Selecting the right array format for your study

Monday 22 August 2011

Nicole Sparkes - Head of High-Throughput Services

Selecting the optimum array format for your study depends on a number of factors, including the application required, the desired data resolution and the available budget. Many pre-designed arrays are now available for various applications and species; however, these may not always be appropriate for high-resolution or high-throughput studies of specific genomic regions or species 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 Genefficiency Genomic Services (Figure 1) and their benefits for different applications.

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Figure 1: Flexible array formats to suit all requirements

Array comparative genomic hybridisation (aCGH) for 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 (Table 1). Such high-resolution arrays are ideal for identifying novel regions of copy number changes.

Table 1: Probe spacing in Agilent Human Genome CGH Microarrays

Array FormatMedian probe spacing
1x1M 2.1 kb
2x400k 5.3 kb
1x244k 8.9 kb
4x180k 13 kb
2x105k 22 kb
8x60k 41 kb
4x44k 43 kb

Focused studies

For large-scale studies examining regions of known genomic variation, the 8x60k array format is a popular choice. Such studies are made possible though the facility to create custom arrays containing very high probe density designed against the genomic regions of interest. These are therefore both more informative and more cost-effective than using high-resolution genome-wide catalogue arrays. The probe density, and therefore spacing of the probes, is defined by the size of the region being studied. If the region under investigation is too large for adequate probe coverage in an 8x60k array, many researchers will consider the 4x180k array format — which offers increased probe resolution but lower sample throughput and therefore moderately increased costs. OGT has designed hundreds of array CGH arrays, 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. For more information on the available OGT and Agilent catalogue arrays (Table 2), or our custom array design service, please contact us.

Table 2: OGT and Agilent aCGH arrays

ApplicationOrganismArray format(s)
aCGH Human 4x44k, 8x60k, 2x105k, 4x180k,1x244k, 2x400k, 1x1M
aCGH Mouse 2x105k, 4x180k, 1x244k,1x1M
aCGH Rat 2x105k, 4x180k, 1x244k,1x1M
aCGH Other (please enquire) Please enquire

 

Methylation

Arrays for detecting DNA methylation status can be designed and selected in much the same way as CGH arrays. A number of Agilent catalogue genome-wide designs covering CPG island and promoter regions are available (Table 3). Alternatively, researchers who are interested in specific regions may choose a more cost-effective custom array design allowing both higher resolution coverage of specific genomic regions enabling higher sample throughput. For more information about the Agilent methylation arrays, or our custom array design service, please contact us.

Table 3: Agilent DNA methylation arrays

ApplicationOrganismArray format(s)
CpG island Human 1x244k
CpG island Mouse 2x105k
Promoter Human 1x244k, 2x400k, 1x1M
Promoter Mouse 1x244k, 2x400k, 1x1M

miRNA and gene expression

As with other microarray applications, a number of pre-designed catalogue whole transcriptome gene expression and miRNA arrays are available for many model organisms (Table 4). Most researchers select whole transcriptome designs as they are available on the more cost-effective 4x and 8x formats, enabling large-scale screening and discovery projects. OGT can also provide custom array designs for novel organisms or targeted designs such as specific high-resolution exon designs to focus on known areas of interest.

Table 4: Agilent miRNA and gene expression arrays

ApplicationOrganismArray format(s)
miRNA Human 8x15k, 8x60k
miRNA Mouse 8x15k, 8x60k
miRNA Rat 8x15k
Gene expression (exon) Human 4x180k, 2x400k
Gene expression (mRNA) Human 4x44k, 8x60k
Gene expression (exon) Mouse 4x180k, 2x400k
Gene expression (mRNA) Mouse 4x44k, 8x60k
Gene expression (exon) Rat 4x180k, 2x400k
Gene expression (mRNA) Rat 4x44k, 8x60k
Gene expression (exon) Other (please enquire) Please enquire
Gene expression (mRNA) Other (please enquire) Please enquire

 

For the latest information about the Agilent miRNA and gene expression arrays, or our custom array design service, please contact us.

Summary

Microarrays are a powerful and truly flexible technology for studying CNV, methylation, miRNA and gene expression. 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 — and status as the world's first Agilent High-Throughput Certified Service Provider — combined with our highly skilled team allows us to provide complete design, project management, and data analysis services to ensure you achieve the highest quality data. We were entrusted with the world's largest copy number variation study where over 2 billion high-quality data points were generated from >20,000 samples in just 20 weeks for the Wellcome Trust Case Control Consortium. Our purpose-built, state-of-the-art laboratories operate under an ISO9001:2008 and ISO27001:2005 certified management system.

For complete peace-of-mind, trust your project to OGT and benefit from our experienced, expert staff and thorough quality management processes. OGT’s services are available to customers worldwide.

Find out more about our Genefficiency Genomic 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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