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The analysis of structural variants, such as copy number variants (CNVs), is an important aspect of clinical genetics research. Whilst many technologies are used for determining CNVs in human DNA, array comparative genomic hybridisation (aCGH) is now established as the gold standard for detection of CNVs across the entire genome, and is used not just in research but also in clinical applications1.

As microarray technology has evolved, the resolution at which CNVs can be detected has steadily increased. Despite this, the design strategy behind many microarray designs has made it difficult or impossible to find aberrations smaller than ~30kb2, despite the fact that smaller aberrations have been demonstrated to be relevant in Mendelian disorders3. In order to tackle this problem, sophisticated probe design approaches have been developed over the last few years, and have made it possible to increase the resolution of arrays much further – targeting important genetic loci in such a way that CNVs can be found even at the exon-level4.

However, in order to develop arrays that can robustly analyse CNVs at this size, a number of factors need to be taken into account during the design process.

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