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Product summary

  • Technology Arrays
  • Application Haematology, Solid tumour
  • Gene Targets 18 + 1500
  • Aberration Types CNVs & LOH
  • Resolution Exon level (18 genes) and whole gene (1500) + LOH (20Mb)
  • Product No. Various
  • Intended use For research use only; not for diagnostic procedures.

Overview

Introduction - Flexible arrays for reliable analysis of CNV and LOH using a single assay

OGT’s range of CytoSure® Cancer +SNP arrays combine long-oligo probes for superior copy number variant (CNV) detection alongside single nucleotide polymorphism (SNP) probes – which function using OGT proprietary technology – for accurate identification of loss-of-heterozygosity (LOH).

Features
  • Unique SNP probe technology allowing the use of any reference sample with no restriction digest
  • Unparalleled performance through design optimisation
  • Fast and easy analysis using CytoSure Interpret® software
  • Versatile array designs across a choice of formats

Capabilities

Unique SNP probe technology allowing the use of any reference sample with no restriction digest

Array comparative genomic hybridisation (aCGH) using 60-mer oligonucleotide probes has been shown to offer higher signal-to-noise ratios, increased sensitivity and increased specificity compared to other technologies1.

With other platforms, the use of 60-mer technology for LOH analysis typically requires a restriction digest, which can compromise sample quality, limits the target SNPs to those overlapping restriction sites, and requires a genotyped reference for comparison. However, due to OGT’s unique SNP technology (Figure 1), there is no restriction digest required, the most informative SNPs can be targeted and any reference sample can be used (e.g. normal tissue from the same individual to enable constitutional abnormalities to be filtered out).

Combined with the in silico and empirical optimisation carried out across all OGT catalogue arrays as well as easy customisation to include any additional regions of interest, OGT’s Cancer +SNP arrays deliver flexible and robust analysis of CNV and LOH combined in a single assay.

Unparalleled performance through design optimisation

The ability of a microarray to detect genetic aberrations accurately is highly dependent on achieving the best possible data quality. OGT leverage years of experience in microarray design to ensure excellent performance in all microarray products. A proprietary pipeline of perl scripts is used to design the best possible probes to target genomic regions of interest, followed by both in silico and empirical optimisation.

Customisation made simple

Additional targets relevant to your research can also easily be targeted by selecting probes from our Oligome™ database containing more than 26 million pre-optimised probes, including additional SNP probes to improve LOH resolution.

Fast and easy analysis using CytoSure Interpret Software

OGT’s CytoSure Interpret Software, which accompanies all CytoSure arrays, is a powerful and easy-to-use package for straightforward analysis of CNV and SNP data (Figure 3), delivering:

  • Feature-rich, highly-customisable analysis workflows to meet any lab’s requirements
  • Automation of the data analysis processes, including batch upload of LIMS information to the database
  • Extensive cancer-specific annotation tracks including regions from the Mitelman Database, the Cancer Gene Consensus Genes, the Atlas of Genetics and Cytogenetics in Oncology and Haematology and the Hurles Haploinsufficiency data2
Versatile array designs across a choice of formats

Three fully customisable Cancer +SNP designs are available (Table 1), designed using different formats to suit any analysis and throughput requirement.

CytoSure Cancer +SNP Arrays workflow

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Content selection

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  • CytoSure Cancer +SNP Arrays
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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. Curtis, C. et al (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10, 588-6102
  2. Hurles, M. et al (2010) Characterising and predicting haploinsufficiency in the human genome. PLoS Genetics 6, 10, e1001154 1-113

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