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CGH - Human Designs


Comparative Genomic Hybridization (CGH) measures DNA copy number differences between and test and reference genome. NimbleGen offers two types of CGH array products: whole-genome and custom targeted arrays. Whole-genome arrays measure DNA copy number gains and losses across entire genomes, while custom targeted arrays can interrogate a single chromosomal region or multiple loci of interest. In addition, custom designs can be created with either uniform or mixed-density probe spacing.

Whole-Genome Tiling
2.1M Whole-Genome Tiling
NimbleGen 2.1M Array Format: 2.1M
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Version Probe Length Median Probe Spacing
Whole Genome Tiling Array Delivery Workflow. Click to learn more... 05541921001 Human CGH 2.1M WG-T v2.0D Arr Del 2.0D 60mer 1169bp
Service Workflow. Click to learn more... B7074-00-01 HG18 CGH 2.1M WG Tiling v2.0D
3x720K Whole-Genome Tiling New Design!
NimbleGen 3x720K Array Format: 3x720K
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Version Probe Length Median Probe Spacing
Whole Genome Tiling Array Delivery Workflow. Click to learn more... 05520797001 Human CGH 3x720K WG-T v3.0 Arr Del 3.0 60mer 2509bp
Service Workflow. Click to learn more... B9475-00-01 HG18 CGH 3x720K WG Tiling v3.0
Whole Genome Tiling Array Delivery Workflow. Click to learn more... 05542065001 Human CGH 3x720K WG-T v2.0 Arr Del 2.0 60mer 3877bp
Service Workflow. Click to learn more... B8441-00-01 HG18 CGH 3x720K WG Tiling v2.0
12x135K Whole-Genome Tiling New Design!
NimbleGen 12x135K Array Format: 12x135K
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Version Probe Length Median Probe Spacing
Whole Genome Tiling Array Delivery Workflow. Click to learn more... 05520878001 Human CGH 12x135K WG-T v3.0 Arr Del 3.0 60mer 12524bp
Service Workflow. Click to learn more... B9474-00-01 HG18 CGH 12x135K WG Tiling v3.0
Whole Genome Tiling Array Delivery Workflow. Click to learn more... 05542219001 Human CGH 12x135K WG-T v2.0 Arr Del 2.0 60mer 21500bp
Service Workflow. Click to learn more... B7829-00-01 HG18 CGH 12x135K WG Tiling v2.0
385K Whole-Genome Tiling
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Version Probe Length Median Probe Spacing
Whole Genome Tiling Array Delivery Workflow. Click to learn more... 05542243001 Human CGH 385K WG-T v2.0 Arr Del 2.0 60mer 7073bp
Service Workflow. Click to learn more... B6902-00-01 HG18 CGH 385K WG Tiling v2.0
Whole Genome Tiling Array Delivery or Service Workflow. Click to learn more... B4366-00-01 HG18 CGH 385K WG Tiling v1.0 1.0 50-75mer 6270bp
4x72K Whole-Genome
NimbleGen 4x72K Array Format: 4x72K
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Version Probe Length Median Probe Spacing
Whole Genome Tiling Array Delivery or Service Workflow. Click to learn more... B6925-00-01 HG18 CGH 4x72K WG Tiling v2.0 2.0 60mer 40046bp
Whole-Genome Exon-Focused
NimbleGen 3x720K Array Format: 3x720K
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Version Probe Length Median Probe Spacing
Whole Genome Exon-Focused Array Delivery Workflow. Click to learn more... 05542073001 Human CGH 3x720K Exon Foc Arr Del 1.0 50-75mer Variable
