Preferences for results from genomic microarrays: comparing parents and health care providers

Variants in Genes Associated with Hearing Loss in Children: Prevalence in a Large Canadian Cohort

OBJECTIVE

The objective of this study was to assess the prevalence of genetic variants associated with hearing loss in a large cohort of children in Canada using high throughput next generation sequencing (NGS).

METHODS

A total of 485 children with hearing loss underwent NGS testing with an 80 gene panel of syndromic and non-syndromic variants known to be associated with hearing loss. Genetic variants were classified as pathogenic, likely pathogenic, likely benign, benign, or variants of uncertain significance (VUS), according to the American College of Medical Genetics and Genomics guidelines.

RESULTS

Across the 80 genes tested, 923 variants, predominantly in 28 genes, were identified in 324 children. Pathogenic variants occurred in 19/80 (23.8%) of the hearing loss related genes tested and confirmed the etiology of hearing loss in 73/485 (15.1%) of children. GJB2 was the most prevalent gene, affecting 28/73 (38.4%) children with confirmed genetic hearing loss in our cohort. Most identified variants (748/923, 81.0%, in 76/80 genes) were of uncertain significance.

CONCLUSION

Genetic testing using NGS identified the etiology in approximately 15% of childhood hearing loss in a Canadian cohort which is lower than what is typically reported. GJB2 was the most common genetic cause of hearing loss. VUS are commonly identified, presenting clinical challenges for counseling.

LEVEL OF EVIDENCE

4 Laryngoscope, 134:3832-3838, 2024.

Utility and Outcomes of the 2019 American College of Medical Genetics and Genomics-Clinical Genome Resource Guidelines for Interpretation of Copy Number Variants with Borderline Classifications at an Academic Clinical Diagnostic Laboratory

In 2019, American College of Medical Genetics and Genomics and the Clinical Genome Resource published updated technical standards for the interpretation and reporting of copy number variants (CNVs), introducing a semiquantitative classification system that aims to foster greater standardization and consistency between laboratories. Evaluation of these guidelines' performance will inform laboratories about the impact of their implementation into clinical practice. A total of 145 difficult-to-classify CNVs, originally assessed by an academic molecular diagnostic laboratory, were re-interpreted/classified according to the American College of Medical Genetics and Genomics-Clinical Genome Resource guidelines. Classifications between interpretation systems were then compared. The concordance rate was 60.7%, and significantly more variants of uncertain significance were obtained when using the guidelines (n = 98) versus the laboratory's classification system (n = 49; P < 0.001). The concordance rate was presumably impacted by the intentionally unclear nature of the selected variants. The difference in variant of uncertain significance rate was largely due to laboratory-specific practices for variant interpretation and reporting, as well as differences in utilization of general population data. Laboratory-specific policies and practices may need to be addressed for true standardization to be achieved. Challenges to consistent guideline utilization are centered around the general lack of high-quality curated data available for CNV interpretations and the inherent subjectivity in the selection of evidence criteria and application of evidence points. Multiple aspects of the guidelines were highlighted as potential opportunities for subsequent refinements to further improve classification standardization.

Genetic Testing in Neurodevelopmental Disorders

Neurodevelopmental disorders are the most prevalent chronic medical conditions encountered in pediatric primary care. In addition to identifying appropriate descriptive diagnoses and guiding families to evidence-based treatments and supports, comprehensive care for individuals with neurodevelopmental disorders includes a search for an underlying etiologic diagnosis, primarily through a genetic evaluation. Identification of an underlying genetic etiology can inform prognosis, clarify recurrence risk, shape clinical management, and direct patients and families to condition-specific resources and supports. Here we review the utility of genetic testing in patients with neurodevelopmental disorders and describe the three major testing modalities and their yields - chromosomal microarray, exome sequencing (with/without copy number variant calling), and FMR1 CGG repeat analysis for fragile X syndrome. Given the diagnostic yield of genetic testing and the potential for clinical and personal utility, there is consensus that genetic testing should be offered to all patients with global developmental delay, intellectual disability, and/or autism spectrum disorder. Despite this recommendation, data suggest that a minority of children with autism spectrum disorder and intellectual disability have undergone genetic testing. To address this gap in care, we describe a structured but flexible approach to facilitate integration of genetic testing into clinical practice across pediatric specialties and discuss future considerations for genetic testing in neurodevelopmental disorders to prepare pediatric providers to care for patients with such diagnoses today and tomorrow.

