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June 15, 2009 (Vol. 29, No. 12)

Solutions for DNA Copy-Number Analysis

NimbleGen CGH: An Array Portfolio from Discovery to High-Throughput Detection

  • Whole-Genome View

    Click Image To Enlarge +
    Figure 2. Whole-genome view of NimbleGen CGH data

    NimbleGen CGH arrays are used to identify DNA copy-number changes associated with a broad range of human diseases including mental retardation, autism, schizophrenia, cancer, and autoimmune disease. Figure 2 shows whole-genome PDF views of pathogenic chromosomal gains and losses associated with mental retardation using the NimbleGen CGH 12x135K Whole-Genome Tiling v3.0 Array. 

    Data is displayed as whole-genome “rainbow” plots where each chromosome is denoted by a different color. CGH analysis of gDNA from a healthy male versus healthy female shows the expected copy-number loss of chromosome X (probes are shifted below the baseline) and gain of chromosome Y (probes are shifted above the baseline), but no other pathogenic copy-number changes are detected.  In contrast, large copy-number gains and losses associated with Trisomy 21 and Velocardiofacial Syndrome are detected, as indicated by the arrows. 

    In addition to whole-genome PDF views, NimbleGen CGH data is provided in GFF  for interactive viewing using SignalMap software. Figure 3 shows a zoom-in view of an ~382 Kb deletion region and an ~35 Kb amplification in a Burkitt Lymphoma cell line detected using the NimbleGen Human CGH 3x720K Whole-Genome Tiling v3.0 Array but missed using a lower-resolution competitor’s array. 

    Data is displayed in SignalMap software alongside annotation tracks (provided with Roche NimbleGen CGH arrays) showing corresponding normal CNVs annotated in the Database of Genomic Variants, segmental duplication regions, and known genes. 

    The NimbleGen CGH array portfolio includes catalog whole-genome and custom targeted designs in 2.1M, 3x720K, and 12x135K array formats for human and nonhuman organisms (e.g., mouse, rat, dog, cow). This flexibility in array format and design, combined with a simple workflow with validated instruments, reagent kits, and software offers a complete solution for DNA copy-number analysis from high-resolution discovery to high-throughput detection. 

  • Click Image To Enlarge +
    Figure 3. Zoom-in view of NimbleGen CGH data