Assessing parental understanding of variant reclassification in pediatric neurology and developmental pediatrics clinics

Canadian College of Medical Geneticists: clinical practice advisory document - responsibility to recontact for reinterpretation of clinical genetic testing

BACKGROUND

Advances in technology and knowledge have facilitated both an increase in the number of patient variants reported and variants reclassified. While there is currently no duty to recontact for reclassified genetic variants, there may be a responsibility. The purpose of this clinical practice advisory document is to provide healthcare practitioners guidance for recontact of previously identified and classified variants, suggest methods for recontact, and principles to consider, taking account patient safety, feasibility, ethical considerations, health service capacity and resource constraints. The target audience are practitioners who order genetic testing, follow patients who have undergone genetic testing and those analysing and reporting genetic testing.

METHODS

A multidisciplinary group of laboratory and ordering clinicians, patient representatives, ethics and legal researchers and a genetic counsellor from the Canadian Association of Genetic Counsellors reviewed the existing literature and guidelines on responsibility to recontact in a clinical context to make recommendations. Comments were collected from the Canadian College of Medical Geneticists (CCMG) Education, Ethics, and Public Policy, Clinical Practice and Laboratory Practice committees, and the membership at large.

RESULTS

Following incorporation of feedback, and external review by the Canadian Association of Genetic Counsellors and patient groups, the document was approved by the CCMG Board of Directors. The CCMG is the Canadian organisation responsible for certifying laboratory and medical geneticists who provide medical genetics services, and for establishing professional and ethical standards for clinical genetics services in Canada.

CONCLUSION

The document describes the ethical and practical factors and suggests a shared responsibility between patients, ordering clinician and laboratory practitioners.

Variant reclassification and recontact research: A scoping review

Purpose

A primary challenge in clinical genetics is accurate interpretation of identified variants and relaying the information to patients and providers. Inconsistencies around handling variant reclassifications and notifying patients, combined with the lack of prescriptive guidelines on re-evaluation, reanalysis, and return of variants, has created practice challenges. Although relevant empirical work has emerged, the scope and outcomes of this research have not been characterized.

Methods

We conducted a systematic literature review of variant reclassification and recontact research (2013-2023) across subdisciplines of medical genetics. Of the 159 nonduplicate records screened, we summarize findings from 54 included research articles describing variant reclassification frequencies, outcomes, and stakeholder perspectives on recontact.

Results

The included articles reported on active reclassification (n = 20), passive reclassification (n = 13), stakeholder surveys (n = 11), qualitative interviews (n = 7), and reanalysis of published or ClinVar data (n = 3). On average, active and passive approaches yielded different reclassification frequencies-31% and 20%, respectively, which were considerably higher than ClinVar (<0.1%-6.4%). Despite a wealth of data on individual stakeholder perspectives and opinions on reclassification, recontact, and consensus on the need for standardization in this space, opinions differ on how to develop and implement standardized processes.

Conclusion

Many active reclassification studies reapplied standard variant classification guideline to previously reported variants-thus demonstrating the number of variants that would be successfully reclassified if reinterpretation and reanalysis were performed routinely. Research gaps identified include the need for understanding practices and opinions of nongenetics providers and engaging in deliberative democracy exercises to reach consensus on these issues.

Variant reclassification and clinical implications

Genomic technologies have transformed clinical genetic testing, underlining the importance of accurate molecular genetic diagnoses. Variant classification, ranging from benign to pathogenic, is fundamental to these tests. However, variant reclassification, the process of reassigning the pathogenicity of variants over time, poses challenges to diagnostic legitimacy. This review explores the medical and scientific literature available on variant reclassification, focusing on its clinical implications.Variant reclassification is driven by accruing evidence from diverse sources, leading to variant reclassification frequency ranging from 3.6% to 58.8%. Recent studies have shown that significant changes can occur when reviewing variant classifications within 1 year after initial classification, illustrating the importance of early, accurate variant assignation for clinical care.Variants of uncertain significance (VUS) are particularly problematic. They lack clear categorisation but have influenced patient treatment despite recommendations against it. Addressing VUS reclassification is essential to enhance the credibility of genetic testing and the clinical impact. Factors affecting reclassification include standardised guidelines, clinical phenotype-genotype correlations through deep phenotyping and ancestry studies, large-scale databases and bioinformatics tools. As genomic databases grow and knowledge advances, reclassification rates are expected to change, reducing discordance in future classifications.Variant reclassification affects patient diagnosis, precision therapy and family screening. The exact patient impact is yet unknown. Understanding influencing factors and adopting standardised guidelines are vital for precise molecular genetic diagnoses, ensuring optimal patient care and minimising clinical risk.