Title
Defining best practice for microarray analyses in nutrigenomic studies
Author
TNO Kwaliteit van Leven TNO Voeding
Garosi, P.
de Filippo, C.
van Erk, M.
Rocca-Serra, P.
Sansone, S.A.
Elliott, R.
Publication year
2005
Abstract
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. © The Authors 2005.
Subject
Biomedical Research
Experimental design
Microarrays
Standardisation
Statistical analysis
Diet
Image analysis
Microarray analysis
Nutrigenomics
Nutrition
RNA extraction
Standardization
Statistical analysis
Animal
DNA microarray
Image processing
Methodology
Animals
Data Interpretation, Statistical
Gene Expression Profiling
Genome
Humans
Image Processing, Computer-Assisted
Nutrition Physiology
Oligonucleotide Array Sequence Analysis
To reference this document use:
http://resolver.tudelft.nl/uuid:fc862770-981f-415a-bf23-426322644127
DOI
https://doi.org/10.1079/bjn20041385
TNO identifier
238996
ISSN
0007-1145
Source
British Journal of Nutrition, 93 (93), 425-432
Document type
article