A primer in genomics for social and behavioral investigators

Genomics is being increasingly utilized in medical research and health care. Countless opportunities exist for social and behavioral scientists to answer novel and important research questions. Evidence that will be produced from such enquiries can help ensure appropriate use of genomic information and realize the potential of genomics to improve patient care and medical outcomes. Here, we provide an accessible overview of different types of genetic and genomic tests and the resulting information produced. There are important nuances that distinguish genetic from genomic tests and different information that each yield. We outline key examples where social and behavioral scientists have made an impact in this field, and opportunities for future research. The intention of this primer is to introduce or clarify genomics concepts to social and behavioral scientists, summarize prior research and outline future research directions. The time is ripe for social and behavioral scientists to engage in genomics and make important contributions to improve clinical and community translation of genomic discoveries.

Patients' views on variants of uncertain significance across indications

As genomic sequencing expands into more areas of patient care, an increasing number of patients learn of the variants of uncertain significance (VUSs) that they carry. Understanding the potential psychosocial consequences of the disclosure of a VUS can help inform pre- and post-test counseling discussions. Medical uncertainty in general elicits a variety of responses from patients, particularly in the growing field of medical genetics and genomics. It is important to consider patients' responses to the ambiguous nature of VUSs across different indications and situational contexts. Genetic counselors and other providers ordering genetic testing should be prepared for the possibility of their patients' misinterpretation of such results. Pre-test counseling should include a discussion of the possibility of VUSs and what it would mean for the patient's care and its potential psychosocial impacts. When a VUS is found, post-test counseling should include additional education and a discussion of the variant's implications and medical management recommendations based on the results. These discussions may help temper subjective interpretations, unrealistic views, and decisional regret.

Epilepsy genetics: clinical impacts and biological insights

Genomics now has an increasingly important role in neurology clinics. Regarding the epilepsies, innovations centred around technology, analytics, and collaboration have led to remarkable progress in gene discovery and have revealed the diverse array of genetic mechanisms and neurobiological pathways that contribute to these disorders. The new genomic era can present a challenge to clinicians, who now find themselves asked to interpret and apply genetic data to their daily management of patients with epilepsy. Navigation of this new era will require genetic literacy and familiarity with research advances in epilepsy genetics. Genetic epilepsy diagnoses now directly affect clinical care, and their importance will only increase as new targeted treatments continue to emerge. At the same time, new genetic insights challenge us to move from a deterministic view of genetic changes to a more nuanced appreciation of genetic risk within complex neurobiological systems that give rise to epilepsy.

Clinical validity assessment of genes for inclusion in multi-gene panel testing: A systematic approach

BACKGROUND

Advances in sequencing technology have led to expanded use of multi-gene panel tests (MGPTs) for clinical diagnostics. Well-designed MGPTs must balance increased detection of clinically significant findings while mitigating the increase in variants of uncertain significance (VUS). To maximize clinical utililty, design of such panels should include comprehensive gene vetting using a standardized clinical validity (CV) scoring system.

METHODS

To assess the impact of CV-based gene vetting on MGPT results, data from MGPTs for cardiovascular indications were retrospectively analyzed. Using our CV scoring system, genes were categorized as having definitive, strong, moderate, or limited evidence. The rates of reported pathogenic or likely pathogenic variants and VUS were then determined for each CV category.

RESULTS

Of 106 total genes, 42% had definitive, 17% had strong, 29% had moderate, and 12% had limited CV. The detection rate of variants classified as pathogenic or likely pathogenic was higher for genes with greater CV, while the VUS rate showed an inverse relationship with CV score. No pathogenic or likely pathogenic findings were observed in genes with a limited CV.

CONCLUSION

These results demonstrate the importance of a standardized, evidence-based vetting process to establish CV for genes on MGPTs. Using our proposed system may help to increase the detection rate while mitigating higher VUS rates.

Communication of genetic information to families with inherited rhythm disorders

Given the dynamic nature of the electrical activity of the heart and ongoing challenges in the diagnostics of inherited heart rhythm disorders, genetic information can be a vital aspect of family management. Communication of genetic information is complex, and the responsibility to convey this information to the family lies with the proband. Current practice falls short, requiring additional support from the clinician and multidisciplinary team. Communication is a 2-part iterative process, reliant on both the understanding of the probands and their ability to effectively communicate with relatives. With the surge of high-throughput genetic testing, results generated are increasingly complex, making the task of communication more challenging. Here we discuss 3 key issues. First, the probabilistic nature of genetic test results means uncertainty is inherent to the practice. Second, secondary findings may arise. Third, personal preferences, values, and family dynamics also come into play and must be acknowledged when considering how best to support effective communication. Here we provide insight into the challenges and provide practical advice for clinicians to support effective family communication. These strategies include acknowledging and managing genetic uncertainty, genetic counseling and informed consent, and consideration of personal and familial barriers to effective communication. We will explore the potential for developing resources to assist clinicians in providing patients with sufficient knowledge and support to communicate complex information to their at-risk relatives. Specialized multidisciplinary clinics remain the best equipped to manage patients and families with inherited heart rhythm disorders given the need for a high level of information and support.

