Genetics of Epilepsy in the Era of Precision Medicine: Implications for Testing, Treatment, and Genetic Counseling

Clinical signatures of genetic epilepsies precede diagnosis in electronic medical records of 32,000 individuals

PURPOSE

An early genetic diagnosis can guide the time-sensitive treatment of individuals with genetic epilepsies. However, most genetic diagnoses occur long after disease onset. We aimed to identify early clinical features suggestive of genetic diagnoses in individuals with epilepsy through large-scale analysis of full-text electronic medical records.

METHODS

We extracted 89 million time-stamped standardized clinical annotations using Natural Language Processing from 4,572,783 clinical notes from 32,112 individuals with childhood epilepsy, including 1925 individuals with known or presumed genetic epilepsies. We applied these features to train random forest models to predict SCN1A-related disorders and any genetic diagnosis.

RESULTS

We identified 47,774 age-dependent associations of clinical features with genetic etiologies a median of 3.6 years before molecular diagnosis. Across all 710 genetic etiologies identified in our cohort, neurodevelopmental differences between 6 to 9 months increased the likelihood of a later molecular diagnosis 5-fold (P < .0001, 95% CI = 3.55-7.42). A later diagnosis of SCN1A-related disorders (area under the curve [AUC] = 0.91) or an overall positive genetic diagnosis (AUC = 0.82) could be reliably predicted using random forest models.

CONCLUSION

Clinical features predictive of genetic epilepsies precede molecular diagnoses by up to several years in conditions with known precision treatments. An earlier diagnosis facilitated by automated electronic medical records analysis has the potential for earlier targeted therapeutic strategies in the genetic epilepsies.

Genetic testing for the epilepsies: A systematic review

OBJECTIVE

Numerous genetic testing options for individuals with epilepsy have emerged over the past decade without clear guidelines regarding optimal testing strategies. We performed a systematic evidence review (SER) and conducted meta-analyses of the diagnostic yield of genetic tests commonly utilized for patients with epilepsy. We also assessed nonyield outcomes (NYOs) such as changes in treatment and/or management, prognostic information, recurrence risk determination, and genetic counseling.

METHODS

We performed an SER, in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses), using PubMed, Embase, CINAHL, and Cochrane Central through December of 2020. We included studies that utilized genome sequencing (GS), exome sequencing (ES), multigene panel (MGP), and/or genome-wide comparative genomic hybridization/chromosomal microarray (CGH/CMA) in cohorts (n ≥ 10) ascertained for epilepsy. Quality assessment was undertaken using ROBINS-I (Risk of Bias in Non-Randomized Studies of Interventions). We estimated diagnostic yields and 95% confidence intervals with random effects meta-analyses and narratively synthesized NYOs.

RESULTS

From 5985 nonduplicated articles published through 2020, 154 met inclusion criteria and were included in meta-analyses of diagnostic yield; 43 of those were included in the NYO synthesis. The overall diagnostic yield across all test modalities was 17%, with the highest yield for GS (48%), followed by ES (24%), MGP (19%), and CGH/CMA (9%). The only phenotypic factors that were significantly associated with increased yield were (1) the presence of developmental and epileptic encephalopathy and/or (2) the presence of neurodevelopmental comorbidities. Studies reporting NYOs addressed clinical and personal utility of testing.

SIGNIFICANCE

This comprehensive SER, focused specifically on the literature regarding patients with epilepsy, provides a comparative assessment of the yield of clinically available tests, which will help shape clinician decision-making and policy regarding insurance coverage for genetic testing. We highlight the need for prospective assessment of the clinical and personal utility of genetic testing for patients with epilepsy and for standardization in reporting patient characteristics.

Developmental and epileptic encephalopathy: Personal utility of a genetic diagnosis for families

Objectives

Identifying genetic pathogenic variants improves clinical outcomes for children with developmental and epileptic encephalopathy (DEE) by directing therapy and enabling accurate reproductive and prognostic information for families. We aimed to explore the additional personal utility of receiving a genetic diagnosis for families.

Methods

Semi-structured interviews were conducted with fifteen families of children with a DEE who had received a genetic diagnosis. The interviews stimulated discussion focusing on the impact of receiving a genetic diagnosis for the family. Interview transcripts were analyzed using the six-step systematic process of interpretative phenomenological analysis (IPA).

Results

Three key themes were identified: "Importance of the label," "Relief to end the diagnostic journey," and "Factors that influence personal utility." Families reported that receiving a genetic label improved their knowledge about the likely trajectory of the DEE, increased their hope for the future, and helped them communicate with others. The relief of finally having an answer for the cause of their child's DEE alleviated parental guilt and self-blame as well as helped families to process their grief and move forward. Delay in receipt of a genetic diagnosis diluted its psychological impact.

Significance

To date, the factors associated with the personal utility of a genetic diagnosis for DEEs have been under appreciated. This study demonstrates that identifying a genetic diagnosis for a child's DEE can be a psychological turning point for families. A genetic result has the potential to set these families on an adaptive path toward better quality of life through increased understanding, social connection, and support. Early access to genetic testing is important as it not only increases clinical utility, but also increases personal utility with early mitigation of family stress, trauma, and negative experiences.