Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays

DNA sequencing and genomics laboratory, Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland. .
BMC Research Notes 12/2009; 2(1):249. DOI: 10.1186/1756-0500-2-249
Source: PubMed


Nucleic acid detection based on ligation reaction or single nucleotide extension of ssDNA probes followed by tag microarray hybridization provides an accurate and sensitive detection tool for various diagnostic purposes. Since microarray quality is crucial for reliable detection, these methods can benefit from correcting for microarray artefacts using specifically adapted techniques.
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.

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    • "The application of LDR coupled to a universal array (UA-LDR) for microbial identification has been described by various authors [27–29], especially for clinical diagnostics. Cremonesi et al. [11] successfully applied the methodology to detect and identify bacterial species causing mastitis in dairy ruminants, also including species that are of great interest as responsible of foodborne disease and food spoilage. "
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    04/2014; 2014:156323. DOI:10.1155/2014/156323
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    • "The microarray experiments were performed on Arrayit or Agilent microarray platforms. The 16 compartment slides purchased from Arrayit (Sunnyvale, CA, USA) were designed and used as described previously [42]. Briefly, for hybridisation to Arrayit microarrays, a mixture containing 20 μl of PCR/lambda exonuclease reaction, 5X SSC, 20 μg of herring sperm DNA (Sigma-Aldrich, Steinheim, Germany) and 5 pmol of control oligo in a final volume of 60 μl was applied to each subarray according to manufacturer's instructions. "
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