CytoSure™ Cancer +SNP Arrays (8x60k and 4x180k)
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).
CytoSure Cancer +SNP arrays deliver:
- 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
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.
Figure 1. A schematic of the OGT SNP probe technology. Separate probes target both the reference (major) and non-reference (minor) allele. A fluorescent signal is only received from the probe if DNA fragments containing the respective alleles are present in the sample. By comparing fluorescence intensity between the two probes, the allelic status at each SNP position can be ascertained.
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.
Figure 2. Screenshots from CytoSure Interpret, displaying results from an unoptimised and optimised array on the same sample with a confirmed ~1600 bp deletion. All CytoSure catalogue arrays go through stages of 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
Figure 3. Shown here is a CLL research sample run on the CytoSure Consortium Cancer +SNP array (8x60k) with a deletion and corresponding LOH. CytoSure Interpret offers an intuitive user interface for easy interpretation of genetic findings. Samples kindly provided by Dr Jon Strefford, University of Southampton.
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.
|Copy number resolution||LOH resolution|
|Backbone||Average gene resolution (Hg19)|
|CytoSure Haematological Cancer +SNP||1 probe every 117kb||1 probe every 68kb||30Mb|
|CytoSure Cancer +SNP||1 probe every 44kb||1 probe every 25kb||20Mb|
|CytoSure Consortium Cancer +SNP||1 probe every 36kb||1 probe every 23kb||10Mb|
Table 1. CytoSure Cancer +SNP arrays selection guide. For a complete list of genes covered by each array, email firstname.lastname@example.org
CytoSure Haematological Cancer +SNP array (8x60k)
This design offers a balance between throughput and resolution, allowing investigation of large CNV and LOH in a cost-effective manner. This array delivers:
- Whole-genome coverage for CNV and LOH analysis
- Enhanced resolution across regions relevant for research into CLL, MM, MPN and MDS (Chronic Lymphocytic leukaemia, Multiple Myeloma, Myeloproliferative Neoplasms, Myelodyspastic Syndromes)
CytoSure Cancer +SNP array (4x180k)
This design, developed in collaboration with Dr Jacqueline Schoumans (Head of the Cancer Cytogenetic Unit at Lausanne University Hospital), focuses on CNV detection across the target regions and delivers:
- Whole-genome coverage for CNV and LOH analysis
- Whole-gene CNV resolution across more than 1500 cancer-associated genes
- Exon resolution across 18 genes (Table 2)
Table 2. Genes covered at single-exon resolution on the CytoSure Cancer +SNP array.
CytoSure Consortium Cancer +SNP array (4x180k)
This design focuses on the content recommended by the Cancer Cytogenetics Microarray Consortium (CCMC) now known as the Cancer Genomics Consortium (CGC), with more probes dedicated to SNP analysis than the other arrays. The recommended content is intended to help standardise research across cancer genomics, similar to the successful model introduced by ISCA/ICCG, now known as ClinGen. The array delivers:
- Whole-genome coverage for CNV and LOH analysis
- Enhanced coverage of 130 cancer-associated genomic regions
- Whole-gene CNV resolution of more than 500 cancer-associated genes
|CytoSure Haematological Cancer +SNP (8x60k)
Slide with eight arrays of 60,000 spots; CytoSure Interpret analysis software
|020070||Get a quote|
|CytoSure Cancer +SNP (4x180k)||Slide with four arrays of 180,000 spots; CytoSure Interpret analysis software||700090||Get a quote|
|CytoSure Consortium Cancer +SNP (4x180k)||Slide with four arrays of 180,000 spots; CytoSure Interpret analysis software||020071||Get a quote|
|CytoSure Genomic DNA Labelling Kit||24 reactions: dyes, nucleotide mix, random primers, enzyme||020020||Get a quote|
|CytoSure HT Genomic DNA Labelling Kit
||96 reactions: dyes, nucleotide mix, random primers, enzyme||500040||Get a quote|
|Clean-up Columns||24 columns for the clean-up of DNA||500020||Get a quote|
|Clean-up Plates||96-well plate for the clean-up of DNA||500041||Get a quote|
|CytoSure Interpret Software||Class-leading data analysis software provided with CytoSure arrays - complimentary with all array purchases||020022||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 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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CytoSure™ Array Handbook (4x44k and 4x180k formats)
CytoSure™ Array Handbook (8x15k and 8x60k formats)
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