Evaluation of low density array technology for quantitative parallel measurement of multiple genes in human tissue.
BACKGROUND
Low density arrays (LDAs) have recently been introduced as a novel approach to gene expression profiling. Based on real time quantitative RT-PCR (QRT-PCR), these arrays enable a more focused and sensitive approach to the study of gene expression than gene chips, while offering higher throughput than more established approaches to QRT-PCR. We have now evaluated LDAs as a means of determining the expression of multiple genes simultaneously in human tissues and cells.


RESULTS
Comparisons between LDAs reveal low variability, with correlation coefficients close to 1. By performing 2-fold and 10-fold serial dilutions of cDNA samples in the LDAs we determined a clear linear relationship between the gene expression data points over 5 orders of magnitude. We also showed that it is possible to use LDAs to accurately and quantitatively detect 2-fold changes in target copy number as well as measuring genes that are expressed with low and high copy numbers in the range of 1 x 10(2)-1 x 10(6) copies. Furthermore, the data generated by the LDA from a cell based pharmacological study were comparable to data generated by conventional QRT-PCR.


CONCLUSIONS
LDAs represent a valuable new approach for sensitive and quantitative gene expression profiling.
Goulter
Andrew B
AB
Pharmagene Laboratories Ltd, Royston, Hertfordshire, SG8 5HD, UK. andrew.goulter@pharmagene.com
Harmer
Daniel W
DW
Clark
Kenneth L
KL
D017931:DNA Primers; D004730:Endothelium, Vascular / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000032:analysis / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods; D013917:Thrombin / Q000494:pharmacology
D017931:DNA Primers; D012333:RNA, Messenger; D013917:Thrombin