Microarrays
Gene expression
Chip-on-Chip
Methylation
Comparative Genomic Hybridization (CGH)
Sequence Capture

Comparative Genomic Hybridization (CGH)

Comparative Genomic Hybridization (CGH) measures DNA copy number differences between a 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.

Key features of NimbleGen microarrays – ultra-high density (up to 2.1M probes on a single slide) and long oligo probes – enable the highest resolution and most comprehensive array CGH platform for whole-genome analysis. With the design flexibility offered by NimbleGen’s array synthesis technology, chromosomal aberrations identified in whole-genome surveys can be further examined at ultra-high resolution using custom targeted CGH arrays.

Advantages

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. 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. 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. 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. 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.

Specifications and Array Formats available

 
  2.1M 3x720K 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

For more information, please click the link below: http://www.nimblegen.com/products/