Negative Controls

Negative control probes are randomly permutated sequences that should not hybridize to the DNA template. Negative controls are important for methylation studies because of a decrease in sequence complexity after bisulfite treatment. The mean signal of these probes defines the system background. It is a comprehensive measurement of background, including signal resulting from cross-hybridization and nonspecific extension and imaging system background. The GenomeStudio platform uses the average signal and standard deviation of 600 negative controls to establish detection limits for the methylation probes. Performance of negative controls should be monitored in both green and red channels.