Service Workflow. Click to learn more... B8442-00-01 HG18 CGH 3x720K WG Exon-Focused
Chromosome-Specific
NimbleGen 385K Array Format: 385K
Source: UCSC
Build: HG18, NCBI 36
Recommended Storage: Store arrays desiccated at room temperature.
Description Delivery Workflow. Click to learn more... Catalog Number Design Name Probe Length Median Probe Spacing
Chromosome 1 Tiling Array Delivery or Service Workflow. Click to learn more... B3732001-00-01 HG18 CHR1 FT 50-75mer 531
Chromosome 2 Tiling Array Delivery or Service Workflow. Click to learn more... B3733001-00-01 HG18 CHR2 FT 50-75mer 575
Chromosome 3 Tiling Array Delivery or Service Workflow. Click to learn more... B3734001-00-01 HG18 CHR3 FT 50-75mer 475
Chromosome 4 Tiling Array Delivery or Service Workflow. Click to learn more... B3735001-00-01 HG18 CHR4 FT 50-75mer 450
Chromosome 5 Tiling Array Delivery or Service Workflow. Click to learn more... B3736001-00-01 HG18 CHR5 FT 50-75mer 425
Chromosome 6 Tiling Array Delivery or Service Workflow. Click to learn more... B3737001-00-01 HG18 CHR6 FT 50-75mer 404
Chromosome 7 Tiling Array Delivery or Service Workflow. Click to learn more... B3738001-00-01 HG18 CHR7 FT 50-75mer 365
Chromosome 8 Tiling Array Delivery or Service Workflow. Click to learn more... B3739001-00-01 HG18 CHR8 FT 50-75mer 341
Chromosome 9 Tiling Array Delivery or Service Workflow. Click to learn more... B3740001-00-01 HG18 CHR9 FT 50-75mer 255
Chromosome 10 Tiling Array Delivery or Service Workflow. Click to learn more... B3741001-00-01 HG18 CHR10 FT 50-75mer 305
Chromosome 11 Tiling Array Delivery or Service Workflow. Click to learn more... B3742001-00-01 HG18 CHR11 FT 50-75mer 310
Chromosome 12 Tiling Array Delivery or Service Workflow. Click to learn more... B3743001-00-01 HG18 CHR12 FT 50-75mer 310
Chromosome 13 Tiling Array Delivery or Service Workflow. Click to learn more... B3744001-00-01 HG18 CHR13 FT 50-75mer 225
Chromosome 14 Tiling Array Delivery or Service Workflow. Click to learn more... B3745001-00-01 HG18 CHR14 FT 50-75mer 200
Chromosome 15 Tiling Array Delivery or Service Workflow. Click to learn more... B3746001-00-01 HG18 CHR15 FT 50-75mer 175
Chromosome 16 Tiling Array Delivery or Service Workflow. Click to learn more... B3747001-00-01 HG18 CHR16 FT 50-75mer 165
Chromosome 17 Tiling Array Delivery or Service Workflow. Click to learn more... B3748001-00-01 HG18 CHR17 FT 50-75mer 160
Chromosome 18 Tiling Array Delivery or Service Workflow. Click to learn more... B3749001-00-01 HG18 CHR18 FT 50-75mer 170
Chromosome 19 Tiling Array Delivery or Service Workflow. Click to learn more... B3750001-00-01 HG18 CHR19 FT 50-75mer 105
Chromosome 20 Tiling Array Delivery or Service Workflow. Click to learn more... B3751001-00-01 HG18 CHR20 FT 50-75mer 134
Chromosome 21 Tiling Array Delivery or Service Workflow. Click to learn more... B3752001-00-01 HG18 CHR21 FT 50-75mer 70
Chromosome 22 Tiling Array Delivery or Service Workflow. Click to learn more... B3753001-00-01 HG18 CHR22 FT 50-75mer 65
Chromosome X Tiling Array Delivery or Service Workflow. Click to learn more... B3754001-00-01 HG18 CHRX FT 50-75mer 340
Chromosome Y Tiling Array Delivery or Service Workflow. Click to learn more... B3755001-00-01 HG18 CHRY FT 50-75mer 20
Custom