Attitudes, knowledge and consequences of uncertain genetic findings in hypertrophic cardiomyopathy

With the surge of next-generation sequencing (NGS) technologies making almost all genetic tests more affordable and available, cardiac genetic testing now routinely encompasses a large number of genes within a panel setting. The additional sensitivity of this practice is limited and has the potential to inflict a spectrum of uncertainty. We sought to explore attitudes, preferences, recall and psychological consequences of informative and uninformative genetic results amongst probands diagnosed with hypertrophic cardiomyopathy (HCM). We conducted semi-structured interviews and analysed the qualitative data using a framework analysis process. In general, we found probands were more concerned with their clinical diagnosis than gene result and in some, recall and understanding of genetic diagnosis was poor. Several participants expected genetic testing would alleviate uncertainty, often holding an altruistic view of participation in testing, removing their sense of self and failing to appreciate fully the familial implications. With the key utility of HCM genetic testing and counselling being for greater risk prediction for at-risk relatives, effective communication within the family is critical. While communication appeared adequate, further questioning found it was often vague, failing to translate into meaningful action by relatives. Based on these findings, a framework of key outcomes to assist multidisciplinary teams in genetic counselling of probands receiving an HCM gene result was developed.

Personal utility in genomic testing: a systematic literature review

Researchers and clinicians refer to outcomes of genomic testing that extend beyond clinical utility as 'personal utility'. No systematic delineation of personal utility exists, making it challenging to appreciate its scope. Identifying empirical elements of personal utility reported in the literature offers an inventory that can be subsequently ranked for its relative value by those who have undergone genomic testing. A systematic review was conducted of the peer-reviewed literature reporting non-health-related outcomes of genomic testing from 1 January 2003 to 5 August 2016. Inclusion criteria specified English language, date of publication, and presence of empirical evidence. Identified outcomes were iteratively coded into unique domains. The search returned 551 abstracts from which 31 studies met the inclusion criteria. Study populations and type of genomic testing varied. Coding resulted in 15 distinct elements of personal utility, organized into three domains related to personal outcomes: affective, cognitive, and behavioral; and one domain related to social outcomes. The domains of personal utility may inform pre-test counseling by helping patients anticipate potential value of test results beyond clinical utility. Identified elements may also inform investigations into the prevalence and importance of personal utility to future test users.

Analytical and Clinical Validity Study of FirstStepDx PLUS: A Chromosomal Microarray Optimized for Patients with Neurodevelopmental Conditions

Introduction:

Chromosomal microarray analysis (CMA) is recognized as the first-tier test in the genetic evaluation of children with developmental delays, intellectual disabilities, congenital anomalies and autism spectrum disorders of unknown etiology.

Array Design:

To optimize detection of clinically relevant copy number variants associated with these conditions, we designed a whole-genome microarray, FirstStep^Dx PLUS (FSDX). A set of 88,435 custom probes was added to the Affymetrix CytoScanHD platform targeting genomic regions strongly associated with these conditions. This combination of 2,784,985 total probes results in the highest probe coverage and clinical yield for these disorders.

Results and Discussion:

Clinical testing of this patient population is validated on DNA from either non-invasive buccal swabs or traditional blood samples. In this report we provide data demonstrating the analytic and clinical validity of FSDX and provide an overview of results from the first 7,570 consecutive patients tested clinically. We further demonstrate that buccal sampling is an effective method of obtaining DNA samples, which may provide improved results compared to traditional blood sampling for patients with neurodevelopmental disorders who exhibit somatic mosaicism.

Parents' perceptions of the usefulness of chromosomal microarray analysis for children with autism spectrum disorders

Clinical guidelines recommend chromosomal microarray analysis (CMA) for all children with autism spectrum disorders (ASDs). We explored the test's perceived usefulness among parents of children with ASD who had undergone CMA, and received a result categorized as pathogenic, variant of uncertain significance, or negative. Fifty-seven parents participated in a semi-structured telephone interview, and 50 also completed a survey. Most parents reported that CMA was helpful for their child and family. Major themes regarding perceived usefulness were: medical care, educational and behavioral interventions, causal explanation, information for family members, and advancing knowledge. Limits to utility, uncertainties and negative outcomes were also identified. Our findings highlight the importance of considering both health and non-health related utility in genomic testing.

