (i.e., P, LP, VUS, LB, B) concordance, and 17 (11%) had a discordance that could affect clinical recommendations (P/LP versus VUS/LB/B). 21% and 63% of variants submitted as P and LP, respectively, were discordant with VUS. Of the 54 originally discordant variants that underwent further review, 32 reached agreement, for a post-review concordance rate of 84% (118/140 variants). This project provides an updated estimate of variant concordance, identifies considerations for LP classified variants, and highlights ongoing sources of discordance. Continued and increased sharing of variant classifications and evidence across laboratories, and the ongoing work of ClinGen to provide general as well as gene- and disease-specific guidance, will lead to continued increases in concordance.

Informed Consent in the Genomics Era

Informed consent, the process of gathering autonomous authorization for a medical intervention or medical research participation, is a fundamental component of medical practice. Medical informed consent assumes decision-making capacity, voluntariness, comprehension, and adequate information. The increasing use of genetic testing, particularly genomic sequencing, in clinical and research settings has presented many new challenges for clinicians and researchers when obtaining informed consent. Many of these challenges revolve around the need for patient comprehension of sufficient information. Genomic sequencing is complex-all of the possible results are too numerous to explain, and many of the risks and benefits remain unknown. Thus, historical standards of consent are difficult to apply. Alternative models of consent have been proposed to increase patient understanding, and several have empirically demonstrated effectiveness. However, there is still a striking lack of consensus in the genetics community about what constitutes informed consent in the context of genomic sequencing. Multiple approaches are needed to address this challenge, including consensus building around standards, targeted use of genetic counselors in nongenetics clinics in which genomic testing is ordered, and the development and testing of alternative models for obtaining informed consent.

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.

Differences in Conceptual Understanding of the "Actionability" of Incidental Findings and the Resultant Difference in Ethical Responsibility: An Empirical Study in Japan

BACKGROUND

The issue of incidental findings encountered in medical researches and in clinical practices becomes controversial in recent years. In what situations should researchers and clinicians disclose incidental findings to study participants or patients? According to previous studies, the concept of "actionability" is one of most important notions in determining the management of incidental findings, however, the understanding of this concept is also inconsistent among people and the inconsistency can affect the management of incidental findings. That is why we surveyed the difference in conceptual understanding of "actionability" for incidental findings with genomic researches in Japan. Methods: We conducted focus groups with individuals conducting genomics research or genetic testing at the National Centers in Japan, all of which are expected to contribute significantly to genomics research and subsequent clinical practice in Japan. Results: As far as our survey and analysis, there exists crucial discrepancy; one might consider that an "actionable" finding should be one that would be useful in treatment or prevention; another might consider if the finding could lead to a definitive diagnosis, it should be considered "actionable," regardless of the treatment potential of the disease; moreover another might considered that a finding that would lead to the opportunity to participate in a clinical trial was "actionable". Conclusion: Based on the present study which we conducted, we have examined thus far the concept of "actionability", which may influence the management of incidental findings. The present study revealed discrepancies in the understanding of this concept among the National Centers in Japan, which all bear similar expectations from society. And this difference in "actionability" would lead to variations in management of incidental findings.

Adapting Clinical Systems to Enable Adolescents' Genomic Choices

BACKGROUND

We offered adolescents personalized choices about the type of genetic results they wanted to learn during a research study and created a workflow to filter and transfer the results to the electronic health record (EHR).

METHODS

We describe adaptations needed to ensure that adolescents' results documented in the EHR and returned to adolescent/parent dyads matched their choices. A web application enabled manual modification of the underlying laboratory report data based on adolescents' choices. The final PDF format of the laboratory reports was not viewable through the EHR patient portal, so an EHR form was created to support the manual entry of discrete results that could be viewed in the portal.

RESULTS

Enabling adolescents' choices about genetic results was a labor-intensive process. More than 350 hours was required for development of the application and EHR form, as well as over 50 hours of a study professional's time to enter choices into the application and EHR. Adolescents and their parents who learned genetic results through the patient portal indicated that they were satisfied with the method of return and would make their choices again if given the option.

CONCLUSION

Although future EHR upgrades are expected to enable patient portal access to PDFs, additional improvements are needed to allow the results to be partitioned and filtered based on patient preferences. Furthermore, separating these results into more discrete components will allow them to be stored separately in the EHR, supporting the use of these data in clinical decision support or artificial intelligence applications.

Quantifying Downstream Healthcare Utilization in Studies of Genomic Testing

OBJECTIVES

The challenges of understanding how interventions influence follow-up medical care are magnified during genomic testing because few patients have received it to date and because the scope of information it provides is complex and often unexpected. We tested a novel strategy for quantifying downstream healthcare utilization after genomic testing to more comprehensively and efficiently identify related services. We also evaluated the effectiveness of different methods for collecting these data.

METHODS

We developed a risk-based approach for a trial of newborn genomic sequencing in which we defined primary conditions based on existing diagnoses and family histories of disease and defined secondary conditions based on unexpected findings. We then created patient-specific lists of services associated with managing primary and secondary conditions. Services were quantified based on medical record reviews, surveys, and telephone check-ins with parents.

