CGH 3x1.4M ISCA Plus Cytogenetic Arrays

3x1.4M Array IconFormat: 3x1.4M
Source: UCSC
Build: HG19, NCBI 37
Recommended Storage: Store arrays desiccated at room temperature.
Description Number of CGH Markers Number of SNPs CNV Resolution (Average) LOH/UPD Resolution Catalog Number Pack Size Workflow Ordering*
CGH 3x1.4M ISCA Plus Cytogenetic Array ~500,000 64,000 15 - 20 Kb > 5 Mb 06527426001 1 Slide Delivery Workflow Icon Contact Us to Purchase
06560938001 4 Slides Delivery Workflow Icon
* Availability of products varies from country to country.
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Advantages

NimbleGen CGH ISCA Plus Cytogenetic Arrays offer flexible and comprehensive analysis tools to investigate chromosome abnormalities. Our high-density microarrays (up to 4.2M features on a single array) offer researchers a cytogenetic array with the advantage of increased resolution, high-quality copy number oligonucleotide data, and SNP probes for detection of LOH (Loss of Heterozyosity).

Unlike other competitive cytogenetic arrays, the ISCA Plus Array offers exon level coverage and the ability to use a single array and select a design file that matches existing ISCA consortium designs (i.e. ISCA 44k, ISCA 60K, ISCA 105K and ISCA 180K). Our arrays utilize a hybridization based approach, allowing laboratories to easily add LOH detection to the same CGH workflow currently in use. Optimized SNPs with a high minor allele frequency are spaced uniformly throughout the genome to ensure informative data generation with greater than 5 Mb LOH resolution capability.

  • Designed for comprehensive detection of chromosomal abnormalities. Targeted coverage of over 418 consolidated regions associated with constitutional cytogenetics including over 4,200 genes referenced from ISCA, OMIM and Decipher databases.
  • Cost-effective and accurate design. Multiplex design allows for maximum analysis for your throughput requirements.
  • Discover chromosome modifications previously undetected by conventional methods. Reveal exon level copy number events and identify loss of heterozygosity with our hybridization based approach to copy number and LOH detection.

Applications

NimbleGen CGH ISCA Plus Cytogenetic Arrays provide high-density exon-level coverage over cytogenetically relevant regions defined by ISCA, OMIM and Decipher databases. If a lower density array is desired, the ISCA Plus Array offers laboratories the option for selection of matching ISCA design files during the analysis step. Figure 1 demonstrates the complete ISCA Plus Array probe content and how the use of different ISCA design files can extract the probe information desired to match currently available ISCA designs from other array manufacturers.

The addition of SNP probe data to an array allows for detection of LOH which can reveal relevant instances of uniparental disomy (UPD) and other potential causes of disease. In Figure 2, chromosome 15 has a normal copy number result, however, a review of the SNP data in the B allele frequency plot reveals additional relevant genomic information missed by a standard CGH array.

Figure 1

NimbleGen CGH ISCA Plus - Comparison Data

Figure 1: Comparison of ISCA array designs. The NimbleGen CGH ISCA Plus Cytogenetic Array design provides comprehensive backbone spacing and probe coverage for target regions.

Figure 2

NimbleGen CGH ISCA Plus - Prader-Willi Data

Figure 2: Chromosome 15 exhibits Prader-Willi Syndrome through LOH analysis. No copy number variations are observed in chromosome 15. However, B allele frequency of SNP probes reveal 64 Mb and 6 Mb regions exhibiting loss of heterozygosity (LOH) from maternal uniparental disomy (UPD).

Workflow

Delivery Workflow IconCGH/CNV Delivery Workflow

Customers can purchase NimbleGen whole-genome or custom targeted arrays and perform CGH/CNV experiments in their own lab or core facility. NimbleGen arrays are synthesized on standard-sized glass microscope slides, compatible with many microarray scanners. NimbleGen provides a comprehensive user’s guide and offers a line of instruments, reagents kits and consumables to support customers with sample labeling, hybridization, scanning, data extraction, and analysis. Please contact Roche NimbleGen for a list of required equipment and reagents. NimbleGen also offers a training program to get you up and running with NimbleGen arrays quickly.

Alternate Design Files

In addition to the standard data analysis files that you received on your design CD, the ISCA Plus Cytogenetic Arrays can also be analyzed with alternate design files in order to extract only the probe information matching the ISCA 44K, 60K, 105K, and 180K designs. For each alternate design there are probe_locations and target_regions .gff files for visualization of the genomic locations and ISCA target regions covered and the .pos and .gcstats files required for DEVA Software analysis. These are available with both HG18 and HG19 coordinates.

Targeted Gene Lists

Software

Roche NimbleGen offers comprehensive data processing and analysis software tools for CGH/CNV analysis. Software available from NimbleGen includes:

  • DEVA automates the feature extraction, primary data analysis, and visualization process for Roche NimbleGen CGH, CNV, and CGX arrays. Using Roche NimbleGen design files and scanned array images, DEVA software will automatically detect new scanned array images, process them, and run the analyses.
  • Nexus Copy Number Standard simplifies CNV genetic aberration analysis with tools including custom annotation tracks, integration of custom databases (e.g. CNVs, genetic disorders), and segmentation algorithms.
  • Nexus Copy Number Discovery includes all the same features as Copy Number Standard plus additional computational modules for advanced analysis.
  • SignalMap Provides a simple and interactive data browsing tool to view and interpret CGH/CNV data in GFF format. A free, 30-day demo version of SignalMap software is available for download.

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