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ICO Amplicon NGS Data Analysis: A Web Tool for Variant Detection in Common High-Risk Hereditary Cancer Genes Analyzed by Amplicon GS Junior Next-Generation Sequencing

Authors

  • Adriana Lopez-Doriga,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
    2. Prevention Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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  • Lídia Feliubadaló,

    Corresponding author
    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
    • Correspondence to: Lídia Feliubadaló, Unitat de Diagnòstic Molecular, Programa de Càncer Hereditari, Laboratori de Recerca Translacional 2, Institut Català d'Oncologia (ICO-IDIBELL), Hospital Duran i Reynals, Gran Via 199-203, L'Hospitalet de Llobregat, Barcelona 08908, Spain. E-mail: lfeliubadalo@iconcologia.net

      Correspondence to: Conxi Lázaro, Unitat de Diagnòstic Molecular, Programa de Càncer Hereditari, Laboratori de Recerca Translacional 2, Institut Català d'Oncologia (ICO-IDIBELL), Hospital Duran i Reynals, Gran Via 199-203, L'Hospitalet de Llobregat, Barcelona 08908, Spain. E-mail: clazaro@iconcologia.net

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  • Mireia Menéndez,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Sergio Lopez-Doriga,

    1. Facultat d'Ingenieria Industrial, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
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  • Francisco D. Morón-Duran,

    1. Prevention Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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  • Jesús del Valle,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Eva Tornero,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Eva Montes,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Raquel Cuesta,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Olga Campos,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Carolina Gómez,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Marta Pineda,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Sara González,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Victor Moreno,

    1. Prevention Program, Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
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  • Gabriel Capellá,

    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
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  • Conxi Lázaro

    Corresponding author
    1. Hereditary Cancer Program, Catalan Institute of Oncology, L'Hospitalet de Llobregat, Barcelona, Spain
    • Correspondence to: Lídia Feliubadaló, Unitat de Diagnòstic Molecular, Programa de Càncer Hereditari, Laboratori de Recerca Translacional 2, Institut Català d'Oncologia (ICO-IDIBELL), Hospital Duran i Reynals, Gran Via 199-203, L'Hospitalet de Llobregat, Barcelona 08908, Spain. E-mail: lfeliubadalo@iconcologia.net

      Correspondence to: Conxi Lázaro, Unitat de Diagnòstic Molecular, Programa de Càncer Hereditari, Laboratori de Recerca Translacional 2, Institut Català d'Oncologia (ICO-IDIBELL), Hospital Duran i Reynals, Gran Via 199-203, L'Hospitalet de Llobregat, Barcelona 08908, Spain. E-mail: clazaro@iconcologia.net

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  • Contract grant sponsors: the Spanish Ministry of Health ISCIII FIS grants (PI10/01422, PI13/00285, CA10/01474, RD06/0020/1050, RD12/0036/008 and RD12/0036/0031); the AGAUR Catalan Government Agency grants 2009-SGR293; the Spanish Association Against Cancer (AECC 2010).

  • Communicated by Madhuri Hegde

ABSTRACT

Next-generation sequencing (NGS) has revolutionized genomic research and is set to have a major impact on genetic diagnostics thanks to the advent of benchtop sequencers and flexible kits for targeted libraries. Among the main hurdles in NGS are the difficulty of performing bioinformatic analysis of the huge volume of data generated and the high number of false positive calls that could be obtained, depending on the NGS technology and the analysis pipeline. Here, we present the development of a free and user-friendly Web data analysis tool that detects and filters sequence variants, provides coverage information, and allows the user to customize some basic parameters. The tool has been developed to provide accurate genetic analysis of targeted sequencing of common high-risk hereditary cancer genes using amplicon libraries run in a GS Junior System. The Web resource is linked to our own mutation database, to assist in the clinical classification of identified variants. We believe that this tool will greatly facilitate the use of the NGS approach in routine laboratories.

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