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What is Comparative Genomic Hybridization?

Comparative Genomic Hybridization (CGH) is a technique that allows the detection of copy number differences between two DNA samples, typically between mutant and wild-type genomes. For an excellent review of CGH and a variety its applications, see the following link.

Gresham et al. 2008
Comparing whole genomes using DNA microarrays. Nature Reviews Genetics

CGH for Deletion Detection

CGH is an powerful method of screening for novel induced deletions, as detailed in the following publication.

Maydan et al. 2007
Efficient high-resolution deletion discovery in Caenorhabditis elegans using oligonucleotide by Array Comparative Genomic Hybridization. Genome Research

Deletions screens can be done with our exon-centric Whole Genome Chip, or with custom chips to probe particular regions of interest with higher probe density. Our Whole Genome Chip targets 98% of the genes in the C. elegans genome, with an average of approximately 20 probes per gene and a median probe spacing of 289 bp.

CGH for SNP Detection

CGH can also be used to detect single nucleotide mutations and polymorphisms (SNPs) when the location of the mutation is known to within 1-2 Mbp, as described in the following publication. Certain types of transitions and transversions are easier than other to detect, and fortunately the mutations most commonly caused by EMS are among those that are easiest to detect. Mapping the mutation to an interval small enough to permit the use of this technique to locate the mutation is greatly simplified by SNP-CGH Mapping, described further below.

Maydan et al. 2009
De Novo Identification of Single Nucleotide Mutations in Caenorhabditis elegans Using Array Comparative Genomic Hybridization. Genetics

Probe Design and Data Analysis

To assist in using CGH for SNP Detection, we have mounted a web application that will generate a list of probes in a target region of your choice, in a file format suitable for submission to NimbleGen for array manufacture. A second application on this website will perform data analysis, calculating Log2Ratios and performing a simple LOESS normalization of the raw data from your experiment.

SNP Detection Website

SNP CGH Mapping

We have developed an easy, rapid and affordable method of mapping mutations that exploits the ability to detect SNPs using CGH. A single genetic cross of a mutant hermaphrodite and a Hawaiian (CB4856) male, followed by a CGH experiment, is sufficient to map a mutation to within 200 kb using this technique. A candidate region of this size more than sufficient to allow an attempt to detect the causative mutation using the SNP Detection method described above. See the following publication for more details.

Flibotte et al. 2008
Rapid high resolution single nucleotide polymorphism-comparative genome hybridization mapping in Caenorhabditis elegans. Genetics