Evaluation of damaging effects of splicing mutations: validation of an in vitro method for diagnostic laboratories.
Clin Chim Acta
; 436: 276-82, 2014 Sep 25.
Article
in En
| MEDLINE
| ID: mdl-24915601
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 ANDMETHODS:
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 "wet" RNA 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.Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
RNA Splicing
/
Clinical Laboratory Techniques
/
Mutation
Type of study:
Diagnostic_studies
/
Prognostic_studies
Limits:
Adult
/
Humans
/
Male
/
Middle aged
Language:
En
Journal:
Clin Chim Acta
Year:
2014
Type:
Article
Affiliation country:
Italy