Title | Comparison of the latest commercial short and long oligonucleotide microarray technologies. |
Publication Type | Journal Article |
Year of Publication | 2006 |
Authors | de Reyniès A, Geromin D, Cayuela J-M, Petel F, Dessen P, Sigaux F, Rickman DS |
Journal | BMC Genomics |
Volume | 7 |
Pagination | 51 |
Date Published | 2006 Mar 15 |
ISSN | 1471-2164 |
Keywords | Cell Line, Tumor, Cluster Analysis, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Reproducibility of Results |
Abstract | BACKGROUND: We compared the relative precision and accuracy of expression measurements obtained from three different state-of-the-art commercial short and long-oligonucleotide microarray platforms (Affymetrix GeneChip, GE Healthcare CodeLink and Agilent Technologies). The design of the comparison was chosen to judge each platform in the context of a multi-project program. RESULTS: All wet-lab experiments and raw data acquisitions were performed independently by each commercial platform. Intra-platform reproducibility was assessed using measurements from all available targets. Inter-platform comparisons of relative signal intensities were based on a common and non-redundant set of roughly 3,400 targets chosen for their unique correspondence toward a single transcript. Despite many examples of strong similarities we found several areas of discrepancy between the different platforms. CONCLUSION: We found a higher level of reproducibility from one-color based microarrays (Affymetrix and CodeLink) compared to the two-color arrays from Agilent. Overall, Affymetrix data had a slightly higher level of concordance with sample-matched real-time quantitative reverse-transcriptase polymerase chain reaction (QRT-PCR) data particularly for detecting small changes in gene expression levels. |
DOI | 10.1186/1471-2164-7-51 |
Alternate Journal | BMC Genomics |
PubMed ID | 16539734 |
PubMed Central ID | PMC1473202 |
Related Faculty:
David Rickman, Ph.D.