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reagents are required beyond those found in a standard molecular genetics laboratory
( Kadandale et al., 2005 ).
There are however some drawbacks. The mapping resolution is dependent on the
availability of DNA sequence differences in the region of interest in the two strains.
Negative results can be ambiguous, especially if rare or low-fidelity enzymes are
used, which may require that additional control reactions be performed. This
approach works well with simple deletions, but not with duplications, translocations,
inversions, and complex deficiencies (indels).
B. Oligonucleotide Array Comparative Genome Hybridization (aCGH)
Complex rearrangements can be characterized on a genome-wide scale using
oligonucleotide array comparative genomic analysis (aCGH) ( Gresham et al.,
2008 ). aCGH is a technology used for high-resolution mapping of chromosomal
copy number variation (CNV) at a genome-wide scale by comparing the ratio of
DNA between two samples from the same organism ( Dhami et al., 2005; Selzer
et al., 2005 ).
The development of a C. elegans specific aCGH platform for identification of
novel single-gene deletions has represented a powerful technology that can be
adapted to the rapid and precise characterization of deficiency mapping strains
( Maydan et al., 2007 ). Currently, aCGH has been used to analyze the structure of
deficiencies and duplications on chromosome III ( Jones et al., 2007 ), chromosome
V( Jones et al., 2009; Zhao et al., 2008 ), and chromosome IV (D. Baillie, pers.
comm.).
Determining the extent of duplications or deletions using aCGH is straightforward
requiring only a sample of genomic DNA from the deficiency strain and a reference
strain. The sensitivity of this approach is sufficient for the analysis of heterozygous
animals ( Maydan et al., 2007 ). This means that the relatively large amount of
genomic DNA required for the hybridization can be easily isolated from balanced
rearrangements strains ( Jones et al., 2007 ). Using available software to visualised
hybridization data CNVs can normally be detected without the need for statistical
analysis or trained personnel. Precise breakpoint positions can be validated using
methods such as PCR ( Jones et al., 2007 )( Fig. 8 ).
1. Advantages and Disadvantages
aCGH is relatively straightforward and at less than $1000 per chip is cost-effective
considering the quantity and resolution of the information attained. Very high-
resolution chips with probes for every kilobase (kb) are available and new high-
density arrays with overlapping probes giving bp resolution for the entire genome
have been developed ( NimbleGenSystemsInc. ). The results can be readily visualized
without the need for statistical analysis. It is fast and breakpoint confirmation takes
only a few weeks to obtain. Finally, little or no previous knowledge about the
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