Evaluation of damaging effects of splicing mutations

Validation of an in vitro method for diagnostic laboratories

Chiara Di Resta, Martina Manzoni, Massimo Zoni Berisso, Gabriele Siciliano, Sara Benedetti, Maurizio Ferrari

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Background: Pre-mRNA splicing defects may have an important impact on clinical phenotype in several diseases, but often their pathogenic role is difficult to demonstrate. The aim of this study was to validate an in vitro method to assess the effects of putative splicing variants. Materials and methods: We studied three novel variants in vitro using a novel minigene approach and compared results with in silico and ex vivo strategies from patient samples. Results: For the c.1146C>T variant in the LMNA gene, in vitro and ex vivo studies were concordant with the prediction obtained by in silico tools, confirming the loss of 13. bp at the end of exon 6. In the second case (c.1140+1G>A, SCN5A gene), in vitro experiments identified the insertion of 94 intronic bp in exon 9 as well as exon 9 skipping, but these results were not correctly predicted by ex vivo data and in silico tools. In the third case (c.1608+1C>T, LMNA gene) in vitro and ex vivo studies suggested the recognition of an exonic cryptic site leading to the loss of 29. bp in exon 9, not predicted by in silico analysis. Conclusion: Our results revealed how in silico tools are often unreliable requiring wetRNA analysis. Since ex vivo studies are not always feasible, the use of an in vitro construct represents an efficient and useful method for the evaluation of damaging effects of unknown splicing variants, especially in diagnostic laboratories.

Original languageEnglish
Pages (from-to)276-282
Number of pages7
JournalClinica Chimica Acta
Volume436
DOIs
Publication statusPublished - Sep 25 2014

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Exons
Computer Simulation
Mutation
Genes
RNA Precursors
Defects
In Vitro Techniques
Phenotype
Experiments

Keywords

  • Expression vectors
  • In silico tools
  • In vitro studies
  • Minigene
  • RNA analysis
  • Splicing defects

ASJC Scopus subject areas

  • Biochemistry
  • Clinical Biochemistry
  • Biochemistry, medical
  • Medicine(all)

Cite this

Evaluation of damaging effects of splicing mutations : Validation of an in vitro method for diagnostic laboratories. / Di Resta, Chiara; Manzoni, Martina; Zoni Berisso, Massimo; Siciliano, Gabriele; Benedetti, Sara; Ferrari, Maurizio.

In: Clinica Chimica Acta, Vol. 436, 25.09.2014, p. 276-282.

Research output: Contribution to journalArticle

Di Resta, Chiara ; Manzoni, Martina ; Zoni Berisso, Massimo ; Siciliano, Gabriele ; Benedetti, Sara ; Ferrari, Maurizio. / Evaluation of damaging effects of splicing mutations : Validation of an in vitro method for diagnostic laboratories. In: Clinica Chimica Acta. 2014 ; Vol. 436. pp. 276-282.
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