Agilent CGH Arrays
The Agilent's CGH microarrays enable the scientist to confidently characterize chromosomal aberrations associated with developmental abnormalities, disease susceptibility, and differential drug responses. Highly-sensitive 60-mer oligonucleotide probes deliver the resolution needed to accurately examine chromosomal changes and to analyze complex and challenging samples. Versatile probe selection and customization options allow the scientist to target regions of interest, without compromising on data quality or cost.
Agilent CGH microarray platform combines sensitivity, flexibility and coverage, allowing scientists to finely view chromosomal variations and elucidate their relationship to disease susceptibility.
Sample Requirements
1. For optimal performance, use high quality, intact template genomic DNA; make sure that the DNA is free of RNA and protein contamination. High-quality genomic DNA samples should have an A260/A280 ratio of 1.8 to 2.0, indicating the absence of contaminating proteins.
2. Many organic compounds such as guanidinium isothiocyanate, alcohol and phenol as well as cellular contaminants such as carbohydrates, absorb strongly at A230.
3. An A260/A230 ratio of >2.0 is indicative of pure genomic DNA. Intact genomic DNA should appear as a compact, high-molecular weight band in an agarose gel, with no lower molecular weight smear. A small amount of degradation is not likely to interfere with downstream processing.
4. The samples will be quantitated by pico green for accurate assessment of double-stranded gDNA concentration.
| Microarray format | gDNA input µg | Volume of gDNA µl |
|---|---|---|
| 1x244K | 0.5-3.0 | 20.2 |
| 2x105K or 4x44K | 0.5-3.0 | 20.2 |
| 8x15K | 0.2-0.5 | 10.1 |
5. The input amount of DNA for the experimental labeling reaction must be the same as for the reference sample labeling reaction. Inaccurate DNA quantitation can lead to different DNA inputs into the experimental and reference labeling reactions, which increases assay noise (DLRSD). Different DNA isolation methods can create different quantitation artifacts, so a higher risk of assay noise exists when the experimental and reference DNA samples are isolated from different sources (for example, experimental DNA isolated from blood and reference DNA obtained from a Coriell cell line). To minimize assay noise, especially when experimental and reference samples are isolated from different sources, measure the DNA concentration with both a spectrophotometer (e.g. Nanodrop) and a fluorometer (e.g. Qubit) to give you two independent methods of measurement.
Agilent CGH Data
GSR Microarrays provides raw array data and Feature Extracted data. Genomic Workbench software can be purchased from Agilent to do the copy number analysis