Background: Automated DNA sequencing produces large amounts of data that need to be analyzed by appropriate software. Personalization of software can be a difficult and time-consuming task, especially if a large number of mutations have to be analyzed. Methods: The Applied BioSystems SeqScape software, based on the KB basecaller algorithm, is a versatile tool that can be used for mutational analysis and for data quality assessment of sequences belonging to any gene of interest. Using this software we analyzed over 1400 sequences of CFTR exons and adjacent intronic zones, representing over 500,000 bases. Results: We present an up to date specific template and a linked set of instructions for automated labeling of all point mutations and polymorphisms of the CFTR gene, whose mutations cause cystic fibrosis (the most common genetic disease among Caucasian individuals). We also describe our refined software settings for mutational analysis, in order to keep to a minimum the need of manual validation. Conclusions: The use of our template greatly simplifies the mutational analysis of the CFTR gene, reducing human intervention. In our opinion, it might not only be useful to researchers that already perform CFTR mutational analysis by sequencing methods but it should also improve the approach in those laboratories that already use ABI PRISM instrumentation for a limited mutational analysis of the CFTR gene. Similar mutational templates can also be used for other disease causing genes, thus improving molecular genetics protocols.

A template for mutational data analysis of the CFTR gene / Ferraguti, Giampiero; Pierandrei, Silvia; Bruno, SABINA MARIA; Ceci, Fabrizio; Strom, Roberto; Lucarelli, Marco. - In: CLINICAL CHEMISTRY AND LABORATORY MEDICINE. - ISSN 1434-6621. - STAMPA. - 49:9(2011), pp. 1447-1451. [10.1515/cclm.2011.604]

A template for mutational data analysis of the CFTR gene

FERRAGUTI, Giampiero;PIERANDREI, SILVIA;BRUNO, SABINA MARIA;CECI, Fabrizio;STROM, Roberto;LUCARELLI, Marco
2011

Abstract

Background: Automated DNA sequencing produces large amounts of data that need to be analyzed by appropriate software. Personalization of software can be a difficult and time-consuming task, especially if a large number of mutations have to be analyzed. Methods: The Applied BioSystems SeqScape software, based on the KB basecaller algorithm, is a versatile tool that can be used for mutational analysis and for data quality assessment of sequences belonging to any gene of interest. Using this software we analyzed over 1400 sequences of CFTR exons and adjacent intronic zones, representing over 500,000 bases. Results: We present an up to date specific template and a linked set of instructions for automated labeling of all point mutations and polymorphisms of the CFTR gene, whose mutations cause cystic fibrosis (the most common genetic disease among Caucasian individuals). We also describe our refined software settings for mutational analysis, in order to keep to a minimum the need of manual validation. Conclusions: The use of our template greatly simplifies the mutational analysis of the CFTR gene, reducing human intervention. In our opinion, it might not only be useful to researchers that already perform CFTR mutational analysis by sequencing methods but it should also improve the approach in those laboratories that already use ABI PRISM instrumentation for a limited mutational analysis of the CFTR gene. Similar mutational templates can also be used for other disease causing genes, thus improving molecular genetics protocols.
2011
automated sequence analysis; cftr mutational analysis; cystic fibrosis; seqscape software
01 Pubblicazione su rivista::01a Articolo in rivista
A template for mutational data analysis of the CFTR gene / Ferraguti, Giampiero; Pierandrei, Silvia; Bruno, SABINA MARIA; Ceci, Fabrizio; Strom, Roberto; Lucarelli, Marco. - In: CLINICAL CHEMISTRY AND LABORATORY MEDICINE. - ISSN 1434-6621. - STAMPA. - 49:9(2011), pp. 1447-1451. [10.1515/cclm.2011.604]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11573/377194
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