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 (3x720K, 12x135K) 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:

• Known Genes: 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.
• Exon-Intron Boundaries: Indicates the exon-intron boundaries of all genes in 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: Indicates all transcription initiation sites for build HG18 as reported in the UCSC Genome browser.
• Structural Variants: Displays all copy number variants as reported in the Database of Genomic Variants (http://projects.tcag.ca/variation).
• Cytogenetic Ideogram: Displays the cytogenetic bands, in grayscale format, for each chromosome as reported in the UCSC Genome browser.
• miRNA: Indicates all miRNAs as reported in the miRBase database (http://microrna.sanger.ac.uk/). Each feature represents the entire hairpin sequence for the miRNA.
• Segmental Duplications: Displays regions of genomic duplication >1 kb in size and with > 90T 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 Duplications database.

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.

Roche NimbleGen offers ultra-high resolution CGH arrays with up to 2.1 million probes for comprehensive analysis of DNA copy number variation in humans and model organisms. In addition to the 2.1M array format, 3x720K and 12x135K 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

Applications	References
Genetics Research
Detect whole-chromosome and submicroscopic copy number gains and losses down to exon-level resolution Fine-map chromosomal breakpoints in patient cohorts Identify inherited CNVs associated with recurrent de novo abnormalities	Helbig I., et al. “15q13.3 microdeletions increase risk of idiopathic generalized epilepsy,” Nature Genetics: 41, 160-162 (2009)
	Hegde MR, et al. “Microarray-based mutation detection in the dystrophin gene,” Human Mutation: 29, 1091-99 (2008)
	Saillour Y, et al. “Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method,” Human Mutation: 29, 1083-90 (2008)
	Mefford HC, et al. “Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes,” The New England Journal of Medicine: 359(16):1685-99 (2008)
	Ballif, B.C., et al., “Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-12.2,” Nature Genetics 39, 1071-3 (2007)
Cancer Research
Perform genome-wide analysis of chromosomal imbalances in tumors Discover oncogenes and tumor suppressor genes using exon-level resolution custom targeted arrays	Lenz G, et al. “Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways,” PNAS: 105, 13520-13525 (2008)
	Natrajan, R., et al., “Delineation of a 1Mb breakpoint region at 1p13 in Wilms tumors by fine-tiling oligonucleotide array CGH,” Genes Chromosomes Cancer 46, 607-15 (2007)
	Stallings, R.J., et al., “High-resolution analysis of chromosomal breakpoints and genomic instability identifies PTPRD as a candidate tumor suppressor gene in neuroblastoma,” Cancer Research 66, 3673-80 (2006)
CNV Research
Characterize “normal” human genome variation down to gene- and exon-level resolution Discover common and rare structural variants associated with complex disease (e.g. autism, psychiatricdisorders, diabetes) Perform higher-throughput validation of CNV loci associated with complex disease	Itsara, A., et al., “Population analysis of large copy number variants and hotspots of human genetic disease,” American Journal of Human Genetics 84, 148-161, (2009)
	Marques-Bonet T., et al., “A burst of segmental duplications in the genome of the African great ape ancestor,” Nature 457, 877-881 (2009)
	Wheeler, D.A., et al., “The complete genome of an individual by massively parallel DNA sequencing,” Nature 452, 872-6 (2008)
	Walsh, T., et al., “Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia,” Science 320, 539-43 (2008)
	Roohi, J., et al., “Disruption of contactin 4 in 3 subjects with autism spectrum disorder,” Journal of Medical Genetics Mar 18 [Epub ahead of print] (2008)
	Balciuniene, J., et al., “Recurrent 10q22-q23 deletions: a genomic disorder on 10q associated with cognitive and behavioral abnormalities,” American Journal of Human Genetics 80, 938-47 (2007)
Model Organism Research
Characterize phenotypic variation between strains Rapidly map structural variants in mutagenized strains Identify disease-specific loci in animal models of human disease	Nicholas, T.J., et al., “The genomic architecture of segmental duplications and associated copy number variants in dogs,” Genome Research Feb 3. [Epub ahead of print] (2009)
	Chen, W, et al., “Mapping DNA structural variation in dogs,” Genome Research Jan 28. [Epub ahead of print] (2009)
	Lee, A.S., et al., “Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies,” Human Molecular Genetics 17, 1127-36 (2008)
	Graubert, T.A., et al., “A high-resolution map of segmental DNA copy number variation in the mouse genome,” PLoS Genetics 3, e3 (2007)
	Guryev, V., et al., “Distribution and functional impact of DNA copy number variation in the rat,” Nature Genetics 40, 538-45 (2007)
	Jones, M.R., et al., “Oligonucleotide array comparative genomic hybridization (oaCGH) based characterization of genetic deficiencies as an aid to gene mapping in Caenorhabditis elegans,” BMC Genomics 8, 402 (2007)

	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.

Specifications:

	NEW! 2.1M	NEW! 3x720K	NEW! 12x135K	385K	4x72K
Arrays per Slide	1	3	12	1	4
Total Number of Probes	2,100,000	3 x 720,000	12 x 135,000	385,000	4 x 72,000
Feature Size	13μm x 13μm	13μm x 13μm	13μm x 13μm	16μm x 16μm	16μm x 16μm
Array Size	62mm x 14mm	19mm x 14mm	8.9mm x 6.5mm	17.4mm x 13mm	7.8mm x 5.7mm
Slide Size	1 x 3 in. (25 x 76 mm)

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.

	2.1M	3x720K	12x135K	385K	4x72K
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 AND Service Workflows
	- 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 v2.5
  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.
• NimbleScan CGH Plugin
  If you are a CGH 2.1M array customer and are still using NimbleScan v2.4, the NimbleScan CGH PlugIn provides an option for applying a spatial correction to the raw data generated from the arrays.

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.

• NimbleGen CGH Microarrays and Services
  Brochure (PDF Format 1.13MB)
• NimbleGen Human CGH Whole-Genome Arrays
  Brochure (PDF Format 889KB)
• NimbleGen CGH HD2 Arrays
  Datasheet (PDF Format 422KB)
• NimbleGen Arrays User’s Guide: CGH Analysis (Version 5.1)
  User’s Guide (PDF Format 3.6MB)
• Descriptions of HG18 Annotation Files
  Datasheet (PDF Format 49KB)
• Human Genome HG18 Annotation Files
  Annotation Files (ZIP Format 10.6MB)
  What files are included in this download?
• High Resolution Copy Number Analysis of Parkinson’s Samples Using Nexus Copy Number and Roche NimbleGen Microarrays
  Whitepaper (PDF Format 964KB)
• A Performance Comparison of Two CGH Segmentation Analysis Algorithms: DNACopy and segMNT
  Technical Note (PDF Format 203KB)
• Microarray-Based Comparative Genomic Hybridization (Array CGH): Identifying Chromosomal Abnormalities Associated with Mental Retardation and Developmental Delay
  Application Note (PDF Format 173KB)

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