"Something Extra on Chromosome 5": Parents' Understanding of Positive Prenatal Chromosomal Microarray Analysis (CMA) Results

This study aims to explore how couples' understanding of the nature and consequences of positive prenatal chromosomal microarray analysis (CMA) results impacts decision-making and concern about pregnancy. We interviewed 28 women and 12 male partners after receiving positive results and analyzed the transcripts to assess their understanding and level of concern about the expected clinical implications of results. Participant descriptions were compared to the original laboratory interpretation. When diagnosed prenatally, couples' understanding of the nature and consequences of copy number variants (CNVs) impacts decision-making and concern. Findings suggest women, but less so partners, generally understand the nature and clinical implications of prenatal CMA results. Couples feel reassured, perhaps sometimes falsely so, when a CNV is inherited from a "normal" parent and experience considerable uncertainty when a CNV is de novo, frequently precipitating a search for additional information and guidance. Five factors influenced participants' concern including: the pattern of inheritance, type of possible phenotypic involvement, perceived manageability of outcomes, availability and strength of evidence about outcomes associated with the CNV, and provider messages about continuing the pregnancy. A good understanding of results is vital as couples decide whether or not to continue with their pregnancy and seek additional information to assist in pregnancy decision-making.

Comparing genetic counselor's and patient's perceptions of needs in prenatal chromosomal microarray testing

OBJECTIVE

Chromosome microarray analysis is poised to take a significant place in the prenatal setting given its increased yield over standard karyotyping, but concerns regarding ethical and counseling challenges remain, especially associated with the risk of uncertain and incidental findings. Guidelines recommend patients receiving prenatal screening to undergo genetic counseling prior to testing, but little is known about women's specific pre-testing and post-testing informational needs, as well as their preference for return of various types of results.

METHODS

The present study surveys 199 prenatal genetic counselors who have counseled patients undergoing chromosome microarray analysis testing and 152 women who have undergone testing on the importance of understanding pre-test information, return of various types of results, and resources made available following an abnormal finding.

RESULTS

Counselors and patients agree on many aspects, although findings indicate patients consider all available information very important, while genetic counselors give more varying ratings.

CONCLUSION

Counseling sessions would benefit from information personalized to a patient's particular needs and a shared decision-making model, to reduce informational overload and avoid unnecessary anxiety. Additionally, policies regarding the return of various types of results are needed. © 2015 John Wiley & Sons, Ltd.

Parents' Perspectives on Variants of Uncertain Significance from Chromosome Microarray Analysis

Chromosomal microarray analysis (CMA) for unexplained anomalies and developmental delay has improved diagnosis rates, but results classified as variants of uncertain significance (VUS) may challenge both clinicians and families. We explored the impact of such results on families, including parental knowledge, understanding and interpretation. Semi-structured telephone interviews were conducted with parents (N = 14) who received genetic counseling for a VUS in their child. Transcripts were analyzed through an iterative coding process. Participants demonstrated a range of recall and personal interpretation regarding whether test results provided a causal explanation for their children's health issues. Participants maintained contradictory interpretations, describing results as answers while maintaining that little clarification of their child's condition had been provided. Reported benefits included obtaining medical services and personal validation. Parents described adaptation/coping processes similar to those occurring after positive test results. Recall of terminology, including "VUS" and precise CMA abnormalities, was poor. However, most demonstrated conceptual understanding of scientific uncertainty. All participants expressed intentions to return for recommended genetics follow-up but had misconceptions about how this would occur. These results provide insight into the patient-and-family experience when receiving uncertain genomic findings, emphasize the importance of exploring uncertainty during the communication process, and highlight areas for potential attention or improvement in the clinical encounter.

Analyzing communication in genetic consultations--a systematic review

OBJECTIVE

To systematically review studies that have analyzed communication within medical consultations involving genetic specialists and report on their findings and design.

METHODS

Drawing from PRISMA and appropriate guidelines for reviewing qualitative research, a systematic search of seven databases was conducted, followed by selection of studies for inclusion based on a set of criteria. Three authors conducted data extraction and narrative synthesis.

RESULTS

Twenty-two studies were identified and were heterogeneous in setting, design, and methods, with many including limited descriptions of health professionals involved. Despite this variability, studies generally pursued the following three main objectives: searching for structural patterns within consultations, investigating communication and genetic counseling concepts, and linking process with input- and outcome-measures. Structural patterns identified included clinician dialog dominating consultations, and talk being mostly biomedical. Counseling and communication concepts investigated were: risk communication, the negotiation of power and knowledge, and adherence to genetic counseling ideals. Attempts to link consultation data to input- or outcome-measures were often unsuccessful.

CONCLUSION

More interdisciplinary research, grounded in appropriate theoretical frameworks, is needed to explore inherent complexities in this setting.

PRACTICE IMPLICATIONS

Findings from this review can be used to guide the design of future research into the process of genetic consultations.