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

BACKGROUND: 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 m...

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Detalles Bibliográficos
Autores principales: Ritari, Jarmo, Paulin, Lars, Hultman, Jenni, Auvinen, Petri
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799435/
https://www.ncbi.nlm.nih.gov/pubmed/20003444
http://dx.doi.org/10.1186/1756-0500-2-249
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author Ritari, Jarmo
Paulin, Lars
Hultman, Jenni
Auvinen, Petri
author_facet Ritari, Jarmo
Paulin, Lars
Hultman, Jenni
Auvinen, Petri
author_sort Ritari, Jarmo
collection PubMed
description BACKGROUND: 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. FINDINGS: 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. CONCLUSIONS: 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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spelling pubmed-27994352009-12-30 Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays Ritari, Jarmo Paulin, Lars Hultman, Jenni Auvinen, Petri BMC Res Notes Technical Note BACKGROUND: 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. FINDINGS: 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. CONCLUSIONS: 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. BioMed Central 2009-12-14 /pmc/articles/PMC2799435/ /pubmed/20003444 http://dx.doi.org/10.1186/1756-0500-2-249 Text en Copyright ©2009 Ritari et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Note
Ritari, Jarmo
Paulin, Lars
Hultman, Jenni
Auvinen, Petri
Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
title Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
title_full Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
title_fullStr Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
title_full_unstemmed Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
title_short Application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
title_sort application of hybridization control probe to increase accuracy on ligation detection or minisequencing diagnostic microarrays
topic Technical Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799435/
https://www.ncbi.nlm.nih.gov/pubmed/20003444
http://dx.doi.org/10.1186/1756-0500-2-249
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