Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays

Authors

  • Marianne Tuefferd,

    Corresponding author
    1. JE2492 Department, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France
    • JE2492, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France, Europe
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    • These authors contributed equally to this work.

  • An De Bondt,

    1. Functional Genomics Department, Johnson & Johnson Pharmaceutical Research & Development, a Division of Janssen Pharmaceutica, Beerse, Belgium
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    • These authors contributed equally to this work.

  • Ilse Van Den Wyngaert,

    1. Functional Genomics Department, Johnson & Johnson Pharmaceutical Research & Development, a Division of Janssen Pharmaceutica, Beerse, Belgium
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  • Willem Talloen,

    1. Functional Genomics Department, Johnson & Johnson Pharmaceutical Research & Development, a Division of Janssen Pharmaceutica, Beerse, Belgium
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  • Tobias Verbeke,

    1. Business & Decision, Life Science Department, Benelux Division, Brussels, Belgium
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  • Benilton Carvalho,

    1. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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  • Djork-Arne Clevert,

    1. Institute of Bioinformatics, Johannes Kepler Universität Linz, Austria
    2. Department of Nephrology and Internal Intensive Care, Charité University Medicine, Berlin, Germany
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  • Marco Alifano,

    1. JE2492 Department, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France
    2. Department of Thoracic Surgery, Hôtel-Dieu Hospital, Paris V University, Paris, France
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  • Nandini Raghavan,

    1. Non-Clinical Biostatistics Department, Johnson & Johnson Pharmaceutical Research & Development, Raritan, NJ 08869, USA
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  • Dhammika Amaratunga,

    1. Non-Clinical Biostatistics Department, Johnson & Johnson Pharmaceutical Research & Development, Raritan, NJ 08869, USA
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  • Hinrich Göhlmann,

    1. Functional Genomics Department, Johnson & Johnson Pharmaceutical Research & Development, a Division of Janssen Pharmaceutica, Beerse, Belgium
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    • These authors contributed equally to this work.

  • Philippe Broët,

    1. JE2492 Department, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France
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    • These authors contributed equally to this work.

  • Sophie Camilleri-Broët

    1. JE2492 Department, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France
    2. Faculté Paris-Descartes, Assistance Publique - Hôpitaux de Paris (AP-HP), Paris, France
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    • These authors contributed equally to this work.


Abstract

SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. DNA from formalin-fixed paraffin-embedded material (FFPE) is partially degraded which limits the application of those technologies for retrospective studies. We present the use of Affymetrix GeneChip SNP6.0 for identification of copy number alterations in fresh frozen (FF) and matched FFPE samples. Fifteen pairs of adenocarcinomas with both frozen and FFPE embedded material were analyzed. We present an optimization of the sample preparation and show the importance of correcting the measured intensities for fragment length and GC-content when using FFPE samples. The absence of GC content correction results in a chromosome specific “wave pattern” which may lead to the misclassification of genomic regions as being altered. The highest concordance between FFPE and matched FF were found in samples with the highest call rates. Nineteen of the 23 high level amplifications (83%) seen using FF samples were also detected in the corresponding FFPE material. For limiting the rate of “false positive” alterations, we have chosen a conservative False Discovery Rate (FDR). We observed better results using SNP probes than CNV probes for copy number analysis of FFPE material. This is the first report on the detection of copy number alterations in FFPE samples using Affymetrix GeneChip SNP6.0. © 2008 Wiley-Liss, Inc.

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