CytoSure™ ISCA and ISCA v2 Arrays

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Designed in collaboration with the International Standards for Cytogenomic Arrays (ISCA) Consortium, to deliver standardised, evidence-based designs to the cytogenetic research community.

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For more information about any OGT product or service, please contact us.

Overview

CytoSure ISCA and ISCA v2 arrays deliver standardised, evidence-based designs to the cytogenetics research community, focusing on disease- and syndrome-associated genome regions, in addition to offering whole genome‘backbone’ coverage. All arrays are provided with full training and support which includes the complimentary, industry-leading CytoSure Interpret Software for intuitive, single-click data analysis.

Every Cytosure ISCA array provides:

  • Accurate detection of CN and LOH on a single array*
  • Gold-standard detection of CN changes with complete coverage of the ISCA regions
  • A range of array formats to suit your requirements
  • Easy identification of sample mix-up via spike-in controls
  • Fast and easy data generation and interpretation

I would definitely recommend OGT to any colleague. The platform has been easy to transfer to, improving our processes, and we’re very happy using it within our area of developmental delay. If anyone ever asks me if it was worth the effort of transferring to OGT, the answer is a clear yes. Kath Smith, Consultant Clinical Scientist at Sheffield Children's NHS Foundation Trust 

Ordering Information

Product Contents Cat. No. Price
CytoSure ISCA v2 (4x44k) Microarray with four arrays of 44,000 spots; CytoSure Interpret Software 020042 Get a quote
CytoSure ISCA v2 (8x60k) Microarray with eight arrays of 60,000 spots, featuring spike-in control; CytoSure Interpret Software 020040 Get a quote
CytoSure ISCA v2 (4x180k) Microarray with four arrays of 180,000 spots, featuring spike-in control; CytoSure Interpret Software 020041 Get a quote
CytoSure ISCA +SNP (8x60k) Microarray with eight arrays of 60,000 spots, featuring spike-in control; CytoSure Interpret Software 020052 Get a quote
CytoSure ISCA UPD (4x180k) Microarray with four arrays of 180,000 spots, featuring spike-in control; CytoSure Interpret Software 020050 Get a quote
CytoSure ISCA +SNP (4x180k) Microarray with four arrays of 180,000 spots, featuring spike-in control; CytoSure Interpret Software 020051 Get a quote

CytoSure™ products are for research use only; not for use in diagnostic procedures.

* CytoSure ISCA +SNP and ISCA UPD only.

Details

Accurate detection of CN and LOH on a single array

CytoSure ISCA and ISCA +SNP arrays comprise a research-validated collection of specific probes that enable reliable detection of copy number (CN) changes for research into a variety of genetic disorders. CytoSure ISCA +SNP arrays combine long oligonucleotide probes for accurate CN detection with single nucleotide polymorphism (SNP) probes for precise identification of loss of heterozygosity (LOH) and uniparental disomy (UPD). Combining CN and SNP detection on a single array enables cost-effective detection of a broader range of aberations — without the requirement for additional investment in equipment or training.

Gold-standard detection of CN changes with complete coverage of the ISCA regions

Array comparative genomic hybridisation (aCGH) is the gold-standard for detecting CN; however, it has not always been possible to combine this technique with LOH and UPD detection, meaning either two separate arrays were needed or inferior SNP-based CN detection platforms1 were used. CytoSure ISCA+SNP arrays offer complete coverage of the ISCA-defined regions ensuring uncompromising detection of CN changes in these important regions in addition to accurate LOH detection. One of the challenges in combining CN and SNP content is the selection of probes that reliably detect and discriminate between SNP alleles while working under hybridisation conditions developed for CN detection. For each SNP, two probes have been designed; comparing the difference in signal intensity of the two probes allows the discrimination between homozygous and heterozygous SNPs (Figure 1). Unlike alternative platforms, this unique approach does not require restriction digest of the sample, allowing the use of any reference DNA.

ISCAfig1

Figure 1: The principles of SNP calling. When a homozygous SNP is present, the labelled target will only hybridise to one of the probes. This is displayed in the B-allele frequency plot (BAF) plot within CytoSure Interpret Software with a score of 1 or 0. If a heterozygous SNP ispresent, both probes will hybridise, which is displayed in the BAF plot with a score of 0.5. Image courtesy of Prof. Joris Vermeesch and Simon Ardui, Centre of Human Genetics, KU Leuven.

A range of array formats to suit your requirements

CytoSure ISCA and ISCA +SNP arrays are available in a range of formats (Table 1) to match your resolution and throughput requirements. All CytoSure arrays have been research-validated using CytoSure Genomic DNA Labelling Kits, which 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.

