Molecular Genetic Characterization of Patients With Focal Epilepsy Using a Customized Targeted Resequencing Gene Panel

Tsai, Meng Han; Chan, Chung Kin; Chang, Ying; Lin, Chih Hsiang; Liou, Chia Wei; Chang, Wen‐Cheng; Ng, Ching Ching; Lim, Kheng Seang

doi:10.3389/fneur.2018.00515

Cited by 19 publications

(16 citation statements)

References 44 publications

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“…Using a broad exome-based approach, we identified molecular diagnoses in 12%, which is less than in syndromic epilepsies,13 but comparable to the small-scale study by Perucca et al evaluating diagnostic ES with targeted gene analysis in NAFE 14. In contrast, our diagnostic yield is remarkably higher than that reported by Hildebrand et al and Tsai et al , who found diagnostic variants in only 0.8% and 1.85% of cases, respectively 15 16. First, the lower hit rate may be explained by the broader inclusion criteria of these studies, not accounting for age of onset and a positive family history.…”

Section: Discussionsupporting

confidence: 77%

“…One small-scale diagnostic ES study used a targeted analysis approach in 40 patients with NAFE and a suspected genetic background, resulting in a diagnostic yield of 12.5% 14. Two further studies used narrower panel approaches limited to known focal epilepsy genes, both resulting in hit rates of only less than 2% 15 16. These contrasting findings demonstrate the uncertainty about genetic testing outcomes for this relevant epilepsy subgroup, and there is a strong need to evaluate comprehensive genetic–diagnostic approaches in clinically well-characterised cohorts.…”

Section: Introductionmentioning

confidence: 99%

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Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes

et al. 2020

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BackgroundThe genetic architecture of non-acquired focal epilepsies (NAFEs) becomes increasingly unravelled using genome-wide sequencing datasets. However, it remains to be determined how this emerging knowledge can be translated into a diagnostic setting. To bridge this gap, we assessed the diagnostic outcomes of exome sequencing (ES) in NAFE.Methods112 deeply phenotyped patients with NAFE were included in the study. Diagnostic ES was performed, followed by a screen to detect variants of uncertain significance (VUSs) in 15 well-established focal epilepsy genes. Explorative gene prioritisation was used to identify possible novel candidate aetiologies with so far limited evidence for NAFE.ResultsES identified pathogenic or likely pathogenic (ie, diagnostic) variants in 13/112 patients (12%) in the genes DEPDC5, NPRL3, GABRG2, SCN1A, PCDH19 and STX1B. Two pathogenic variants were microdeletions involving NPRL3 and PCDH19. Nine of the 13 diagnostic variants (69%) were found in genes of the GATOR1 complex, a potentially druggable target involved in the mammalian target of rapamycin (mTOR) signalling pathway. In addition, 17 VUSs in focal epilepsy genes and 6 rare variants in candidate genes (MTOR, KCNA2, RBFOX1 and SCN3A) were detected. Five patients with reported variants had double hits in different genes, suggesting a possible (oligogenic) role of multiple rare variants.ConclusionThis study underscores the molecular heterogeneity of NAFE with GATOR1 complex genes representing the by far most relevant genetic aetiology known to date. Although the diagnostic yield is lower compared with severe early-onset epilepsies, the high rate of VUSs and candidate variants suggests a further increase in future years.

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Section: Discussionsupporting

confidence: 77%

Section: Introductionmentioning

confidence: 99%

Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes

et al. 2020

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“…Family B was diagnosed through a microfluidic multiplex polymerase chain reaction–based multigene panel (Fluidigm Access 48.48 Array). Amplified products were barcoded and sequenced using an Illumina MiSeq system followed by standardized bioinformatic analysis and Sanger sequencing . The functional impact of variant was predicted using Polymorphism Phenotyping 2 (PolyPhen‐2; http://genetics.bwh.harvard.edu/pph2/), Protein Variation Effect Analyzer (PROVEAN; http://provean.jcvi.org/index.php), and MutationTaster (http://www.mutationtaster.org).…”

Section: Methodsmentioning

confidence: 99%

“…Amplified products were barcoded and sequenced using an Illumina MiSeq system followed by standardized bioinformatic analysis and Sanger sequencing. 19,20 The functional impact of variant was predicted using Polymorphism Phenotyping 2 (PolyPhen-2; http://genetics.bwh.harvard.edu/ pph2/), 21 Protein Variation Effect Analyzer (PROVEAN; http://provean.jcvi.org/index.php), 22 and MutationTaster (http://www.mutationtaster.org). 23 Segregation analysis was performed in the family members where DNA samples were available.…”

