Reuse of bacterial artificial clones microarrays by stripping with sodium hydroxide

Abstract

© 2018, Medical Association of Thailand. All rights reserved. Background: Array comparative genomic hybridization [CGH] was established as the method of choice for fast and accurate detection of numerical chromosomal abnormalities. However, the main limitation is due to the price of the array themselves. The present study tried to demonstrate a method for stripping DNA-DNA duplexes in bacterial artificial clone [BAC] array by using sodium hydroxide (NaOH)/stress corrosion cracking [SCC]. Additionally, after stripping, the microarray can be reused for further experiments. Objective: To compare the accuracy in detected chromosomal aberrations between new and stripped slide by using NaOH/SCC as an array-stripping agent. Materials and Methods: An experimental study was performed in an academic medical center. Two human known cell lines from fibroblast cell were used with whole genome amplification and microarray step according to the BlueGnome 24Sure protocol. Data processing was analyzed with Bluefuse software analysis. All detected copy number changes were compared to known aberrations listed in public databases. A 4 mM NaOH/0.5x SCC at 63°C was used as an array-stripping agent. The main outcome measure was the percentage agreement of chromosome interpretation between new and stripped microarray slide. Results: The present study demonstrated that the stripped slides with NaOH/SCC at appropriate temperature (63°C) have almost identical hybridization pattern and 100% agreement of chromosome interpretation to the new slides. Conclusion: The authors found that stripping BAC microarray by mild alkali treatment (4 mM NaOH/0.5x SCC) at appropriate temperature (63°C) do not compromise the results. It has been validated and showed 100% agreement of chromosome interpretation. The reused microarray slide is a cost-effective method to develop microarray experiment.