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Acute Leukemias

Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks

Leukemia volume 20, pages 1385–1392 (2006)Cite this article

Abstract

A plethora of studies have documented that gene expression profiling using DNA microarrays for various types of hematological malignancies provides novel information, which may have diagnostic and prognostic implications. However, to successfully use microarrays for this purpose, the quality and reproducibility of the whole procedure need to be guaranteed. Critical steps of the method are handling, processing and storage of the leukemic sample, purification of tumor cells (or lack thereof), RNA extraction methods, quality control of RNA, labeling techniques, hybridization, washing, scanning, spot filtering, normalization and initial interpretation, and finally the biostatistical analysis. These items have been extensively discussed and evaluated in different multi-center quality rounds within the three networks, that is, I-BFM-SG, the German Competence Network ‘Acute and Chronic Leukemias’ and the European LeukemiaNet. Based on the exchange of knowledge and experience between the three networks over the last few years, we have formulated guidelines for performing microarray experiments in leukemia. We confine ourselves to leukemias, but many of these requirements also apply to lymphomas or other clinical samples, including solid tumors.

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Acknowledgements

The excellent technical assistance of Marcel Tauscher in performing the multi-center quality rounds is gratefully acknowledged. Dick de Ridder is acknowledged for his expert opinion on bioinformatical software packages. The activities of the Genomics/Proteomics project of the German Competence Network ‘Acute and Chronic Leukemias’ have been supported by BMBF Grant 01GI0378.

Author information

Author notes

  1. F J T Staal, G Cario, G Cazzaniga, M Schrappe, M Stanulla and J J M van Dongen: On behalf of: I-BFM-SG Task Force on gene expression profiling.

  2. F J T Staal and G Cario: These authors contributed equally to this work (Appendix A).

  3. T Haferlach, M Heuser, W-K Hofmann, L U Wingen and B Schlegelberger: On behalf of: Genomics/Proteomics group of the German Competence Network ‘Acute and Chronic Leukemias’ (Appendix A).

  4. T Haferlach, W-K Hofmann and K Mills: On behalf of: WP13 Gene Profiling of European LeukemiaNet (Appendix A).

Authors and Affiliations

  1. Department of Immunology, Erasmus Medical Center, Rotterdam, The Netherlands

    F J T Staal & J J M van Dongen

  2. General Pediatric Clinic, University of Schleswig-Holstein, Kiel, Germany

    G Cario & M Schrappe

  3. Pediatric Clinic, University of Milan, Monza, Italy

    G Cazzaniga

  4. MLL Münchner Leukämielabor GmbH, Munich, Germany

    T Haferlach

  5. Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany

    M Heuser, L U Wingen & B Schlegelberger

  6. Medical Clinic III, Charité, Campus Benjamin Franklin, Berlin, Germany

    W-K Hofmann

  7. Department of Haematology, Wales College of Medicine, University of Cardiff, Cardiff, UK

    K Mills

  8. Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany

    M Stanulla

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  1. F J T Staal
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Corresponding author

Correspondence to B Schlegelberger.

Appendix A

Appendix A

I-BFM-SG Task Force on gene expression profiling: G Cario, Kiel (DE); G Cazzaniga, Monza (IT); J Cloos, Amsterdam (NL); M den Boer, Rotterdam (NL); A Hall, Newcastle (UK); J Harbott, Giessen (DE); J Irving, Newcastle (UK); S Izraeli, Tel Aviv (IL); F Niggli, Zurich (CH); U Ozbek, Istanbul (TR); B Schaefer, Zurich (CH); FJT Staal, Rotterdam (NL); MS Staege, Halle (DE); M Stanulla, Hannover (DE); G te Kronnie, Padua (IT); O Teuffel, Zurich (CH); F van Delft, London (UK); JJM van Dongen, Rotterdam (NL); M Zwaan, Amsterdam (NL). Genomics/ Proteomics group of the German Competence Network ‘Acute and Chronic Leukemias’: S Balabanov, Tübingen; TH Brümmendorf, Tübingen; L Bullinger, Ulm; H Döhner, Ulm; J Duyster, München; R Eils, Heidelberg; O Frank, Mannheim; T Haferlach, München; R Hehlmann, Mannheim; M Heuser, Hannover; A Hochhaus, Mannheim; W-K Hofmann, Berlin/Frankfurt; P Lichter, Heidelberg; A Neubauer, Marburg; M Ritter, Marburg; B Schlegelberger, Hannover; C Schoch, München; W Seifarth, Mannheim; M Tauscher, Hannover; C Thiede, Dresden; N von Bubnoff, München; LU Wingen, Hannover; C Zheng, Mannheim. WP13 Gene Profiling of European LeukemiaNet: T Haferlach, Munich (DE); G Basso, Padova (IT); MC Bené, Nancy (FR); L Bullinger, Ulm (DE); S Chiaretti, Rome (IT); H Döhner, Ulm (DE); M Dugas, Munich (DE); S Ferrari, Modena (IT); R Foa, Rome (IT); JM Hernandez Rivas, Salamanca (ES); W-K Hofmann, Berlin (DE); JH Jansen, Nijmegen (NL); A Kohlmann, Munich (DE); G te Kronnie, Padua (IT); E Macintyre, Paris (FR); JV Melo, London (UK); K Mills, Cardiff (UK); A Neubauer, Marburg (DE); C Preudhomme, Lille (FR); B Schlegelberger, Hannover (DE); W Seifarth, Mannheim (DE); J de Vos, Montpellier (FR); BD Young, London (UK).

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Staal, F., Cario, G., Cazzaniga, G. et al. Consensus guidelines for microarray gene expression analyses in leukemia from three European leukemia networks. Leukemia 20, 1385–1392 (2006). https://doi.org/10.1038/sj.leu.2404274

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