CytoSure™ ISCA +SNP Array

The CytoSure ISCA +SNP array delivers:

• Confident detection of CNV and LOH on a single array
• Superior aberration detection sensitivity and specificity with complete coverage of the ISCA* regions
• Accurate analysis of consanguineous samples
• Fast and easy data generation and interpretation

Ordering Information

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

Confident detection of CNV and LOH on a single array

aCGH is the gold standard for detecting CNV¹, however, until recently it was not possible to combine this technique with LOH and UPD detection, meaning either 2 separate arrays were needed or inferior SNP-based CNV detection platforms¹ were used. The CytoSure ISCA +SNP array combines aCGH-based CNV detection with fully research-validated SNP content allowing confident and cost-effective copy number changes and identification of LOH. One of the challenges in combining CNV and SNP content is the selection of probes that reliably detect and discriminate between SNP alleles while working under hybridisation conditions developed for copy number detection. The SNP probes utilised in OGT’s CytoSure ISCA +SNP array have been fully optimised and research-validated to ensure confident detection of regions of LOH at high resolution using the standard CytoSure aCGH protocol — allowing rapid and easy integration into your existing workflow. Any reference DNA can be used and restriction digest of the sample is not required. For optimum performance, this array should be combined with CytoSure Genomic DNA Labelling Kits, which offer high signal intensities enabling easier allele discrimination.

Figure 1: CytoSure Interpret Software clearly displays the percentage of homozygous and heterozygous SNPs for each chromosome and each chromosome arm. 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 tabulated. Chromosome 3 data comes from a consanguineous sample where regions of LOH of 62.38mb and 6.07mb have been detected^†. Chromosome 15 data show isodisomy  where a region of LOH of 22.5mb has been detected^‡.

Superior aberration detection sensitivity and specificity with complete coverage of the ISCA regions

Oxford Gene Technology (OGT) has worked in collaboration with the International Standards for Cytogenomic Arrays (ISCA) consortium to develop the CytoSure ISCA range of arrays. These arrays provide standardised, evidence-based content focusing on disease and syndrome-associated genome regions, in addition to offering whole genome ‘backbone’coverage. The array design utilises 60-mer oligonucleotide probes, which have been shown to offer higher signal-to-noise ratios and increased sensitivity and specificity¹. The CytoSure ISCA +SNP array offers complete coverage of the ISCA defined regions, at the same resolution to the CytoSure ISCA 8x60k array, ensuring uncompromised detection of copy number changes in these important regions.

Table 1: UPD-linked syndromes identified using the CytoSure ISCA +SNP array. Isodisomy can be detected when running individual samples. Heterodisomy can be detected when parental samples are available.

Accurate analysis of consanguineous samples

Understanding the complex genetic composition of consanguineous samples is simplified using innovative array design and CytoSure Interpret Software. From the thousands of SNPs present in the human genome, informative SNPs were identified — those with an allele frequency of approximately 50%. Probes with the ability to discriminate between the SNP alleles while working under the standard hybridisation and washing procedures were designed. Two types of probes are printed on the array for each informative SNP — one for each allele. After loading the array data into CytoSure Interpret Software the first step in the analysis process is to examine the signal intensity of each allele-specific probe. CytoSure Interpret Software utilises a novel algorithm, which automatically measures the difference between the signal intensities of each allele pair thereby identifying which allele is present in the sample (Figure 1). Continuous stretches of homozygous SNPs are scored and those regions with a score above a threshold of 300 are considered to be significant. This threshold is user definable but recommended values have been calculated based on validation studies.

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 CNV and SNP data. Innovative features such as the Accelerate Workflow enable the automation of data analysis workflows, minimising the need for user intervention and maximising the consistency and speed of data interpretation. CytoSure Interpret Software also includes extensive annotation tracks covering syndromes, genes, exons, CNVs 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.

Ordering Information

Related products

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

* International Standards for Cytogenomic Arrays. ^†Data kindly provided by Emory Genetics Laboratory.^‡Data kindly provided by Diane Pickering, University of Nebraska Medical Center.^§Resolution of LOH detection for Beckwith-Wiedemann Syndrome is 10mb.

References

1. Miller, C. et al (2009) The pitfalls of platform comparison: DNA copy number array technologies asessed. BMC Genomics 10, 588-610