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Assessing the Enrichment Performance in Targeted Resequencing Experiments

Authors

  • Peter Frommolt,

    Corresponding author
    1. Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Universität zu Köln, Cologne, Germany
    2. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
    • Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Universität zu Köln, Cologne, Germany.
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  • Ali T. Abdallah,

    1. Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Universität zu Köln, Cologne, Germany
    2. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
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  • Janine Altmüller,

    1. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
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  • Susanne Motameny,

    1. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
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  • Holger Thiele,

    1. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
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  • Christian Becker,

    1. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
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  • Kathryn Stemshorn,

    1. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
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  • Matthias Fischer,

    1. Klinik und Poliklinik für Kinderheilkunde, Abteilung für Pädiatrische Onkologie und Hämatologie, Klinikum der Universität zu Köln, Cologne, Germany
    2. Zentrum für Molekulare Medizin Köln (ZMMK), Universität zu Köln, Cologne, Germany
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  • Tobias Freilinger,

    1. Neurologische Klinik und Poliklinik, Klinikum Großhadern, München, Germany
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  • Peter Nürnberg

    1. Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Universität zu Köln, Cologne, Germany
    2. Cologne Center for Genomics (CCG), Universität zu Köln, Cologne, Germany
    3. Zentrum für Molekulare Medizin Köln (ZMMK), Universität zu Köln, Cologne, Germany
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  • Communicated Graham R. Taylor

Abstract

Target enrichment strategies are a very common approach to sequence a predefined part of an individual's genome using second-generation sequencing technologies. While highly dependent on the technology and the target sequences selected, the performance of the various assays is also variable between samples and is influenced by the way how the libraries are handled in the laboratory. Here, we show how to find detailed information about the enrichment performance using a novel software package called NGSrich, which we developed as a part of a whole-exome resequencing pipeline in a medium-sized genomics center. Our software is suitable for high-throughput use and the results can be shared using HTML and a web server. Finally, we have sequenced exome-enriched DNA libraries of 18 human individuals using three different enrichment products and used our new software for a comparative analysis of their performance. Hum Mutat 33:635–641, 2012. © 2012 Wiley Periodicals, Inc.

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