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Defining best practice for microarray analyses in nutrigenomic studies

Published online by Cambridge University Press:  08 March 2007

Paola Garosi ,
Carlotta De Filippo ,
Marjan van Erk ,
Philippe Rocca-Serra ,
Susanna-Assunta Sansone  and
Ruan Elliott
Paola Garosi*
Affiliation:
Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK
Carlotta De Filippo
Affiliation:
Department of Pharmacology, University of Florence, Florence, Italy
Marjan van Erk
Affiliation:
TNO Nutrition and Food Research, PO Box 360, 3700 AJ, Zeist, The Netherlands
Philippe Rocca-Serra
Affiliation:
EMBL-EBI, The European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
Susanna-Assunta Sansone
Affiliation:
EMBL-EBI, The European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
Ruan Elliott
Affiliation:
Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK
*
*Corresponding author: Dr Paola Garosi, fax +44 (0) 1603 507723, email, paola.garosi@bbsrc.ac.uk
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Abstract

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Microarrays represent a powerful tool for studies of diet–gene interactions. Their use is, however, associated with a number of technical challenges and potential pitfalls. The cost of microarrays continues to drop but is still comparatively high. This, coupled with the complex logistical issues associated with performing nutritional microarray studies, often means that compromises have to be made in the number and type of samples analysed. Additionally, technical variations between array platforms and analytical procedures will almost inevitably lead to differences in the transcriptional responses observed. Consequently, conflicting data may be produced, important effects may be missed and/or false leads generated (e.g. apparent patterns of differential gene regulation that ultimately prove to be incorrect or not significant). This is likely to be particularly true in the field of nutrition, in which we expect that many dietary bioactive agents at nutritionally relevant concentrations will elicit subtle changes in gene transcription that may be critically important in biological terms but will be difficult to detect reliably. Thus, great care should always be taken in designing and executing microarray studies. This article seeks to provide an overview of both the main practical and theoretical considerations in microarray use that represent potential sources of technical variation and error. Wherever possible, recommendations are made on what we propose to be the best approach. The overall aims are to provide a basic framework of advice for researchers who are new to the use of microarrays and to promote a discussion of standardisation and best practice in the field.

Keywords

MicroarraysStandardisationStatistical analysisExperimental design
Type
Research Article
Information
British Journal of Nutrition , Volume 93 , Issue 4 , April 2005 , pp. 425 - 432
Copyright
Copyright © The Nutrition Society 2005

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