%0 Journal Article
%T Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
%A Jarmo Ritari
%A Lars Paulin
%A Jenni Hultman
%A Petri Auvinen
%J BMC Research Notes
%D 2009
%I BioMed Central
%R 10.1186/1756-0500-2-249
%X Here we demonstrate the application of a per-spot hybridization control oligonucleotide probe and a novel way of computing normalization for tag array data. The method takes into account the absolute value of the detection probe signal and the variability in the control probe signal to significantly alleviate problems caused by artefacts and noise on low quality microarrays.Diagnostic microarray platforms require experimental and computational tools to enable efficient correction of array artefacts. The techniques presented here improve the signal to noise ratio and help in determining true positives with better statistical significance and in allowing the use of arrays with poor quality that would otherwise be discarded.Nucleic acid detection by ligation and single-nucleotide extension minisequencing techniques take advantage of the catalytic selectivity of DNA ligase and polymerase enzymes, respectively, to recognize a unique position in a target DNA strand. In ligation assays, two specific ssDNA oligonucleotide detection probes are designed to hybridize adjacently on target DNA strand so that the 3' end of the label-carrying probe recognizes a discriminating position and is ligated to the phosphorylated 5' end of the other probe in the presence of a matching target molecule (figure 1A) [1,2]. Ligation detection can also be implemented as a single probe which is circularized upon ligation [3]. In minisequencing, the target is recognized through the addition of a specific labeled dideoxynucleotide to the 3' end of the oligonucleotide detection primer annealed immediately upstream of a discriminating position in the target (figure 1B) [4,5]. Both methods allow tagging of the probes for detection on a microarray platform containing complementary tag sequences providing uniform thermodynamic hybridization properties for all probes. The relatively high throughput and superior accuracy over traditional microarray and PCR based methods have motivated the application of l
%U http://www.biomedcentral.com/1756-0500/2/249