What is the diagnostic yield of genetic testing when used for children with newly presenting early-life epilepsy?
In this cohort study of 775 children, diagnostic yields overall were 40%, with epilepsy gene-sequencing panels and whole-exome sequencing having substantially greater diagnostic yields than chromosomal microarray. In the absence of a clinically identified cause, testing yields were greater than 15% and as high as 47% depending on patient subgroups.
Genetic testing, especially with sequencing-based methods, should be incorporated into the routine initial evaluation of early-life epilepsy.
Early-life epilepsies are often a consequence of numerous neurodevelopmental disorders, most of which are proving to have genetic origins. The role of genetic testing in the initial evaluation of these epilepsies is not established.
To provide a contemporary account of the patterns of use and diagnostic yield of genetic testing for early-life epilepsies.
Design, Setting, and Participants
In this prospective cohort, children with newly diagnosed epilepsy with an onset at less than 3 years of age were recruited from March 1, 2012, to April 30, 2015, from 17 US pediatric hospitals and followed up for 1 year. Of 795 families approached, 775 agreed to participate. Clinical diagnosis of the etiology of epilepsy were characterized based on information available before genetic testing was performed. Added contributions of cytogenetic and gene sequencing investigations were determined.
Genetic diagnostic testing.
Main Outcomes and Measures
Laboratory-confirmed pathogenic variant.
Of the 775 patients in the study (367 girls and 408 boys; median age of onset, 7.5 months [interquartile range, 4.2-16.5 months]), 95 (12.3%) had acquired brain injuries. Of the remaining 680 patients, 327 (48.1%) underwent various forms of genetic testing, which identified pathogenic variants in 132 of 327 children (40.4%; 95% CI, 37%-44%): 26 of 59 (44.1%) with karyotyping, 32 of 188 (17.0%) with microarrays, 31 of 114 (27.2%) with epilepsy panels, 11 of 33 (33.3%) with whole exomes, 4 of 20 (20.0%) with mitochondrial panels, and 28 of 94 (29.8%) with other tests. Forty-four variants were identified before initial epilepsy presentation. Apart from dysmorphic syndromes, pathogenic yields were highest for children with tuberous sclerosis complex (9 of 11 [81.8%]), metabolic diseases (11 of 14 [78.6%]), and brain malformations (20 of 61 [32.8%]). A total of 180 of 446 children (40.4%), whose etiology would have remained unknown without genetic testing, underwent some testing. Pathogenic variants were identified in 48 of 180 children (26.7%; 95% CI, 18%-34%). Diagnostic yields were greater than 15% regardless of delay, spasms, and young age. Yields were greater for epilepsy panels (28 of 96 [29.2%]; P < .001) and whole exomes (5 of 18 [27.8%]; P = .02) than for chromosomal microarray (8 of 101 [7.9%]).
Conclusions and Relevance
Genetic investigations, particularly broad sequencing methods, have high diagnostic yields in newly diagnosed early-life epilepsies regardless of key clinical features. Thorough genetic investigation emphasizing sequencing tests should be incorporated into the initial evaluation of newly presenting early-life epilepsies and not just reserved for those with severe presentations and poor outcomes.
Berg AT, Coryell J, Saneto RP, Grinspan ZM, Alexander JJ, Kekis M, Sullivan JE, Wirrell EC, Shellhaas RA, Mytinger JR, Gaillard WD, Kossoff EH, Valencia I, Knupp KG, Wusthoff C, Keator C, Dobyns WB, Ryan N, Loddenkemper T, Chu CJ, Novotny EJ, Koh S. Early-Life Epilepsies and the Emerging Role of Genetic Testing. JAMA Pediatr. Published online July 31, 2017. doi:10.1001/jamapediatrics.2017.1743