Selecting the right CytoSure array format for your study

Selecting the optimum array format for your study depends on a number of factors, including the application, the desired data resolution and the available budget. Many pre-designed arrays are now available for various applications; however, these may not always be appropriate for high-resolution or high-throughput studies of specific genomic regions of interest. At Oxford Gene Technology (OGT), we have extensive experience of designing and running tens of thousands of arrays. This article details the different array formats available through our CytoSure™ product range (Figure 1) and their benefits for different study designs.

Figure 1: Flexible array formats to suit all requirements

Array comparative genomic hybridisation (aCGH) or copy number variation (CNV) applications

aCGH is now recognised as the gold-standard approach to identifying DNA CNV¹. The choice of array is primarily decided by the type of study being undertaken and the number of samples to be analysed.

Genome-wide studies

Higher resolution array formats, such as the 1x1M or 2x400k arrays, are often chosen for genome-wide discovery studies. Such arrays offer more content and less spacing between probes allowing the whole genome to be examined in as much detail as possible. Such high-resolution arrays are ideal for identifying novel regions of copy number changes. OGT offer these array formats as part of our CytoSure custom design service allowing complete flexibility in probe content and design.

Focused studies

For large-scale studies examining regions of known genomic variation, the 8x and the 4x array formats are a popular choice. We use these formats for our focused CytoSure catalogue arrays, including the CytoSure Aneuploidy array. This array uses the 8x15k format which allows multiple samples to be processed in a cost efficient manner.  Although low resolution, this is perfectly suited to the application — the detection of whole chromosome gains and losses in miscarriage samples. These formats are both informative and more cost-effective than using high-resolution but low multiplexing arrays. The probe density, and therefore spacing of the probes, is defined by the array format. The 8x60k array offers a lower resolution compared to the 4x180k array, so many researchers will consider the 4x180k array format — which offers increased probe resolution but lower sample throughput and therefore moderately increased costs. These formats are also a popular choice for custom arrays especially for focussed studies.  Such studies are made possible through the facility to create custom arrays containing high probe density designed against the genomic regions of interest. OGT has designed hundreds of array CGH arrays utilizing this approach; please contact us for more details.

Combination approach

A different approach is to use a combination of focused and genome-wide probe design. This type of array provides researchers with high probe density across genomic regions of interest coupled with a lower density genomic ‘backbone’ of probes enabling  discovery of novel variants outside of the specific regions of interest. This type of array design typically utilises the 8x60k or 4x180k format. OGT’s CytoSure ISCA arrays for detection of cytogenetic aberrations are examples of this array design strategy. The combination approach is also often used in custom studies because of the flexible but cost efficient design strategy, allowing the detection of small aberrations in defined regions while ensuring that larger aberrations in the rest of the genome are not missed.

For more information on the available OGT catalogue arrays (Table 1), or our custom array design service, please contact us.

Table 1: CytoSure catalogue arrays

Summary

 Microarrays are a powerful and truly flexible technology for studying copy number changes. Selecting the right array format is imperative to ensure cost-effective delivery of informative results.OGT's proven track record in microarray technology and services — combined with our highly skilled bioinformatics team allows us to provide you with the right array to ensure you achieve the highest quality data. In addition to providing the complete solution for aCGH processing in your lab — including arrays, DNA labelling kits, software and automation — we also offer CytoSure Services for high-quality processing of your samples in our purpose-built, state-of-the-art laboratories. CytoSure Services operate under an ISO9001:2008 and ISO27001:2005 certified management system and are also accredited to ISO/IEC 17025:2005 — one of the highest accreditations attainable by an analytical genomic services laboratory.

For complete peace-of-mind, trust your project to OGT and benefit from our experienced, expert staff and thorough quality management processes.

Find out more about CytoSure products and CytoSure Services

 References:

1. Curtis, C. et al (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10, 588-610

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