CytoSure - frequently asked questions

CytoSure Microarrays - product formats and equipment required

What CytoSure products are available?

Currently, we offer the following products:

  • CytoSure ISCA — a choice of microarray slide formats containing either 4 x 44,000, 4 x 180,000 or 8 x 60,000 spots. Each array targets approximately 500 regions with a 75kb, 25kb, and 60kb backbone coverage respectively.
  • CytoSure Syndrome Plus – a microarray slide containing two arrays, each with 105,000 spots. Each array targets over 200 syndromes; 410 genes covering autism, heart disease, mental retardation (MR) and eye diseases with a 3 kb resolution and a 40 kb backbone coverage.    Additional information.
  • CytoSure Chromsome X – a microarray slide containing two arrays, each with 105,000 spots. Probe design focus is on exon regions at 1.6 kb resolution with general backbone coverage at 4 kb.  Additional information.
  • CytoSure labelling kit – optimised genomic DNA labelling kit – 24 reactions, including clean-up columns, cy dyes, nucleotide mix, random primers, enzyme and collection tubes.                                                                               Additional information.
  • CytoSure Interpret software is a powerful and easy-to-use tool enabling effortless translation of data into meaningful results. This software is complimentary to CytoSure users and does not require a license fee. Discover more and request your free demo version.
  • There are also several new applications in development. Contact us for more information.
What type of cytogenetic arrays do you have?
  • CytoSure ISCA — a choice of microarray slide formats containing either 4 x 44,000, 4 x 180,000 or 8 x 60,000 spots. Each array targets approximately 500 regions with a 75kb, 25kb, and 60kb backbone coverage respectively.
  • CytoSure Syndrome Plus — a microarray slide containing two arrays, each with 105,000 spots. Each array targets over 200 syndromes; 410 genes covering autism, heart disease, mental retardation (MR) and eye regions with a 3 kb resolution and a 40 kb backbone coverage.       Additional information.
  • CytoSure Chromosome X (2x105k) — a microarray slide containing two arrays, each with 105,000 spots. Probe design focus is on exon regions at 1.6 kb resolution with general backbone coverage at 4 kb.                          Additional information.
  • CytoSure Chromosome X (4x44k) — a microarray slide containing four arrays, each with 44,000 spots.       Additional information.
What formats are available?

CytoSure products are available in a variety of formats.

See our CytoSure selection guide for an overview of all array formats.

What equipment do I need to run CytoSure arrays in the laboratory?
For more information on the equipment required to run oligo arrays in your laboratory, visit our easy-to-use decision-making guide, to lead you through a checklist of what equipment and resources are required. Alternatively, you can contact one of our experts or register your details, and one of our experts will contact you.
I already have a scanner, will my scanner work with CytoSure arrays?
Not all scanners are compatible with CytoSure arrays. The scanner must be able to scan at 5 µm resolution. You may need to check that the feature extraction software can extract high density (orange packed arrays). For the next generation of arrays, the scanner will need to be able to scan at a resolution of at least 2.5 µm. Please contact us and one of our experts will be able to discuss your scanner and compatibility in more detail with you.

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CytoSure microarrays - array designs, resolution, gene coverage and function

What is the resolution of CytoSure cytogenetic arrays?

CytoSure products are available in a variety of formats.

See our CytoSure selection guide for an overview of all array formats.

Which syndromic regions are covered in CytoSure ISCA and Syndrome Plus arrays?

See CytoSure ISCA arrays genetic disorder list

See CytoSure Syndrome Plus array genetic disorder list.

Which genes are covered in CytoSure Chromosome X arrays?
See CytoSure Chromosome X protocol booklet appendix.
What version of the human genome is used in the array design?
Human genome build 36
A colleague of mine has designed a Syndrome array using Agilent’s eArray platform – why use CytoSure?
We supply our proprietary CytoSure analysis software free of charge to our customers to enable analysis of the results. In addition, we offer full project consultation, support and training (at your laboratory or on-site at our premises).
Our CytoSure arrays also demonstrate greater probe density in syndrome regions.
What are the differences between CytoSure ISCA and Syndrome Plus and Agilent CGH arrays?
CytoSure ISCA and Syndrome Plus arrays are biased towards areas of the genome of interest to constitutional cytogeneticists. Support and training are available to customers, please contact us for more information.
What type of probes do you use on CytoSure cytogenetic arrays?
We have a database of over 20 million 60mer probes. These probes are designed to perform equally over the whole array.
How much time is required to run a CytoSure experiment?
Contact one of our cytogenetic experts to discuss your experimental procedure in detail.
I am interested in cancer cytogenetics – can you recommend arrays for this application?
Yes, we recommend using:
  • Oligome™ - a database of more than 20 million oligonucleotide probes designed to the latest release of the human genome - build 36
  • Our custom design service
  • We plan to expand our family of cytogenetic arrays and will release cancer specific arrays in the future

Please contact us to discuss your specific requirements with one of our experts.

