Usher syndrome (USH) is a clinically and genetically heterogeneous disorder 
characterized by visual and hearing impairments. Clinically, it is subdivided 
into three subclasses with nine genes identified so far. In the present study, 
we investigated whether the currently available Next Generation Sequencing (NGS) 
technologies are already suitable for molecular diagnostics of USH. We analyzed 
a total of 12 patients, most of which were negative for previously described 
mutations in known USH genes upon primer extension-based microarray genotyping. 
We enriched the NGS template either by whole exome capture or by Long-PCR of the 
known USH genes. The main NGS sequencing platforms were used: SOLiD for whole 
exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the 
Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH 
gene regions displaying an overall coverage higher than 25×, whereas whole exome 
sequencing yielded a similar coverage for only 50% of those regions. Overall 
this integrated analysis led to the identification of 11 novel sequence 
variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. 
However, at least two cases were not genetically solved. Our result highlights 
the current limitations in the diagnostic use of NGS for USH patients. The limit 
for whole exome sequencing is linked to the need of a strong coverage and to the 
correct interpretation of sequence variations with a non obvious, pathogenic 
role, whereas the targeted approach suffers from the high genetic heterogeneity 
of USH that may be also caused by the presence of additional causative genes yet 
to be identified.