Selecting control genes for RT-QPCR using public microarray data

Popovici, Vlad; Goldstein, Darlene R; Antonov, Janine; Jaggi, Rolf; Delorenzi, Mauro; Wirapati, Pratyaksha (2009). Selecting control genes for RT-QPCR using public microarray data. BMC bioinformatics, 10, p. 42. London: BioMed Central 10.1186/1471-2105-10-42

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BACKGROUND: Gene expression analysis has emerged as a major biological research area, with real-time quantitative reverse transcription PCR (RT-QPCR) being one of the most accurate and widely used techniques for expression profiling of selected genes. In order to obtain results that are comparable across assays, a stable normalization strategy is required. In general, the normalization of PCR measurements between different samples uses one to several control genes (e.g. housekeeping genes), from which a baseline reference level is constructed. Thus, the choice of the control genes is of utmost importance, yet there is not a generally accepted standard technique for screening a large number of candidates and identifying the best ones. RESULTS: We propose a novel approach for scoring and ranking candidate genes for their suitability as control genes. Our approach relies on publicly available microarray data and allows the combination of multiple data sets originating from different platforms and/or representing different pathologies. The use of microarray data allows the screening of tens of thousands of genes, producing very comprehensive lists of candidates. We also provide two lists of candidate control genes: one which is breast cancer-specific and one with more general applicability. Two genes from the breast cancer list which had not been previously used as control genes are identified and validated by RT-QPCR. Open source R functions are available at http://www.isrec.isb-sib.ch/~vpopovic/research/ CONCLUSION: We proposed a new method for identifying candidate control genes for RT-QPCR which was able to rank thousands of genes according to some predefined suitability criteria and we applied it to the case of breast cancer. We also empirically showed that translating the results from microarray to PCR platform was achievable.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > Forschungsbereich Pathologie > Forschungsgruppe Molekularbiologie

UniBE Contributor:

Antonov, Janine and Jaggi, Rolf

ISSN:

1471-2105

Publisher:

BioMed Central

Language:

English

Submitter:

Factscience Import

Date Deposited:

04 Oct 2013 15:13

Last Modified:

17 Dec 2014 20:45

Publisher DOI:

10.1186/1471-2105-10-42

PubMed ID:

19187545

Web of Science ID:

000264007300001

BORIS DOI:

10.7892/boris.32304

URI:

https://boris.unibe.ch/id/eprint/32304 (FactScience: 197365)

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