CytoSure™ Epilepsy Research Array
Exon-focused, high-resolution, 4x180k aCGH array design covering medically-relevant genes for epilepsy research.
Epilepsy is a group of neurological diseases characterised by epileptic seizures. The prevalence of Epilepsy is around 1%, meaning that around 65 million people worldwide are living with the disease. Genetics is believed to be involved in the majority of cases, either directly or indirectly. Over 200 single-gene defects have been described1, but copy number variants (CNVs) also play a key role in this disease. One study found 25 of 315 (7.9%) epilepsy patients had CNVs that may contribute to their phenotype2. A more recent study identified 437 CNVs in 323/805 (40%) individuals with epilepsy (1–4 per patient) ranging from 18kb to 142Mb3, many of which were associated with the disease.
CytoSure disease-focused research arrays are designed to accurately identify small intragenic CNVs in genes associated with specific disorders. The content for the CytoSure Epilepsy Research Array has been designed and optimised in collaboration with leading molecular genetics experts at Emory University.
The CytoSure Epilepsy Research array delivers:
- Accurate detection of copy number variation — a perfect complement to sequencing analysis
- 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 higher signal-to-noise ratios and industry-leading CytoSure Interpret Software
Number of genes targeted:
Examples of diseases covered by the array:
Epilepsy, brain malformations, SCID
|CytoSure Epilepsy Research array
||Microarray with four arrays of 180,000 spots; CytoSure Interpret Software
|Get a quote|
CytoSure™ products are for research use only; not for use in diagnostic procedures.
- Kumar, D. ed. (2008) Genomics and clinical medicine. Oxford: Oxford University Press. p. 279.
- Mefford, H.C. et al (2011) Rare copy number variants are an important cause of epileptic encephalopathies. Annals of Neurology 70, 974–985
- Olson, H. et al (2014) Copy number variation plays an important role in clinical epilepsy. Annals of Neurology 75(6), 943–958
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 Epilepsy Research Array contact us and talk to one of our representatives.
|CytoSure Epilepsy Research Array (8x60k)||Microarray with four arrays of 180,000 spots; CytoSure Interpret Software||700112||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
CytoSure Array Handbook (4x44k and 4x180k formats) - High-throughput labelling
CytoSure Array Handbook (4x44k and 4x180k formats) - Low-throughput labelling
CytoSure Array Handbook (8x15k and 8x60k formats) - High-throughput labelling
CytoSure Array Handbook (8x15k and 8x60k formats) - Low-throughput labelling
Comprehensive genomic analysis — complementing sequencing with high-resolution CNV detection
Examining the medical exome
Switching from NimbleGen to CytoSure Arrays (North America version)
Switching from NimbleGen to CytoSure Arrays (Rest of the world version)
Evaluation of DNA labelling kits for enhanced microarray results
Gene genie: The laboratory informatics used in genomics
This article, which appeared in the latest issue of Scientific Computing World, addresses the data interpretation challenges presented by high resolution genome analysis techniques such as microarray and sequencing. Exclusive access to OGT Cytogenetics Ne
Utility of microarrays in molecular genetics research
Presented at the ACMG meeting 2010, Dr. Madhuri Hegde of Emory Genetics Laboratory details how arrays are currently being used for accurate detection of molecular disorders.