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Product summary

  • Technology Arrays
  • Application Cytogenetics & rare disease
  • Areas of interest Rare disease
  • Gene Targets 212
  • Aberration Types CNVs
  • Resolution Exon Level
  • Examples of diseases covered Epilepsy, brain malformations, SCID
  • Product No. 700112
  • Intended use For research use only; not for diagnostic procedures.

Overview

Introduction

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.

The content for the CytoSure® Epilepsy Research Array has been designed and optimised in collaboration with leading molecular genetics experts at Emory University.

Features
  • Targeted content and high-quality probe design - detect single or multiple exonic CNVs in the genes that matter
  • Customisable multiplex designs - high-throughput, cost-effective analysis
  • Simplified data interpretation - using industry-leading CytoSure Interpret® Software
  • Optimised labelling kits and integrated sample tracking probes - confident analysis and reporting

Capabilities

Targeted content

Inherited genetic disorders can be caused by a variety of chromosomal aberrations, including point mutations and small CNVs (Figure 1). Different methodologies are combined to accurately detect these changes, with one of the most successful combinations being targeted NGS and array comparative genomic hybridisation (aCGH)4. Using highly-targeted, exon-focused arrays as part of this combined approach has been shown to detect small CNVs (Figure 2).

The concept of using highly targeted gene-focused arrays to screen specific loci has been developed in collaboration with leading molecular genetics experts at Emory University and has now been implemented in multiple labs worldwide.

Probe design

To detect these micro aberrations, highly optimised probes are required. The probes have been selected from OGT’s proprietary Oligome™ database — a database of over 25 million in silico optimised oligonucleotide probes. CytoSure arrays utilise 60-mer oligonucleotide probes, which have been shown to offer higher signal-to-noise ratios through increased specificity and sensitivity5. To further improve performance, during the design process multiple probes are designed for each of the target regions. These probes are tested in competitive hybridisation experiments and ranked based on technical performance — with only the best performing probes being chosen for the final array design. In addition, further experimental validation using clinical research samples has been performed by Emory University who collaborated in the design and optimisation of CytoSure Disease- Focused Research arrays.

Cost-effective, customisable analysis

Genetic analysis is typically done in batches to ensure cost-effective processing. However, collecting sufficient samples for rare disorders can significantly delay time to reporting. Through combining informative probes for multiple molecular disorders on a single array, CytoSure Disease-Focused Research arrays allow immediate and accurate processing of diverse samples, thereby reducing both time-to-results and cost.

Each CytoSure Disease-Focused Research array can be modified to create bespoke custom arrays, to suit your specific requirements. The customisation process is made easy with a dedicated project manager from our team of experienced computational biologists assigned to each new project. Additional content, specific to your research interest, can easily be selected from any existing array, our Oligome™ database of pre-optimised probes, or designed de novo to your specifications using our proprietary probe design pipeline. Delivery of your custom array only occurs once you are completely satisfied with the design. A number of array formats are available to suit your design and throughput requirements, with the most typical being 8x60k or 4x180k.

Easy data interpretation using industry-leading CytoSure Interpret Software

All CytoSure arrays are provided with CytoSure Interpret Software which 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. In addition, extensive annotation tracks covering syndromes, genes, exons, CNV and recombination hotspots — each of which link to publicly available databases — can be used to provide results in context (Figure 3).

Optimised labelling kits and integrated sample tracking probes

All CytoSure arrays have been validated using CytoSure Genomic DNA Labelling Kits; these labelling kits have been developed and optimised to enable rapid delivery of high-quality results with excellent signal-to-noise ratios. The kits offer faster and simpler DNA labelling and clean-up than alternative enzymatic labelling procedures with improved data quality. Two kit formats are available; the CytoSure Genomic DNA Labelling Kit for 24 samples processed in tubes or the CytoSure HT Genomic DNA Labelling Kit for plate-based processing of up to 96 samples. For best results, CytoSure Genomic DNA Labelling Kits should be used with all CytoSure arrays to give the best derivative log ratio spread (DLRS) values and signal-to-noise ratios ensuring accurate detection of even the smallest aberration.

Increasing numbers of aCGH samples combined with higher-throughput array formats means that it is imperative to track samples throughout the labelling, hybridisation and analysis process to maintain sample identity. CytoSure Sample Tracking Spike-ins are uniquely designed to enable reliable sample tracking and easy identification of sample mix-up using OGT’s CytoSure Disease-Focused Research arrays and class-leading CytoSure Interpret Software.

CytoSure Epilepsy Research Array workflow

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Content selection

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  • CytoSure Epilepsy Research Array
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Scanning

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  • Agilent C or SureScan
  • Innopsys Innoscan 710 & 900
  • Axon / Molecular devices GenePix 4300 & 4400
  • NimbleGen MS200 / Tecan Power Scanner

What our customers say

References

  1. Kumar, D. ed. (2008) Genomics and clinical medicine. Oxford: Oxford University Press. p. 279.
  2. Mefford, H.C. et al (2011) Rare copy number variants are an important cause of epileptic encephalopathies. Annals of Neurology 70, 974–985
  3. Olson, H. et al (2014) Copy number variation plays an important role in clinical epilepsy. Annals of Neurology 75(6), 943–958
  4. Detection limit of intragenic deletions with targeted array comparative genomic hybridization. BMC Genetics, 2013, 14:116
  5. The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 2009, 10:588

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