Why are CytoSure arrays labelled "For research use only"?
Currently there is no regulatory approval for any arrays in cytogenetics and until there is regulatory approval, they will be listed as "For research use only".

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Sample preparation and labelling

How much starting DNA is required?
Currently, 1 µg of DNA is required for non-amplified labelling.
What labelling method does OGT use for its CytoSure arrays?
We recommend our Genomic DNA Labelling Kit. Our labelling kit, with our unique formulation, gives you more efficient use of reagents with no loss of signal intensity. The labelling kit is optimised for use in combination with CytoSure arrays and Interpret software for easier interpretation of results. However, the Agilent labelling kit is also compatible, as are other labelling kits on the market. Please contact us for more information on kit compatibility.
Do I need to do a dye swap?
Large aberrations (as defined by your laboratory) can be detected without a dye swap. However, dye swaps do provide greater certainty with small aberrations.

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Data analysis

I’ve heard oligo arrays have higher noise compared with BAC arrays?
All our data presented is raw and unsmoothed. However, our data has been normalised. In general, BAC array data is the result of averaging multiple spots. Our oligo arrays are designed with 1,000s of probes in the target sites, so although the data might appear to be noisier, there is greater certainty in the outcome of data analysis since there are many more data points.
Oligo arrays can detect many more aberrations which may complicate finding the pathogenic aberration?
CytoSure software incorporates copy number variation (CNV) annotation (derived from database of genomic variants - DGV) to flag up those aberrations that are unlikely to be disease causing. CNV information is a significant area of research in the scientific community.
What are the recombination hotspots?
These are areas of genome surrounded by segmental duplications (which are 95% identical and are separated by 50 kb – 10 Mb of DNA). These are likely to be regions of the genome that can undergo NAHR (non-alleic homologous recombination). Our CytoSure arrays use areas as defined by Eichler et al. These regions are annotated in the software.
Can CytoSure Interpret software be used with other non-OGT arrays?
It is designed to support only our CytoSure arrays. However, if you wish to do a comparison of your own arrays, we can convert files to our format.
Which feature extracted file formats are compatible with CytoSure Interpret software?
Agilent and Genepix.
Does CytoSure Interpret software provide automatic aberration detection?
Yes. The software is equipped with an implementation of the Circular Binary Segmentation (CBS) algorithm enabling automatic segmentation of data into regions of equal copy number.
How long does the automatic aberration detection take?
On a 105k Syndrome Plus dataset, the CBS algorithm takes between 4 and 9 minutes, depending on computer hardware. CytoSure Interpret software has a new 'batch-processing' function that allows the processing of multiple files in the background or overnight for later review.
Is the data annotated in any way in CytoSure Interpret software?

Yes. The software provides the following annotation 'tracks' to ease data interpretation:

  • Ensembl genes
  • Ensembl exons
  • Syndromic regions
  • CNV regions (from the Database of Genomic Variants - DGV)
  • Recombination hotspots
  • Patient data from the DECIPHER database
  • BAC/MLPA probes
Is there a way to store experimental results and review them using CytoSure Interpret software?
Yes. The software allows users to save full details of aberration calls into a database, which can then be viewed as separate annotation track, and managed within the software.
Can CytoSure Interpret software generate reports for analysed data?
Yes. The software allows users to create HTML or tab-delimited reports of aberration calls in a dataset.
Can I get a copy of CytoSure Interpret software?
We can provide you with a fully functional demonstration version of the software available. Please contact us for more information.

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How to evaluate CytoSure

How much do CytoSure products cost?
Contact us for current promotional packages and volume discount quotations.
How much does a license for CytoSure analysis software cost?
The comprehensive CytoSure analysis software is complimentary to our customers so does not require a license fee.
Do you have special introduction CytoSure packages to get started?
Go to our current Testing and Evaluation promotional packages.
Do you offer training on CytoSure products?
Training is offered with our Evaluation package In addition we offer full training at your laboratory or on-site at our premises.

CytoSure™ products are for research use only