Comparison of gene coverage of mouse oligonucleotide microarray platforms

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• The increasing use of DNA microarrays for genetical genomics studies necessitates platforms with comprehensive genome coverage.
• Evaluating effective gene coverage across different microarray platforms is crucial for accurate genetic research.

Purpose of the Study:

• To compare the effective gene coverage of various commercial and noncommercial oligonucleotide microarray platforms in the mouse genome.
• To develop a standardized method for assessing microarray probe annotation and gene targeting accuracy.

Main Methods:

• In-house gene annotation of probes using vendor-provided information.
• Annotation of microarray probes with Entrez Gene IDs and chromosomal positions from UCSC Genome Browser.
• Estimation of gene coverage as the percentage of unique Entrez Genes tested by each platform.

Main Results:

• A MySQL database was created mapping 25,416 mouse genes to probes across nine platforms.
• Sentrix (90.47%) and Operon v.4/MEEBO (84.03%) showed the highest mouse genome coverage.
• Significant variations in coverage, redundant probes, and unspecific probes were observed among platforms.

Conclusions:

• The developed software, ArrayGene, enables researchers to create custom databases and compare gene coverage across microarray platforms for any organism.
• The Sentrix commercial microarray, utilizing the MEEBO oligoset, provides the best available mouse genome coverage.
• Standardized vendor information guidelines are recommended for accurate platform evaluation.