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Quality control of DNA with on-chip electrophoresis for oligonucleotide-array comparative genomic hybridization
Breast Cancer Research volume 7, Article number: P4.42 (2005)
Comparative genomic hybridization (CGH) is an effective tool for the detection of genomic copy number aberrations. Many conditions such as cancer and developmental disorders occur when modifications, such as amplifications or deletions, to the genome lead to changes in gene copy number. The use of oligonucleotide-array CGH (aCGH) provides a much more sensitive assay for the detection of genomic variance than traditional CGH methods.
The Agilent 2100 bioanalyzer and associated RNA assays are now established industry standards for checking the integrity of RNA samples. Furthermore, the on-chip electrophoresis capabilities for DNA analysis play an important role in the quality-control assessment of DNA used in the context of aCGH. One important function of the bioanalyzer is to provide an assessment of the intactness of the input (genomic) DNA. For instance, current DNA amplification methods with φ 29 require an intact template but genomic DNA extracted from formalin-fixed paraffin embedded tissues exhibit a wide range of fragmentation patterns. It is extremely useful to know the quality of the DNA before using it in expensive and time-consuming reactions such as labeling and amplification. Here we look at the use of the bioanalyzer in the context of aCGH quality control, monitoring critical steps in the workflow including DNA amplification, digestion of template and labeling.
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Buhlmann, C., Mueller, O., Salowsky, R. et al. Quality control of DNA with on-chip electrophoresis for oligonucleotide-array comparative genomic hybridization. Breast Cancer Res 7, P4.42 (2005) doi:10.1186/bcr1172
- Comparative Genomic Hybridization
- Developmental Disorder
- Gene Copy Number
- Fragmentation Pattern
- Genomic Copy