A large resource of deletion strains (also known as genetic deficiencies) accounting for over 70% of the Caenorhabditis elegans genome has been generated by various research groups over the past three decades . These genetic deficiencies have proven advantageous for a variety of purposes including; characterization of mutant alleles , identification of specific loci affecting developmental processes , investigation of genome replication and stability [4, 5] and, most significantly, as tools for positional cloning of unmapped mutations to discrete regions of the genome [1, 6–8].
The full potential of these biological tools has however been limited due to the lack of high resolution characterization at a genome wide scale. The mapping of physical breakpoint positions within each deficiency strain is required to allow the deleted gene complement for that strain to be precisely defined. Additionally, genetic deficiencies may exhibit molecular complexity preventing their reliable use in mapping experiments .
Previously, characterization of genetic deficiencies has been performed by fairly low resolution or labor intensive techniques such as genetic linkage mapping, PCR analysis  and, more recently, by the application of snip-SNP [9, 10] and as a consequence many available deficiency strains remain poorly characterized.
Oligonucleotide array Comparative Genomic Analysis (oaCGH) is an emerging technology for high resolution mapping of chromosomal copy number changes at a genome wide scale through the comparison of the DNA ratio between two samples from the same organism [11, 12]. The recent development of a C. elegans specific oaCGH platform for identification of novel single gene deletions  represents a powerful technology that can be adapted to the rapid and precise characterization of deficiency mapping strains.
In this study we demonstrate the successful application of oaCGH to the physical characterization of deficiency strains in C. elegans. We use this data to annotate a physical deficiency map within a 5 Mb region of chromosome III and demonstrate the application of this map to aid in the molecular identification of previously generated mutations known to reside within this region.