Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip super( registered )platforms for the optimization of the assessment of expression patterns in non human primate (NHP) samples

• Published in: BMC bioinformatics Vol. 5
• Main Authors: Wang, Zhining, Lewis, Mark G, Nau, Martin E, Arnold, Alma, Vahey, Maryanne T
• Format: Journal Article
• Language: English
• Published: 01.01.2004
• ISSN: 1471-2105
• DOI: 10.1186/1471-2105-5-165

Background: While researchers have utilized versions of the Affymetrix human GeneChip super( registered )for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably hybridizing with their orthologs in NHP. By aligning probe sequences with expressed sequence tags (ESTs) in NHP, inter-species conserved (ISC) probesets, which have two or more probes complementary to ESTs in NHP, were identified on human GeneChip super( registered )platforms. The utility of human GeneChips super( registered )for the assessment of NHP expression patterns can be effectively evaluated by analyzing the hybridization behaviour of ISC probesets. Appropriate normalization methods were identified that further improve the reliability of human GeneChips super( registered )for interspecies (human vs NHP) comparisons. Results: ISC probesets in each of the seven Affymetrix GeneChip super( registered )platforms (U133Plus2.0, U133A, U133B, U95Av2, U95B, Focus and HuGeneFL) were identified for both monkey and chimpanzee. Expression data was generated from peripheral blood mononuclear cells (PBMCs) of 12 human and 8 monkey (Indian origin Rhesus macaque) samples using the Focus GeneChip super( registered ). Analysis of both qualitative detection calls and quantitative signal intensities showed that intra-species reproducibility (human vs. human or monkey vs. monkey) was much higher than interspecies reproducibility (human vs. monkey). ISC probesets exhibited higher interspecies reproducibility than the overall expressed probesets. Importantly, appropriate normalization methods could be leveraged to greatly improve interspecies correlations. The correlation coefficients between human (average of 12 samples) and monkey (average of 8 Rhesus macaque samples) are 0.725, 0.821 and 0.893 for MAS5.0 (Microarray Suite version 5.0), dChip and RMA (Robust Multi-chip Average) normalization method, respectively. Conclusions: It is feasible to use Affymetrix human GeneChip super( registered )platforms to assess the expression profiles of NHP for intra-species studies. Caution must be taken for interspecies studies since unsuitable probesets will result in spurious differentially regulated genes between human and NHP. RMA normalization method and ISC probesets are recommended for interspecies studies.