摘要
Several nuclear genes have been found to be linked to ichthyosis, and Next Generation Sequencing approach on panels of targeted genes has turned out to be particularly useful in analyzing diseases characterized by significant genetic and phenotypic heterogeneity. We developed a panel of 26 genes to be screened with the Ion Personal Genome Machine (PGM) for causative mutations relating to ichthyosis. Sequencing runs were obtained from a patient with ichthyosis using the Ion Torrent PGM and then processed with Ion Torrent Suite, Variant Caller, Coverage Analysis and wANNOVER tools. No causative mutations were found using Variant Caller and wANNOVER softwares, whereas the “Coverage Analysis” tool revealed a common large deletion in STS gene in a patient with X-linked ichthyosis. Identification of indels in Next Generation Sequencing (NGS) data is a veritable challenge. This study demonstrates the efficacy and effectiveness of using NGS approach to detect large deletions without resorting to specific algorithms for “indel” detection. Our results indicate that the NGS panel is a useful, rapid and cost-effective screening test for patients whose features are suggestive of a genetic etiology involving one of the genes embedded in the panel. It is an excellent alternative to Sanger sequencing as for costs, ease of analysis, and turnaround time.
Several nuclear genes have been found to be linked to ichthyosis, and Next Generation Sequencing approach on panels of targeted genes has turned out to be particularly useful in analyzing diseases characterized by significant genetic and phenotypic heterogeneity. We developed a panel of 26 genes to be screened with the Ion Personal Genome Machine (PGM) for causative mutations relating to ichthyosis. Sequencing runs were obtained from a patient with ichthyosis using the Ion Torrent PGM and then processed with Ion Torrent Suite, Variant Caller, Coverage Analysis and wANNOVER tools. No causative mutations were found using Variant Caller and wANNOVER softwares, whereas the “Coverage Analysis” tool revealed a common large deletion in STS gene in a patient with X-linked ichthyosis. Identification of indels in Next Generation Sequencing (NGS) data is a veritable challenge. This study demonstrates the efficacy and effectiveness of using NGS approach to detect large deletions without resorting to specific algorithms for “indel” detection. Our results indicate that the NGS panel is a useful, rapid and cost-effective screening test for patients whose features are suggestive of a genetic etiology involving one of the genes embedded in the panel. It is an excellent alternative to Sanger sequencing as for costs, ease of analysis, and turnaround time.
作者
Francesco Calì
Giuseppa Maria Luana Mandarà
Giuseppa Ruggeri
Corrado Romano
Valeria Chiavetta
Alda Ragalmuto
Roberto Salluzzo
Valentino Romano
Marilena Galati Tardanico
Carmelo Schepis
Francesco Calì;Giuseppa Maria Luana Mandarà;Giuseppa Ruggeri;Corrado Romano;Valeria Chiavetta;Alda Ragalmuto;Roberto Salluzzo;Valentino Romano;Marilena Galati Tardanico;Carmelo Schepis(Laboratory of Molecular Genetics, Unit of Medical Genetics, IRCCS Associazione Oasi Maria SS., Troina (EN), Italy;Unit of Medical Genetics, Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy;Unit of Paediatrics and Medical Genetics, IRCCS Associazione Oasi Maria SS., Troina (EN), Italy;Department of Physics and Chemistry, University of Palermo, Palermo, Italy;Unit of Dermatology, IRCCS Associazione Oasi Maria SS., Troina (EN), Italy)
