High frequency of mosaic pathogenic variants in genes causing epilepsy-related neurodevelopmental disorders

Abstract

PurposeMosaicism probably represents an underreported cause of genetic disorders due to detection challenges during routine molecular diagnostics. The purpose of this study was to evaluate the frequency of mosaicism detected by next-generation sequencing in genes associated with epilepsy-related neurodevelopmental disorders.MethodsWe conducted a retrospective analysis of 893 probands with epilepsy who had a multigene epilepsy panel or whole-exome sequencing performed in a clinical diagnostic laboratory and were positive for a pathogenic or likely pathogenic variant in one of nine genes (CDKL5, GABRA1, GABRG2, GRIN2B, KCNQ2, MECP2, PCDH19, SCN1A, or SCN2A). Parental results were available for 395 of these probands.ResultsMosaicism was most common in the CDKL5, PCDH19, SCN2A, and SCN1A genes. Mosaicism was observed in GABRA1, GABRG2, and GRIN2B, which previously have not been reported to have mosaicism, and also in KCNQ2 and MECP2. Parental mosaicism was observed for pathogenic variants in multiple genes including KCNQ2, MECP2, SCN1A, and SCN2A.ConclusionMosaic pathogenic variants were identified frequently in nine genes associated with various neurological conditions. Given the potential clinical ramifications, our findings suggest that next-generation sequencing diagnostic methods may be utilized when testing these genes in a diagnostic laboratory.

Diagnostic outcomes for genetic testing of 70 genes in 8565 patients with epilepsy and neurodevelopmental disorders

“…This finding is particularly true for early onset epileptic encephalopathy, which has been reported to have a higher proportion of monogenic causes than other epilepsies . Additionally, relatively high rates of mosaicism have been reported in many genes associated with epilepsy, supporting the need for NGS as opposed to Sanger sequencing for diagnostic testing of these genes . Positive diagnostic yields of multigene epilepsy panels are reported to range from 18% to 28%, indicating that this type of testing has high clinical utility for individuals with epilepsy and/or NDD .…”

“…Targeted exons were amplified from genomic DNA using either multiplex polymerase chain reaction (Raindance Technologies, Lexington, MA, USA) or RNA probe capture using a custom Agilent SureSelect kit (Agilent Technologies, Santa Clara, CA, USA) to produce DNA libraries for NGS. NGS data were generated, and sequence variants were identified, filtered, and evaluated with a custom bioinformatics pipeline as previously described . Regions of interest were defined as coding exons, ±20 base pairs (bp) of flanking intronic sequence of both coding and noncoding exons, and 20 bp of 5′ and 3′ untranslated region sequence.…”

Epilepsy genetics: Current knowledge, applications, and future directions

“…The parent may have a past history of FS only and the mild nature of seizures, if present, may reflect the degree of mosaicism . Other genes are also noted to have a degree of observed mosaicism . All these factors emphasize the potential benefit of familial testing in patients with Dravet syndrome or GEFS+ phenotypes in the context of thorough pre‐ and post‐genetic counseling.…”

“…108,111,[116][117][118][119][120] A recent report identified "second hit" mutations present in DEPDC5 from the resected brain tissue of individuals with an already identified germline mutation. 121 Deep sequencing of DNA from fibroblasts and/or lymphoblasts may also rule in a somatic mutation, 122,123 and it may also be used to detect the presence of somatic (germline) mosaicism in a parent. 124,125 This would have significant implications for counseling purposes and the prenatal testing options that may be offered.…”

“…123,157,158 Other genes are also noted to have a degree of observed mosaicism. 122 All these factors emphasize the potential benefit of familial testing in patients with Dravet syndrome or GEFS+ phenotypes in the context of thorough pre-and post-genetic counseling. Lastly, it has been recognized that known SCN1A-mutation negative individuals, when later sequenced by NGS methods, have been shown to be positive and thereby missed on initial Sanger sequencing.…”