CytoSure™ Eye Disease Research Array
Exon-focused, high-resolution, 4x180k aCGH array design covering relevant genes for inherited eye disease research
Copy number variants (CNV) as well as single nucleotide variants (SNV) play an important role in many kinds of eye disease. CNVs have been described in both relatively common eye disorders such as late age-related macular degeneration1 and intraocular pressure2, as well as rare eye diseases such as Ocular Behcet’s disease3 and Graves ophthalmopathy4. Eye abnormalities are also present in one-third of inherited, systemic diseases. For example, a dislocated lens in the eye is associated with Marfan syndrome, a connective tissue disease associated with heart problems. The CytoSure Eye Disease Research Array targets genes important for research into syndromic and non-syndromic inherited retinal and choroidal dystrophies, as well as ocular developmental disorders
CytoSure disease-specific arrays are designed to accurately identify small intragenic CNVs in genes associated with specific disorders. The content for the CytoSure Eye Disease Research Array has been designed and optimised in collaboration with leading molecular genetics experts at Emory University.
The CytoSure Eye Disease Research array delivers:
- Accurate detection of copy number variation
- Array content taken from the medical research exome array — fully optimised and research-validated by Emory University
- Multiplex (4x180k) format is cost-effective and allows for higher sample throughput
- Easy data interpretation using optimised protocols for high signal-to-noise ratios and industry-leading CytoSure Interpret Software
Number of genes targeted:
Examples of diseases covered by the array:
Retinitis pigmentosa, Stargardt disease, macular dystrophy, flecked-retina disorders, congenital stationary night blindness, Bardet-Biedl syndrome, Usher syndrome.
Array content fully optimised and research-validated
CytoSure disease-focused research arrays have been designed and optimised in collaboration with leading molecular genetics experts at Emory University. Each gene is targeted by multiple exon-specific probes, allowing accurate detection of copy number variations (CNVs) encompassing single and multiple exons. While Sanger sequencing, and increasingly targeted next generation sequencing (NGS), are being used to detect specific point mutations, it is not possible to use these techniques to accurately detect CNV. As such, many molecular genetics researchers are choosing to complement sequencing studies with array comparative genomic hybridisation (aCGH) — the gold-standard for CNV detection.
CytoSure arrays utilise 60mer oligonucleotide probes, which have been shown to offer higher signal-to-noise ratios through increased specificity and sensitivity1. To further improve performance, each array has been verified by Emory to ensure only the best performing probes were used.
The optimised array design coupled with the powerful CytoSure Interpret Software that accompanies each array ensures sensitive detection of aberrations as small as a few hundred bases within each gene exon.
These arrays provide a cost-effective, routine option for detailed research into small, exon-specific aberrations.
OGT has the experience and expertise required to optimise the design of microarrays, which is why we chose to partner with them". Dr Madhuri Hegde, Executive Director, Emory Genetics Lab, United States of America
Highly targeted optimised probes
Using a proprietary probe design algorithm, it is possible to design highly targeted, optimised probes throughout the majority of the genome. A range of probe performance metrics were evaluated to ensure optimal array performance. A poorly performing probe can result in inaccurate data and even false calls. All of our probes are first tested in silico and scored on quality. Probes with the highest score are printed on an array and tested in the laboratory. These probes are ranked on performance, and only the most accurate, best performing probes are used in the final designs. Probes have been designed to target over 128,000 exons across 4645 genes (the complete probe set is found on the Medical Research Exome Array) and a subset of these probes are then used for the disease-focused research arrays. Using optimised probes enables the detection of small amplifications and deletions.
The targeted, optimised probes deliver:
- An average resolution of 1 probe per 125bp in targeted exons.
- A minimum of 4 probes per targeted exon
- Targeting of exome flanking regions (150bp 5’ and 3’ of each exon)
- Targeting of introns, and gene flanking regions (average resolution of 1 probe per 1kb)
- Coverage of genomic backbone
Easy data interpretation
CytoSure Interpret Software is a powerful, easy-to-use package for the analysis of aCGH data. Innovative features such as the Accelerate Workflow enable standardised and automated data analysis, including automatic aberration detection and classification. It includes extensive annotation tracks covering syndromes, genes, exons, CNVs and recombination hotspots — each of which link to publicly available databases such as ISCA, Decipher and the Database of Genomic Variants (Figure 1) providing results in context. It is possible to select which tracks are displayed allowing only tracks of specific interest to be viewed (e.g. syndrome-specific tracks) ensuring easy data interpretation. Each track can reference NCBI36 (hg18), GRCh37 (hg19) or GRCh38 (hg38) information. Annotations within a track can be coloured allowing easy visualisation. It is also possible to customise which information from the tracks is saved in the report (e.g. how many common variants overlap with an aberration).