RESULTS

By focusing on services that genomic testing would most likely influence in the short-term, we reduced the number of services in our analyses by more than 90% compared with analyses of all observed services. We also identified the same services that were ordered in response to unexpected findings as were identified during expert review and by confirming whether recommendations were completed. Data also showed that quantifying healthcare utilization with surveys and telephone check-ins alone would have missed the majority of attributable services.

CONCLUSIONS

Our risk-based strategy provides an improved approach for assessing the short-term impact of genomic testing and other interventions on healthcare utilization while conforming as much as possible to existing best-practice recommendations.

Exome sequencing in newborns with congenital deafness as a model for genomic newborn screening: the Baby Beyond Hearing project

PURPOSE

Genomic newborn screening raises practical and ethical issues. Evidence is required to build a framework to introduce this technology safely and effectively. We investigated the choices made by a diverse group of parents with newborns when offered tiered genomic information from exome sequencing.

METHODS

This population-derived cohort comprised infants with congenital deafness. Parents were offered exome sequencing and choice regarding the scope of analysis. Options were choice A, diagnostic analysis only; choice B, diagnostic analysis plus childhood-onset diseases with medical actionability; or choice C, diagnostic analysis plus childhood-onset diseases with or without medical actionability.

RESULTS

Of the 106 participants, 72 (68%) consented to receive additional findings with 29 (27.4%) selecting choice B and 43 (40.6%) opting for choice C. Family size, ethnicity, and age of infant at time of recruitment were the significant predictors of choice. Parents who opted to have additional findings analysis demonstrated less anxiety and decisional conflict.

CONCLUSIONS

These data provide evidence from a culturally diverse population that choice around additional findings is important and the age of the infant when this choice is offered impacts on their decision. We found no evidence that offering different levels of genomic information to parents of newborns has a negative psychological impact.

Challenges in reporting pathogenic/potentially pathogenic variants in 94 cancer predisposing genes - in pediatric patients screened with NGS panels

The benefit of reporting unsolicited findings in Next Generation Sequencing (NGS) related to cancer genes in children may have implications for family members, nevertheless, could also cause distress. We aimed to retrospectively investigate germline variants in 94 genes implicated in oncogenesis, in patients referred to NGS testing for various rare genetic diseases and reevaluate the utility of reporting different classes of pathogenicity. We used in silico prediction software to classify variants and conducted manual review to examine unsolicited findings frequencies in 145 children with rare diseases, that underwent sequencing - using a 4813 gene panel. The anonymized reanalysis revealed 18250 variants, of which 126 were considered after filtering. Six pathogenic variants (in BRCA1,BMPR1A,FANCA,FANCC,NBN genes) with cancer related phenotype and three unsolicited variants (in BRCA2,PALB2,RAD50 genes) were reported to patients. Additionally, three unsolicited variants in ATR, BLM (in two individuals), and FANCB genes presented potential cancer susceptibility, were not reported to patients. In retrospect, 4.8% (7/145) of individuals in our cohort had unsolicited NGS findings related to cancer. More efforts are needed to create an updatable consensus in reporting variants in cancer predisposing genes, especially for children. Consent process is crucial to inform of both value and risk of additional genetic information.

Consent for clinical genome sequencing: considerations from the Clinical Sequencing Exploratory Research Consortium

Implementing genome and exome sequencing in clinical practice presents challenges, including obtaining meaningful informed consent. Consent may be challenging due to test limitations such as uncertainties associated with test results and interpretation, complexity created by the potential for additional findings and high patient expectations. We drew on the experiences of research teams within the Clinical Sequencing Exploratory Research (CSER1) Consortium on informed consent for clinical genome and exome sequencing (CGES) to negotiate consensus considerations. We present six considerations for clinicians and 12 key points to communicate as they support patients in deciding whether to undergo CGES. These considerations and key points provide a helpful starting point for informed consent to CGES, grounded in the Clinical Sequencing Exploratory Research (CSER1) experience.

A Next-Generation Sequencing Primer-How Does It Work and What Can It Do?

Next-generation sequencing refers to a high-throughput technology that determines the nucleic acid sequences and identifies variants in a sample. The technology has been introduced into clinical laboratory testing and produces test results for precision medicine. Since next-generation sequencing is relatively new, graduate students, medical students, pathology residents, and other physicians may benefit from a primer to provide a foundation about basic next-generation sequencing methods and applications, as well as specific examples where it has had diagnostic and prognostic utility. Next-generation sequencing technology grew out of advances in multiple fields to produce a sophisticated laboratory test with tremendous potential. Next-generation sequencing may be used in the clinical setting to look for specific genetic alterations in patients with cancer, diagnose inherited conditions such as cystic fibrosis, and detect and profile microbial organisms. This primer will review DNA sequencing technology, the commercialization of next-generation sequencing, and clinical uses of next-generation sequencing. Specific applications where next-generation sequencing has demonstrated utility in oncology are provided.