SCN1A duplications and deletions detected in Dravet syndrome: Implications for molecular diagnosis

Carla Marini, Ingrid E. Scheffer, Rima Nabbout, Davide Mei, Kathy Cox, Leanne M. Dibbens, Jacinta M. McMahon, Xenia Iona, Rochio Sanchez Carpintero, Maurizio Elia, Maria Roberta Cilio, Nicola Specchio, Lucio Giordano, Pasquale Striano, Elena Gennaro, J. Helen Cross, Sara Kivity, Miriam Y. Neufeld, Zaid Afawi, Eva AndermannDaniel Keene, Olivier Dulac, Federico Zara, Samuel F. Berkovic, Renzo Guerrini, John C. Mulley

Research output: Contribution to journalArticle

Abstract

Objective: We aimed to determine the type, frequency, and size of microchromosomal copy number variations (CNVs) affecting the neuronal sodium channel α 1 subunit gene (SCN1A) in Dravet syndrome (DS), other epileptic encephalopathies, and generalized epilepsy with febrile seizures plus (GEFS+). Methods: Multiplex ligation-dependent probe amplification (MLPA) was applied to detect SCN1A CNVs among 289 cases (126 DS, 97 GEFS+, and 66 with other phenotypes). CNVs extending beyond SCN1A were further characterized by comparative genome hybridization (array CGH). Results: Novel SCN1A CNVs were found in 12.5% of DS patients where sequence-based mutations had been excluded. We identified the first partial SCN1A duplications in two siblings with typical DS and in a patient with early-onset symptomatic generalized epilepsy. In addition, a patient with DS had a partial SCN1A amplification of 5-6 copies. The remaining CNVs abnormalities were four partial and nine whole SCN1A deletions involving contiguous genes. Two CNVs (a partial SCN1A deletion and a duplication) were inherited from a parent, in whom there was mosaicism. Array CGH showed intragenic deletions of 90 kb and larger, with the largest of 9.3 Mb deleting 49 contiguous genes and extending beyond SCN1A. Discussion: Duplication and amplification involving SCN1A are now added to molecular mechanisms of DS patients. Our findings showed that 12.5% of DS patients who are mutation negative have MLPA-detected SCN1A CNVs with an overall frequency of about 2-3%. MLPA is the established second-line testing strategy to reliably detect all CNVs of SCN1A from the megabase range down to one exon. Large CNVs extending outside SCN1A and involving contiguous genes can be precisely characterized by array CGH.

Original languageEnglish
Pages (from-to)1670-1678
Number of pages9
JournalEpilepsia
Volume50
Issue number7
DOIs
Publication statusPublished - 2009

Keywords

  • Array CGH
  • Deletion
  • Dravet syndrome
  • Duplication
  • Early-onset severe epilepsy
  • Multiplex ligation-dependent probe amplification
  • SCN1A

ASJC Scopus subject areas

  • Clinical Neurology
  • Neurology
  • Medicine(all)

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  • Cite this

    Marini, C., Scheffer, I. E., Nabbout, R., Mei, D., Cox, K., Dibbens, L. M., McMahon, J. M., Iona, X., Carpintero, R. S., Elia, M., Cilio, M. R., Specchio, N., Giordano, L., Striano, P., Gennaro, E., Cross, J. H., Kivity, S., Neufeld, M. Y., Afawi, Z., ... Mulley, J. C. (2009). SCN1A duplications and deletions detected in Dravet syndrome: Implications for molecular diagnosis. Epilepsia, 50(7), 1670-1678. https://doi.org/10.1111/j.1528-1167.2009.02013.x