Figure 1: Chromosome overviews are clearly displayed in CytoSure Interpret Software. Shown here is an overview of the distribution of probes on chromosome 2 in the CytoSure Medical Research Exome array and the currently available standard tracks. These fully customisable tracks simplify the interpretation of aberrations.
The complete solution
All CytoSure arrays have been validated using CytoSure Genomic DNA Labelling Kits; these labelling kits have been uniquely developed and optimised to enable rapid delivery of high-quality results with excellent signal-to-noise ratios. Two formats are available; the CytoSure Genomic DNA Labelling Kit is sufficient for 24 samples and is ideal for labs running one or two arrays a week. For high-throughput labs, the CytoSure HT Genomic DNA Labelling Kit is recommended as its plate-based protocol allows simultaneous labelling of 96 samples. To achieve the best quality data possible, it is recommended that CytoSure arrays are used in conjunction with CytoSure Genomic DNA Labelling Kits.
For more information about the CytoSure Eye Disease Research Array contact us and talk to one of our representatives.
|CytoSure Eye Disease Research Array (8x60k)||Microarray with four arrays of 180,000 spots; CytoSure Interpret Software||700113||Get a quote|
|CytoSure Genomic DNA Labelling Kit||24 reactions: clean-up columns, dyes, nucleotide mix, random primers, enzyme, collection tubes||020022||Get a quote|
|CytoSure HT Genomic DNA Labelling Kit||96 reactions: 2 purification plates, nucleotide mix, random primers, enzyme, collection tubes||500040||Get a quote|
|CytoSure Sample Tracking Spike-ins A – H||Sample Tracking Probe sufficient for 12 reactions supplied in three aliquots||500050 – 500057||Get a quote|
CytoSure™ products are for research use only; not for use in diagnostic procedures.
1. Curtis, C. et al (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 2009, 10:588
Evaluation of DNA labelling kits for enhanced microarray results
This application note provides a technical evaluation of CytoSure™ Genomic DNA Labelling Kits compared with another leading DNA labelling kit.
The impact of microarray probe design on detecting copy number variants at exon-resolution
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 we undertake to make sure our arrays perform the best they possibly can.
The use of the InnoScan® 710 scanner and Mapix® software with CytoSure™ microarrays
This application note illustrates the use of the InnoScan 710 scanner and Mapix with a range of OGT CytoSure cytogenetic array formats.
Genomic analysis of rare disease
CNV plays an important role in rare disease. See how extensive CNV is across a range of rare diseases and how OGT can help you understand the complete mutation spectrum for each and every sample.
Integrated solutions for the genomic study of inherited disease
Our class-leading products are designed for the robust identification of the whole range of genomic variation, with an emphasis on custom solutions to target the regions important for your research.
Comprehensive genomic analysis — complementing sequencing with high-resolution CNV detection
This whitepaper discusses how researchers at Emory Genetics Laboratory (EGL) are complementing their sequencing results with accurate detection of copy number variants (CNVs) using CytoSure Molecular Arrays.
Evaluating and implementing CytoSure™ microarrays
In this white paper, Kath Smith, Consultant Clinical Scientist at Sheffield Children’s NHS Foundation Trust discusses her laboratory’s experience of transitioning to OGT CytoSure arrays.
Examining the medical exome
In this white paper, genetic scientists Dr Tracey Lewis and Dr Emily Farrow discuss how customisable, exon focused array designs complement next generation sequencing (NGS) for clinical genetic research.
Basics of array comparative genomic hybridisation (aCGH)
This poster illustrates the basics of how aCGH works and some of the applications in which it is used.
What’s wrong with my arrays?
Wet-lab processing is key to achieving the highest quality array data – find the solution to improve your data quality with our poster.