Comparative Genomic Hybridization (CGH)
Comparative Genomic Hybridization (CGH) measures DNA copy number differences between a test and reference genome. Roche NimbleGen offers ultra-high resolution CGH/CNV arrays with up to 4.2 million probes for comprehensive analysis of DNA copy number variation. In addition to the 2.1M array format, multiplex arrays are available for higher throughput and cost-effective analysis of either 3, 6 or 12 samples on a single slide. Roche NimbleGen offers several types of CGH/CNV arrays for a variety of organisms to meet your specific research needs:
- Whole-Genome Designs for comprehensive, unbiased analysis of DNA copy number changes.
- ISCA Plus Designs offer flexible and comprehensive analysis tools to investigate chromosome abnormalities
- CGX (Cytogenetics) Designs for genome-wide analysis of DNA copy number changes with a subset of probes focused in disease-associated regions
- CNV Designs for high-resolution CNV discovery and association studies
- Whole-Genome Exon-Focused Designs for genome-wide analysis of DNA copy number changes with a subset of probes focused in exon regions.
- Custom Designs for DNA copy number analysis of a whole genome, a single chromosomal region, or multiple loci of interest.
Advantages
High Resolution, Improved Performance, Ultimate Confidence
- High Resolution: Up to 4.2 million probes per array enables unbiased, genome-wide detection of CNVs down to ~1.4 – 5 Kb resolution (see Figure 1 and Figure 2).
- Cost-Effective Solution: Utilize NimbleGen multiplex array formats to simultaneously analyze 1, 3, 6 or 12 independent sample pairs on a single slide (see Figure 2).
- Comprehensive CNV Detection: Enhanced probe coverage of low-copy repeat regions of the genome (e.g. segmental duplications) enable increased detection of CNVs associated with pathogenic rearrangements (see Figure 3).
- Improved Performance: NimbleGen Human CGH Whole-Genome Arrays consist of empirically tested probes that provide improved data quality (i.e. signal-to-noise) compared with computationally selected probes (see Figure 4).
- Complete Flexibility: The inherent flexibility of Roche NimbleGen’s array technology enables the rapid prototyping of custom array designs, which can include whole genomes, single chromosomal regions, or multiple loci of interest. Custom designs can be created with uniform or mixed-density probe spacing using the most current genome sequence from any eukaryotic genome.
Figure 1
Figure 1. Test and reference gDNAs were independently labeled with fluorescent dyes, co-hybridized to a NimbleGen Human CGH 2.1M or 385K Whole-Genome Tiling array, and scanned using a 5 µm scanner. Log2-ratio values of the probe signal intensities (Cy3/Cy5) were calculated and plotted versus genomic position using Roche NimbleGen NimbleScan software. Data are displayed in Roche NimbleGen SignalMap software. Figure 1 shows the increased detection of copy number changes using NimbleGen CGH 2.1M Whole-Genome Tiling v2.0D arrays (1.1kb median probe spacing) compared with the 385K Whole-Genome Tiling v1.0 array (6kb median probe spacing). The increased probe density on the 2.1M array enables detection of a novel ~3kb CNV that was identified by only a single probe on the 385K array (blue arrows). In addition, fine structure of a previously reported CNV region was further elucidated using the 2.1M array.
Figure 2
Figure 2. Cross-Platform Analysis of a Large (~4Mb) Deletion Region in Chromosome 22 in a VCFS Sample Referenced Against Normal Genomic DNA: A deletion region associated with Velocardiofacial Syndrome (VCFS) is detected using three different NimbleGen CGH Whole-Genome Tiling arrays, as indicated. Copy number analysis was performed using the segMNT algorithm, available in NimbleScan software. Data are displayed using a GFF file in SignalMap software* alongside annotation tracks (provided with NimbleGen CGH arrays) showing a cytogenetic ideogram, known genes, and “normal” CNVs from the Database of Genomic Variants (http://projects.tcag.ca/variation). The red arrows indicate a presumably “normal” CNV detected by a single probe on the 12x135K array and many probes on the 3x720K and 2.1M arrays.