Please contact your Sales representative to Request a Quote or contact Technical Support with any questions about CGH custom array designs.

  NEW!
NimbleGen 2.1M Array
2.1M		 NEW!
NimbleGen 3x720K Array
3x720K		 NEW!
NimbleGen 12x135K Array
12x135K		 NimbleGen 385K Array
385K		 NimbleGen 4x72K Array
4x72K
Number of 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
Source Customer-defined
Build Customer-defined
Probe Length 50-75mer
Probe Spacing Uniform or mixed-density
Design Options Whole-genome, single or multiple chromosomal regions per array.

To learn more about NimbleGen Array formats, please visit our Array Products page.

Literature

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

FAQ
General
How is NimbleGen array technology different from other platforms? NimbleGen manufactures high-density DNA microarrays using its proprietary Maskless Array Synthesizer (MAS) technology. At the heart of the system is a Digital Micromirror Device (DMD) that uses a solid-state array of miniature aluminum mirrors to create “virtual masks” that replace the physical chromium masks used in traditional arrays. The DMD directs a pattern of UV light projected onto a microscope slide, which when coupled with UV-mediated DNA synthesis in a parallel, combinatorial manner, can generate up to 2.1 million unique probes on a single microarray.
How many features are included on a single array? Individual arrays are available in variety of formats with up to 2.1 million features.
Does NimbleGen offer CGH arrays in multiplex formats? Yes, we offer Human Whole Genome and custom eukaryotic arrays in 3x720K, 12x135K, and 4x72K formats.
What is the resolution of your arrays? Effective resolution varies according to the spacing of individual probes (generally 5-10x the median probe spacing). Our human whole-genome arrays enable resolution down to ~5kb on the 2.1M format. Custom targeted arrays enable higher density probe spacing in specified regions and detection of DNA copy number changes down to exon-level resolution.
Do NimbleGen array designs include non-coding regions of the genome? Yes - NimbleGen offers unbiased whole-genome tiling designs that include genic and intergenic regions.
Can NimbleGen design an array tailored to my specific research needs? Yes - specify genomic regions of interest and NimbleGen will design a custom array to meet your research needs.
What resolution scanner do I need? The NimbleGen MS 200 scanner set at 5 micron resolution is optimal for 385K arrays. The NimbleGen MS 200 scanner set at 2 micron resolution is optimal for 2.1M arrays.
Can NimbleGen CGH distinguish single vs. multi-copy amplifications? Yes.
Sample Processing
What are the sample requirements for CGH? 1-5μg of high-quality unamplified gDNA is required.
What protocol does NimbleGen recommend for DNA isolation? Any protocol that provides high-quality gDNA.
What reference sample should I use? There are several options for choosing a reference sample. For example, for cancer studies choose an individual's own DNA (e.g. tumor vs. germline), DNA from a single individual, or pooled DNA from several individuals (NimbleGen can provide pooled male or female DNA).
Array Design
Are NimbleGen designs up-to-date with the latest genome builds? Yes, NimbleGen technology allows the rapid creation of new array designs based on the latest genome sequence.
Are designs based on earlier genome builds available? Yes.
Does NimbleGen offer non-human CGH designs? Yes - NimbleGen offers whole-genome designs for a wide range of organisms. In addition, NimbleGen can create custom designs for any genome (or region of genome) for which high-quality sequence is available.
Does NimbleGen use only non-unique probes? Generally only unique probes are included in array designs. However, NimbleGen Human Whole Genome v2.0 array designs contain non-unique probes for enhanced coverage of low-copy number repeat regions of the genome (e.g. segmental duplication).
Data Analysis
What software do I need to process NimbleGen CGH arrays in my own lab? Roche NimbleGen's NimbleScan and SignalMap software are required.
What software do I need to view my full service CGH data? Roche NimbleGen's SignalMap software is required for viewing CGH data in GFF format. A free, 30-day demo version of SignalMap is available for download.
Can I analyze my data using other software programs? Yes - NimbleGen data can be viewed and analyzed using a variety of commercially available software programs.
Can I view my data in the UCSC genome browser? Yes.
How do I get gene annotation information? NimbleGen provides a gene annotation track corresponding to your design. Additional annotation tracks can be viewed in the UCSC genome browser.
Array Delivery
Can I purchase NimbleGen arrays for use in my own lab or core facility? Yes.
Which CGH designs are available for array delivery? Whole-Genome and custom targeted array designs in any available array format.
What kits are availble for use with NimbleGen CGH microarrays? NimbleGen Hybridization, Wash Buffer, Array Processing Accessories, and Sample Tracking Control kits. Learn more about our kits...
Can I scan NimbleGen arrays using my Agilent scanner? The 5 micron Agilent scanner can work with NimbleGen arrays.
Does NimbleGen offer training for array delivery customers? Yes - NimbleGen offers on-site Training Workshops at our Madison, WI location.
Can I strip and re-use my CGH microarray? Yes - NimbleGen offers an array re-use kit for stripping and re-hybridizing arrays.
 

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