Determination of optimal microarray designs
Oligonucleotide microarray comparative genomic hybridization (CGH) is a powerful technique to measure DNA copy number in large genomes. Although various constraints on oligonucleotide properties have been suggested to minimize non-specific hybridization and improve the data quality, there have been few experimental validations for CGH experiments. We have determined experimentally the effects of varying several key oligonucleotide microarray design criteria for detection of deletions in C. elegans and humans with NimbleGen’s CGH technology. Our oligonucleotide design recommendations should be applicable for CGH analysis in most species.
Stephane Flibotte and Donald G. Moerman. (2008) Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization. BMC Genomics 9:497. PMID: 18940006 doi:10.1186/1471-2164-9-497
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