Figure 3
Figure 3. Analysis of a Complex CNV Region in Chromosome 17 in a Burkitt Lymphoma Research Sample as Referenced against Normal Genomic DNA. An ~382kb deletion region and an ~35kb amplification are detected using the Human CGH 2.1M Whole-Genome Tiling v2.0D array (Panel A) and the Human CGH 3x720K Whole-Genome Tiling v3.0 array (Panel B) but missed using a lower-resolution competitor’s array. Copy number analysis was performed using NimbleScan software. Data are displayed in GFF format in SignalMap software alongside annotation tracks (provided with Roche NimbleGen CGH arrays) showing corresponding “normal” CNVs, segmental duplications, and known genes. The ~382kb deletion region coincides with segmental duplications that are poorly represented on the competitor’s array. The ~35kb amplification coincides with a “normal” CNV region annotated in the Database of Genomic Variants. The competitor’s array has probe coverage of this region but lacks the resolution to detect the CNV.
Figure 4
Figure 4. NimbleGen Human CGH 3x720K and 12x135K Whole-Genome Tiling v3.0 arrays consist of empirically tested probes that show improved performance compared with the v2.0 arrays. (A) Compared with the v2.0 array (blue), the Human CGH 3x720K Whole-Genome Tiling v3.0 array (orange) offers improved signal-to-noise, which is further enhanced using the NimbleGen MS 200 Microarray Scanner at 2µm resolution (red). (B) A significant decrease in experimental noise, as measured by mad.1dr and DLRS, is achieved using the NimbleGen MS 200 Microarray Scanner at 2µm resolution. Similar results were obtained using the Human CGH 12x135K Whole-Genome v3.0 Array (data not shown).
Workflows
CGH/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.
CGH/CNV Service Workflow
Customers can choose to access NimbleGen whole-genome and custom targeted array technology through NimbleGen's full service microarray processing facility. NimbleGen's CGH/CNV microarray service involves the following:
- Customer selects a catalog whole-genome design or works with the NimbleGen bioinformatics team to create a custom array.
- Customer ships sample(s) to the NimbleGen service lab.
- NimbleGen manufactures the array and performs the hybridization and data analysis.
- Roche NimbleGen ships the following deliverables in DVD format:
- Array design files
- Raw data
- Normalized and processed data (using NimbleGen's segMNT v1.1 copy number analysis algorithm) in GFF, PDF, and TXT formats
- Annotation GFF files
- Customer views data using NimbleGen's SignalMap software and other standard software programs (e.g. Microsoft Excel, Adobe Acrobat).
Availability
Delivery and Service Workflows are not available for every CGH/CNV array design. Please consult the Availability section on this page for a complete list.
Availability
The 4.2M, 3x1.4M, 6x630K, 12x270K, 2.1M, 3x720K, 12x135K, 385K, and 4x72K array formats and the Delivery and Service workflows are not available for every CGH/CNV array design. Use the table below to identify the availability of different formats and workflows across our CGH/CNV design offerings.
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| Whole-Genome Designs | Human | |
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| Mouse | N/A | N/A | N/A | N/A | N/A | |
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| Other | N/A | N/A | N/A | N/A | N/A | N/A | N/A | |
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| ISCA Plus Designs | Human | N/A | |
N/A | N/A | N/A | N/A | N/A | N/A | N/A |
| CGX (Cytogenetics) Designs | Human | N/A | N/A | N/A | N/A | N/A | |
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N/A | N/A |
| CNV Designs | Human | N/A | N/A | N/A | N/A | |
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N/A | N/A | N/A |
| Exon Focused Designs | Human | N/A | N/A | N/A | N/A | N/A | |
N/A | N/A | N/A |
| Chromosome-Specific Designs | Human | N/A | N/A | N/A | N/A | N/A | N/A | N/A | |
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| Custom Designs | Human | |
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| Any array design/format designated "N/A" can be created for Array Delivery through the custom array option. | ||||||||||
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- Service Workflow Only |
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