Reuse of Bacterial Arti(cid:976)icial Clones Microarrays by Stripping with Sodium Hydroxide
Matchuporn Sukprasert MD1, Chonthicha Satirapod MD1, Worawan Lupthalug MD1, Wicharn Choktanasiri MD1, Kungpu Xu PhD2
Affiliation : 1 The Reproductive Endocrinology and Infertility unit, Department of Obstetrics and Gynecology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand 2 Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine and Infertility, Weill Cornell Medical College of Cornell University, New York, United State
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 arti(cid:976)icial 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
(cid:976)ibroblast cell were used with whole genome ampli(cid:976)ication 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.
Keywords : Microarray, Stripping, Sodium hydroxide
