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Open Access Highly Accessed Research article

Diagnosis of Noonan syndrome and related disorders using target next generation sequencing

Francesca Romana Lepri1*, Rossana Scavelli2, Maria Cristina Digilio1, Maria Gnazzo1, Simona Grotta1, Maria Lisa Dentici1, Elisa Pisaneschi1, Pietro Sirleto1, Rossella Capolino1, Anwar Baban1, Serena Russo1, Tiziana Franchin1, Adriano Angioni1 and Bruno Dallapiccola1

Author Affiliations

1 Cytogenetics, Medical Genetics and Pediatric Cardiology, Bambino Gesù Children Hospital, IRCCS, Rome, Italy

2 Illumina, Inc., San Diego, CA 92122, USA

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BMC Medical Genetics 2014, 15:14  doi:10.1186/1471-2350-15-14

Published: 23 January 2014

Abstract

Background

Noonan syndrome is an autosomal dominant developmental disorder with a high phenotypic variability, which shares clinical features with other rare conditions, including LEOPARD syndrome, cardiofaciocutaneous syndrome, Noonan-like syndrome with loose anagen hair, and Costello syndrome. This group of related disorders, so-called RASopathies, is caused by germline mutations in distinct genes encoding for components of the RAS-MAPK signalling pathway. Due to high number of genes associated with these disorders, standard diagnostic testing requires expensive and time consuming approaches using Sanger sequencing. In this study we show how targeted Next Generation Sequencing (NGS) technique can enable accurate, faster and cost-effective diagnosis of RASopathies.

Methods

In this study we used a validation set of 10 patients (6 positive controls previously characterized by Sanger-sequencing and 4 negative controls) to assess the analytical sensitivity and specificity of the targeted NGS. As second step, a training set of 80 enrolled patients with a clinical suspect of RASopathies has been tested. Targeted NGS has been successfully applied over 92% of the regions of interest, including exons for the following genes: PTPN11, SOS1, RAF1, BRAF, HRAS, KRAS, NRAS, SHOC, MAP2K1, MAP2K2, CBL.

Results

All expected variants in patients belonging to the validation set have been identified by targeted NGS providing a detection rate of 100%. Furthermore, all the newly detected mutations in patients from the training set have been confirmed by Sanger sequencing. Absence of any false negative event has been excluded by testing some of the negative patients, randomly selected, with Sanger sequencing.

Conclusion

Here we show how molecular testing of RASopathies by targeted NGS could allow an early and accurate diagnosis for all enrolled patients, enabling a prompt diagnosis especially for those patients with mild, non-specific or atypical features, in whom the detection of the causative mutation usually requires prolonged diagnostic timings when using standard routine. This approach strongly improved genetic counselling and clinical management.

Keywords:
Noonan syndrome; Next generation sequencing; Molecular diagnosis; RASopathies