Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 3' expression arrays

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Standard gene expression arrays often use 3' end interrogation.
• Newer arrays interrogate entire mRNA transcripts and may use DNA targets.

Purpose of the Study:

• To evaluate the performance of the Affymetrix Human Gene 1.0 ST array.
• To compare its reproducibility and concordance with other platforms (Affymetrix HG-U133 Plus 2.0, Illumina HumanRef-8 BeadChip).
• To assess the impact of RNA vs. DNA targets on array performance.

Main Methods:

• Comparative hybridizations using Affymetrix Human Gene 1.0 ST, Affymetrix HG-U133 Plus 2.0, and Illumina HumanRef-8 BeadChip arrays.
• Hybridization of both RNA (cDNA) and DNA targets on HG-U133 Plus 2.0 arrays.
• Assessment of reproducibility and inter-platform concordance using various mapping strategies.

Main Results:

• The Human Gene 1.0 ST array demonstrated the highest overall reproducibility.
• High-intensity probe reproducibility was comparable between the Gene 1.0 ST and Illumina BeadChip arrays.
• The Gene 1.0 ST array showed the best concordance with HG-U133 arrays hybridized with cDNA targets, suggesting target type influences results.

Conclusions:

• The Affymetrix Human Gene 1.0 ST array exhibits excellent reproducibility and reliability.
• The use of DNA targets and full-length transcript interrogation contributes to its robust performance.
• This array represents a reliable tool for comprehensive gene expression profiling.