PubMed Highlight: NGS in molecular diagnosis of Usher syndrome

An increasing number of papers have been published showing how NGS technology could now be effectively applied in the diagnosis of various genetic syndromes. Through WES or target resequencing, this technology could be particularly useful in the case of diseases characterized by an heterogeneous genetic background. However, there still are some limitations, mainly due to the need of a high coverage for a confident call of genetic variants. This issue is discussed in this interesting paper reporting molecular diagnosis of Usher syndrome using 3 different NGS platforms.

PLoS One. 2012;7(8):e43799. Epub 2012 Aug 29.

Molecular diagnosis of usher syndrome: application of two different next generation sequencing-based procedures.

Licastro D, Mutarelli M, Peluso I, Neveling K, Wieskamp N, Rispoli R, Vozzi D, Athanasakis E, D'Eustacchio A, Pizzo M, D'Amico F, Ziviello C, Simonelli F,Fabretto A, Scheffer H, Gasparini P, Banfi S, Nigro V.

Source

Cluster in Biomedicine (CBM) scrl - Genomics, Area Science Park, Basovizza, Trieste, Italy.

Abstract

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.