 

Application Product Name Format Cat. No. CN resolution LOH resolution
Targeted Backbone
Whole genome CN screening, plus high coverage of ISCA defined regions CytoSure ISCA v2 4x44k 020042 1 probe every 52kb
1 probe every 81kb NA
CytoSure ISCA v2 8x60k 020040 1 probe every 48kb
1 probe every 70kb NA
CytoSure ISCA v2 4x180k 020041 1 probe every 19kb
1 probe every 25kb NA
Whole genome CN and LOH screening, plus CN coverage of ISCA defined regions CytoSure ISCA +SNP 8x60k 020052 1 probe every 80kb
1 probe every 141kb 30Mb
Whole genome CN and UPD screening, plus high res. CN coverage of ISCA defined regions CytoSure ISCA UPD 4x180k 020050 1 probe every 20kb 1 probe every 27kb
30Mb
Whole genome CN and LOH screening, plus high res. CN coverage of ISCA defined regions CytoSure ISCA +SNP 4x180k 020051 1 probe every 48kb 1 probe every 70kb
7-10Mb


Table 1: CytoSure ISCA and ISCA +SNP Selection Guide. For a complete list of genes covered, email products@ogt.com.

Easy identification of sample mix-up via spike-in controls

As aCGH is now recognised as the first-tier test for research into numerous cytogenetic aberrations2, many laboratories are scaling up their processes to increase throughput and reduce costs. Parallel processing of higher numbers of samples increases the possibility of sample mix-up. Even automated workflows contain several steps where sample identity can be lost (e.g. pipetting samples into gasket slides). The CytoSure ISCA and ISCA +SNP arrays contain sample tracking probes which, when used in conjunction with CytoSure Sample Tracking Spike-ins, enable researchers to quickly and easily identify any erroneous samples, ensuring only accurate data is reported.

Fast and easy data generation and interpretation

CytoSure Interpret Software, which accompanies all CytoSure arrays, is a powerful, easy-to-use package for the analysis of CN changes and SNP data. Innovative features such as the Accelerate Workflow and automatic aberration classification functionality enable the automation of data analysis workflows, minimising the need for user intervention and maximising the consistency and speed of data interpretation. The unique database enables easy back-up of data, simplified searching and user tracking. CytoSure Interpret Software also includes extensive annotation tracks covering syndromes, genes, exons and CN and recombination hotspots — each of which link to publicly available databases such as ISCA, Ensembl and the Database of Genomic Variants, providing results in context.

Understanding the complex genetic composition of consanguineous samples, samples with UPD and samples with long stretches of LOH is also simplified using CytoSure Interpret Software. Regions of LOH can be identified by viewing the B-allele frequency (BAF) plot or the Allele StatusPlot. CytoSure Interpret Software further simplifies the analysis of LOH using a proprietary ‘LOH Score’ whereby, continuous stretches of homozygous SNPs are scored and those regions with a score above a recommended threshold are considered to be significant (Figure 2). Regions of LOH can also be viewed alongside copy number data simplifying aberration interpretation (Figure 3).

ISCAfig2

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 2: CytoSure Interpret Software clearly displays the percentage of homozygous and heterozygous SNPs for each chromosome. The position of the SNP probes is shown beneath the chromosome image. Red lines indicate homozygous alleles, black heterozygous. Continuous stretches of homozygous alleles, indicating regions of LOH are shown by red rectangles. The details of these regions are also tabulated. To define the genotype of each SNP, the data is segmented using the individual BAF scores and the Circular Binary Segmentation (CBS) algorithm. Following segmentation each SNP is assigned a state which is then displayed in the Allele Status Plot. A Chromosome 3 data from a consanguineous sample where regions of LOH of 48.31Mb, 9.79Mb and 6.38Mb have been detected. B Isodisomy on chromosome 15 where a region of LOH of 20.78Mb has been detected.

ISCAfig3

Figure 3: CytoSure Interpret Software displays changes in copy number alongside regions where LOH has been detected. This aids interpretation of complex aberrations. Image courtesy of Prof. Joris Vermeesch and Simon Ardui, Centre of Human Genetics, KU Leuven.

For more information on CytoSure ISCA and ISCA +SNP arrays, please contact us.

Ordering Information

Product Contents Cat. No. Price
CytoSure ISCA v2 (4x44k) Microarray with four arrays of 44,000 spots; CytoSure Interpret Software 020042 Get a quote
CytoSure ISCA v2 (8x60k) Microarray with eight arrays of 60,000 spots, featuring spike-in control; CytoSure Interpret Software 020040 Get a quote
CytoSure ISCA v2 (4x180k) Microarray with four arrays of 180,000 spots; CytoSure Interpret Software 020041 Get a quote
CytoSure ISCA +SNP (8x60k) Microarray with eight arrays of 60,000 spots, featuring spike-in control; CytoSure Interpret Software 020052 Get a quote
CytoSure ISCA UPD (4x180k) Microarray with four arrays of 180,000 spots; CytoSure Interpret Software 020050 Get a quote
CytoSure ISCA +SNP (4x180k) Microarray with four arrays of 180,000 spots; CytoSure Interpret Software 020051 Get a quote


Related products

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.

References

1. Curtis, C. et al (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics 10, 588-6102
2. Manning, M. and Hudgins, L. (2010). Array-based technology and recommendations for utilization in medical genetics practice for detection of chromosomal abnormalities. Genetics in Medicine 12, 742–745

Data kindly provided by Emory Genetics Laboratory. Data kindly provided by Diane Pickering, University of Nebraska Medical Center.

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