Agilent Technologies introduces microarray and software for comparative genomic hybridization studies in cancer research
Agilent Technologies Inc. (NYSE: A) today introduced its Human Genome CGH Microarray and CGH Analytics software to help cancer biologists and cytogeneticists study genomic alterations in cancer. Comparative genomic hybridization (CGH) is used to study the chromosomal changes that frequently occur in cancer cells, including the loss or duplication of regions of chromosomal DNA.
Agilent’s microarray-based CGH solution enables researchers to rapidly explore chromosomal changes on the same platform they would use to study gene expression changes. This will help researchers more quickly identify new oncogenes, tumor suppressor genes, drug targets and biomarkers in drug discovery research and future applications such as disease sub-classification and diagnostics. Agilent will be hosting a series of e-seminars to help researchers learn how to implement this powerful technique.
The Agilent Human Genome CGH Microarray
The Agilent Human Genome CGH Microarray (G2519A) provides genome-wide coverage with an emphasis on the most commonly studied genomic coding regions and cancer-related genes. It includes 40,000 probes that span the human genome with an average spatial resolution of approximately 75 kb, including coding and noncoding sequences. It includes one probe per gene for RefSeq and Genbank Known Genes and three probes for each of approximately 1,100 known cancer genes of importance. The remaining probes are distributed to cover the rest of the genome, with an emphasis on less well known and predicted gene sequences from public databases.
Designed specifically for CGH experiments, this microarray delivers CGH performance superior to microarrays designed for gene expression (see PNAS, vol. 101, no. 51). Using 60-mer oligonucleotide probes, the microarray provides very high sensitivity, enabling researchers to reliably identify both highly localized and broadly extended single copy deletions, homozygous gene deletions and amplicons. The gene-focused content of the Agilent CGH array facilitates comparison of CGH and gene expression data so that researchers can correlate genomic copy number changes with gene expression changes.
Agilent’s array-CGH solution requires only 25 nanograms of total genomic DNA to detect chromosomal changes across the entire genome. By comparison, scientists using other oligo microarrays have typically needed to use 10 times more DNA and significantly reduce the complexity of their genomic samples, usually by amplifying only specific DNA regions. The use of total genomic DNA improves experimental design and ease of use.
The Agilent CGH Analytics Software
Agilent’s CGH Analytics software (G4175AA) provides a visual environment for exploring array-CGH data. Based on technology developed in Agilent Labs, it uses information visualization theory to leverage visual perception as a means to find interesting patterns in data. The software provides:
- Simultaneous visualization of multiple CGH microarray profiles.
- User-selectable calibration for comparison of profiles.
- Statistical measures to detect aberrant regions.
- Plug-ins for determining optimum intervals of statistical aberrations from single or multiple samples.
- Simultaneous chromosome plotting at multiple zoom levels.
- Preloaded gene annotation information from the most recent genome builds.
- Text and Graphical Aberration Summary reports, exportable for publications and presentations.
The software operates on a standard laboratory PC desktop with the Microsoft(r) Windows(r) operating environment. It is designed with a convenient plug-in architecture for data import and interface with third-party data analysis tools and displays.
Quality Control for CGH Experiments
Agilent also provides quality control capability for all stages of the array-CGH workflow using the Agilent 2100 Bioanalyzer and associated LabChip kits. The DNA 7500 or 12000 LabChip kits can be used to check DNA digestion and labeling efficiency and to infer the quality of array data. Compared to gel electrophoresis, the Bioanalyzer uses less sample while providing digital results at higher resolution, reproducibility and automation. An experimental protocol for array-CGH quality control using the Bioanalyzer is available online at www.chem.agilent.com/scripts/Library.asp?OPT=OL.
E-Seminars and More Information
Agilent will be hosting a series of e-seminars to help researchers learn about and implement microarray-based CGH experiments. The first of these, “Comparative Genomic Hybridization Using Oligonucleotide Microarrays and Total Genomic DNA,” is already available online. Upcoming e-seminars include:
- Feb. 2, 2005: “Interpreting the Consequences of Gene Gain and Loss”
Dr. Michael Bittner
Director, Molecular Diagnostics and Target Validation Division
Translational Genomics Research Institute, TGen
- Feb. 28, 2005: “Practical Considerations for Evaluating Array-CGH Results”
Scott Vacha, Ph.D., Agilent Technologies
Customers can register for and access these e-seminars at: www.agilent.com/chem/eseminars-genomics.
More information about Agilent’s CGH solution is available at www.agilent.com/chem/goCGH, from your local sales representative, or by e-mailing cag_sales-na@agilent.com. More information about Agilent’s microarray and informatics products is available at www.agilent.com/chem/dna.
About Agilent Technologies
Agilent Technologies Inc. (NYSE: A) is a global technology leader in communications, electronics, life sciences and chemical analysis. Agilent had net revenue of $7.2 billion in fiscal year 2004. Information about Agilent is available on the Web at www.agilent.com.
