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How to choose a normalization strategy for miRNA quantitative real-time (QPCR) arrays
Högskolan i Skövde.
Örebro University, School of Health and Medical Sciences. (Tumörbiologi, Bioinformatik)
Högskolan i Skövde.
2011 (English)In: Journal of Bioinformatics and Computational Biology, ISSN 0219-7200, Vol. 9, no 6, 795-812 p.Article in journal (Refereed) Published
Abstract [en]

Low-density arrays for quantitative real-time PCR (qPCR) are increasingly being used as an experimental technique for miRNA expression profiling. As with gene expression profiling using microarrays, data from such experiments needs effective analysis methods to produce reliable and high-quality results. In the pre-processing of the data, one cruciala nalysis step is normalization, which aims to reduce measurement errors and technical variability among arrays that might have arisen during the execution of the experiments. However, there are currently a number of different approaches to choose among and an unsuitable applied method may induce misleading effects, which could affect the subsequent analysis steps and thereby any conclusions drawn from the results. The hoice of normalization method is hence an important issue to consider. In this study we present the comparison of a number of data-driven normalization methods for TaqManlow-density arrays for qPCR and different descriptive statistical techniques that can facilitate the choice of normalization method. The performance of the normalization methods was assessed and compared against each other as well as against standard normalization using endogenous controls. The results clearly show that the data-driven methods reduce variation and represent robust alternatives to using endogenous controls.

Place, publisher, year, edition, pages
2011. Vol. 9, no 6, 795-812 p.
National Category
Medical and Health Sciences Natural Sciences
Research subject
URN: urn:nbn:se:oru:diva-25827DOI: 10.1142/S0219720011005793ISI: 000297096300009OAI: diva2:552276
Available from: 2012-09-17 Created: 2012-09-13 Last updated: 2012-11-29Bibliographically approved
In thesis
1. Identification of miRNA expression profiles for diagnosis and prognosis of prostate cancer
Open this publication in new window or tab >>Identification of miRNA expression profiles for diagnosis and prognosis of prostate cancer
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cancer of the prostate (CaP) is the most common malignancy diagnosed in men in the Western society. During the last years, prostate specific antigen (PSA) has been used as a biomarker for CaP, although a high PSA value is not specific for CaP. Thus, there is an urgent need for new and improved diagnostic markers for CaP.

In this thesis, the aim was to find a miRNA signature for diagnosis of CaP and to elucidate if differences in behavior between transition zone and peripheral zone tumors are reflected in miRNA expression. One of the major findings is anexpression signature based on nine miRNAs that with high accuracy (85%) could classify normal and malignant tissues from the transition zone of the prostate. The results furthermore show that the major differences in miRNA expression are found between normal and malignant tissues, rather than between the different zones. In addition, tumors arising in the peripheral zone have fewer changes in miRNA expression compared to tumors in the transition zone, indicating that the peripheral zone is more prone to tumor development compared to the transition zone of the prostate.

A crucial step in pre-processing of expression data, in order to differentiate true biological changes, is the normalization step. Therefore, an additional aim of this thesis was to compare different normalization methods for qPCR array data in miRNA expression experiments. The results show that data-driven methods based on quantile normalization performs the best. The results also show that in smaller miRNA expression studies, only investigating a few miRNAs, RNU24 is the most suitable endogenous control gene for normalization.

Taken together, the results in this thesis show the importance of miRNAs and the possibility of their future use as biomarkers in the field of prostate cancer.

Place, publisher, year, edition, pages
Örebro: Örebro universitet, 2012. 55 p.
Örebro Studies in Medicine, ISSN 1652-4063 ; 74
Prostate cancer, microRNAs, prostate zones, normalization, endogenous controls
National Category
Medical and Health Sciences Cancer and Oncology
Research subject
urn:nbn:se:oru:diva-25600 (URN)978-91-7668-888-5 (ISBN)
Public defence
2012-10-26, Wilandersalen, Universitetssjukuset (USÖ), Örebro, 13:00 (Swedish)
Available from: 2012-08-30 Created: 2012-08-30 Last updated: 2016-04-19Bibliographically approved

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