Section: Clinical and Molecular Genetic Studymentioning

confidence: 99%

PRRT2 missense mutations cluster near C‐terminus and frequently lead to protein mislocalization

et al. 2019

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Summary Objective Variants in human PRRT2 cause paroxysmal kinesigenic dyskinesia (PKD) and other neurological disorders. Most reported variants resulting in truncating proteins failed to localize to cytoplasmic membrane. The present study identifies novel PRRT2 variants in PKD and epilepsy patients and evaluates the functional consequences of PRRT2 missense variations. Methods We investigated two families with PKD and epilepsies using Sanger sequencing and a multiple gene panel. Subcellular localization of mutant proteins was investigated using confocal microscopy and cell surface biotinylation assay in Prrt2‐transfected cells. Results Two novel PRRT2 variants, p.His232Glnfs*10 and p.Leu298Pro, were identified, and functional study revealed impaired localization of both mutant proteins to the plasma membrane. Further investigation of other reported missense variants revealed decreased protein targeting to the plasma membrane in eight of the 13 missense variants examined (p.Trp281Arg, p.Ala287Thr, p.Ala291Val, p.Arg295Gln, p.Leu298Pro, p.Ala306Asp, p.Gly324Glu, and p.Gly324Arg). In contrast, all benign variants we tested exhibited predominant localization to the plasma membrane similar to wild‐type Prrt2. Most likely pathogenic variants were located at conserved amino acid residues near the C‐terminus, whereas truncating variants spread throughout the gene. Significance PRRT2 missense variants clustering at the C‐terminus often lead to protein mislocalization. Failure in protein targeting to the plasma membrane by PRRT2 variants may be a key mechanism in causing PKD and related neurological disorders.

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“…La encefalopatía epiléptica infantil precoz 9 o epilepsia restringida a mujeres con o sin retraso mental, es causada por una mutación en el gen que codifica la proteína protocadherina-19 (PCDH19; 300460) en el cromosoma Xq22 1-2 . Identificándose en la actualidad 6 mutaciones diferentes en el gen PCDH19 3 .Caracterizado fenotípicamente por encefalopatía epiléptica temprana, múltiples tipos de crisis, asociados con fiebre, retraso mental leve a severo con trastorno del lenguaje y ataxia 4 .Las mutaciones en PCDH19 pueden causar una encefalopatía epiléptica temprana y grave que simula el Síndrome de Dravet, con características clínicas muy similares, incluida la asociación de convulsiones tempranas febriles y afebriles, polimorficas, en salvas, retraso en el desarrollo y el lenguaje, alteraciones del comportamiento y regresión cognitiva 5 .…”

Section: Introductionunclassified

Encefalopatía epiléptica de inicio temprano, pdch19

Vaudagna¹,

Vergara²,

Martínez³

et al. 2019

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IntroducciónLa encefalopatía epiléptica infantil precoz 9 o epilepsia restringida a mujeres con o sin retraso mental, es causada por una mutación en el gen que codifica la proteína protocadherina-19 (PCDH19; 300460) en el cromosoma Xq22 1-2 . Identificándose en la actualidad 6 mutaciones diferentes en el gen PCDH19 3 .Caracterizado fenotípicamente por encefalopatía epiléptica temprana, múltiples tipos de crisis, asociados con fiebre, retraso mental leve a severo con trastorno del lenguaje y ataxia 4 .Las mutaciones en PCDH19 pueden causar una encefalopatía epiléptica temprana y grave que simula el Síndrome de Dravet, con características clínicas muy similares, incluida la asociación de convulsiones tempranas febriles y afebriles, polimorficas, en salvas, retraso en el desarrollo y el lenguaje, alteraciones del comportamiento y regresión cognitiva 5 .

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Molecular Genetic Characterization of Patients With Focal Epilepsy Using a Customized Targeted Resequencing Gene Panel

Cited by 19 publications

References 44 publications

Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes

Diagnostic exome sequencing in non-acquired focal epilepsies highlights a major role of GATOR1 complex genes

PRRT2 missense mutations cluster near C‐terminus and frequently lead to protein mislocalization

Encefalopatía epiléptica de inicio temprano, pdch19

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