High Resolution, Improved Performance, Ultimate Confidence

• High Resolution: Up to 2.1 million probes per array enables unbiased, genome-wide detection of CNVs down to ~5 – 10 Kb resolution (see Figure 1 and Figure 2).
• Cost-Effective Solution: Utilize NimbleGen multiplex array formats to simultaneously analyze 3 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).

Complete Suite of Annotation Files Provided (Free Download)

A complete suite of annotation files is provided with human designs and includes:

Note: Features in some of these files may be more easily viewed by changing the feature style from dots to bars in SignalMap software. To do this, select the track by clicking its Y axis and select Track -> Style -> Bars.

• Genes.gff: Indicates all genes for build hg18 as reported in the UCSC Genome browser (http://genome.ucsc.edu). Genes annotated above the baseline in each track represent features identified on the sense strand, while entries below the baseline represent features identified on the antisense strand.
• Genes_Exon-Intron.gff: Indicates the exon-intron boundaries of all genes for build hg18 as reported in the UCSC Genome browser. Exons are denoted as dark blue bars, and introns are denoted as light blue bars.
• Transcription_Start_Sites.gff: Indicates all transcription initiation sites for build hg18 as reported in the UCSC Genome browser.
• Structural_Variants.gff: Displays all copy number variants as reported in the Database of Genomic Variants (http://projects.tcag.ca/variation).
• 42M_CNV_Regions.gff track*: Displays CNVs identified by the Genome Structural Variation Consortium in a high-resolution CNV discovery project (http://www.sanger.ac.uk/humgen/cnv/42mio). In this study, common CNVs > 500bp were identified from 20 CEU and 20 YRI HapMap samples using a set of NimbleGen CGH arrays that contains approximately 42 million probes tiled across the genome.
• NimbleGen_CNV_Regions.gff track*: Displays CNVs from Asian research samples identified by Roche NimbleGen using high-resolution NimbleGen CGH arrays.
• Segmental_Duplications.gff: Displays regions of genomic duplication > 1kb in size and with > 90% sequence identity after masking high-copy repeat regions (Bailey, et al. Genome Res. 2001; 11:1005-17) as reported in the UCSC Genome browser. The level of similarity is indicated as follows: light to dark gray bars = 90 - 98% similarity, light to dark yellow bars = 98 - 99% similarity, light to dark orange bars ≥ 99% similarity; red = duplications of > 98% that lack sufficient evidence in the Segmental Duplication database.
• Cytogenetic_Ideogram.gff: Displays the cytogenetic bands, in grayscale format, for each chromosome as reported in the UCSC Genome browser.
• miRNA.gff: Indicates all miRNAs as reported in the miRBase database (http://microrna.sanger.ac.uk/). Each feature represents the entire hairpin sequence for the miRNA.

* All of the CNVs shown in the 42M_CNV_Regions and NimbleGen_CNV_Regions are included on the NimbleGen Human CNV Arrays.

Recent advances in high-resolution microarray technology have revealed DNA copy number variation as a significant source of genome variation, now thought to account for more nucleotide variation than SNPs. Until recently, the recognized contribution of genome structural variation to human disease has been limited to rare genomic disorders (e.g. Trisomy 21, Prader-Willi Syndrome). However, with the emergence of high-resolution maps of common copy number variation (CNV) in human populations, the impact of CNVs on a broad range of human disease has become a key research focus.

In addition to the 2.1M array format, multiplex arrays are available for higher throughput and cost-effective analysis of genome-wide copy number variation associated with a broad range of human diseases such as:

• Mendelian disease
• Mental retardation
• Autism
• Schizophrenia
• Cancer
• Autoimmune disease

	2.1M - A single array with 2,100,000 probes.
	3x720K - Three arrays on a single slide each containing 720,000 probes.
	12x135K - Twelve arrays on a single slide each containing 135,000 probes.
	385K - A single array with 385,000 probes.
	4x72K - Four arrays on a single slide each containing 72,000 probes.

Availability

2.1M, 3x720K, 12x135K, 385K, and 4x72K array formats are not available for every CGH array design. Please consult the Availability Guide on this page for a complete list.

CGH Delivery Workflow

Customers can purchase NimbleGen whole-genome or custom targeted arrays and perform CGH 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 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 microarray service involves the following:

1. Customer selects a catalog whole-genome design or works with the NimbleGen bioinformatics team to create a custom array.
2. Customer ships sample(s) to the NimbleGen service lab.
3. NimbleGen manufactures the array and performs the hybridization and data analysis.
4. 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
5. 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 array design. Please consult the Availability Guide on this page for a complete list.

The 2.1M, 3x720K, 12x135K, 385K, and 4x72K array formats and the Delivery and Service workflows are not available for every CGH array design. Use the table below to identify the availability of different formats and workflows across our CGH design offerings. For information on NimbleGen Cytogenetics (CGX) Arrays open the Cytogenetics tab on the Human Designs page.

	2.1M	3x720K	12x135K	385K	4x72K
Human CNV			N/A	N/A	N/A
Human Whole-Genome Tiling
Human Whole-Genome Exon Focused	N/A		N/A	N/A	N/A
Human Chromosome-Specific	N/A	N/A	N/A		N/A
Human Custom
Mouse Whole-Genome Tiling	N/A		N/A		N/A
Mouse Custom
Other Whole-Genome Tiling	N/A	N/A	N/A		N/A
Other Custom
Any array design/format designated "N/A" can be created for Array Delivery through the custom array option.

KEY:
	- Delivery OR Service Workflow
	- Delivery Workflow Only
	- Service Workflow Only
N/A	- Not Available

Roche NimbleGen Software

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

• NimbleScan v2.6
  Provides all the necessary tools for image processing and CGH data analysis. DNA copy number gains and losses are identified using Roche NimbleGen’s segMNT v1.1 algorithm, included in the NimbleScan software.
• SignalMap v1.9
  Provides a simple and interactive data browsing tool to view and interpret CGH data in GFF format.

Partner Solutions

Further in-depth copy number analysis can be carried out with BioDiscovery Inc.’s Nexus Copy Number software which is compatible with NimbleScan data files.

• Nexus Copy Number
  Simplify CNV genetic aberration analysis with tools including custom annotation tracks, integration of custom databases (e.g. CNVs, genetic disorders), and segmentation algorithms.

Brochures & Datasheets

• NimbleGen Copy Number Variation (CNV) Arrays
  Datasheet (PDF Format 1.4MB)
• NimbleGen Human CGH Whole-Genome Arrays
  Brochure (PDF Format 2.2MB)

User Guides

• NimbleGen Arrays User’s Guide: CGH and CNV Arrays (Version 7.0)
  User’s Guide (PDF Format 4.7MB)
• NimbleGen Arrays User’s Guide: CGX Arrays (Version 2.0)
  User’s Guide (PDF Format 5.7MB)

Downloads

• Descriptions of HG18 Annotation Files
  Datasheet (PDF Format 49KB)
• Human Genome HG18 Annotation Files
  Annotation Files (ZIP Format 11.2MB)
  What files are included in this download?

Application Notes & Whitepapers

• Array CGH using DNA from Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Samples
  Technical Note (PDF Format 2MB)
• Detecting Copy Number Variants Associated with Basal Cell Carcinoma in an Arsenic-Exposed Population
  Application Note (PDF Format 1.2MB)
• High Resolution Copy Number Analysis of Parkinson’s Samples Using Nexus Copy Number and Roche NimbleGen Microarrays
  Whitepaper (PDF Format 964KB)

For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.