The impact of microarray probe design on detecting copy number variants at exon-resolution

Friday 13 October 2017

CytoSure™ arrays offer robust copy-number detection with high resolution – detecting CNVs of a few hundred base pairs at the single-exon level. However, a number of different factors need to be taken into account when designing microarrays to make sure that they offer robust performance across the targeted regions. Learn more about the process that we undertake to make sure our arrays perform the best they possibly can.


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.


  1. Kearny, H.M. et al (2011) American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities. Genome in Medicine 13 p676-685
  2. Poultney C.S. et al (2013) Identification of Small Exonic CNV from Whole-Exome Sequence Data and Application to Autism Spectrum Disorder. AJHG Vol 93(4), 607-619
  3. Aradhya S. et al (2012) Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders. Genetics IN Medicine 14, 594–603
  4. Askree S.H. et al (2013) Detection limit of intragenic deletions with targeted array comparative genomic hybridization. BMC Genetics 14:116


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