Reliable and sample saving gene expression analysis approach for diagnostic tool development

• Published in: Health physics (1958) Vol. 103; no. 2; p. 159
• Main Authors: Port, Matthias, Seidl, Christof, Ruf, Christian G, Riecke, Armin, Meineke, Viktor, Abend, Michael
• Format: Journal Article
• Language: English
• Published: United States 01.08.2012
• Subjects: Cell Line, Tumor; Environmental Exposure - adverse effects; False Positive Reactions; Gene Expression Profiling - methods; Gene Expression Profiling - standards; Humans; Oligonucleotide Array Sequence Analysis; Quality Control; Radiation Injuries - diagnosis; Radiation Injuries - genetics; Real-Time Polymerase Chain Reaction; Reproducibility of Results; RNA - genetics
• ISSN: 1538-5159
• DOI: 10.1097/HP.0b013e31824ac318

This work answers the question of whether it is necessary to hybridize individual instead of pooled RNA samples on microarrays for screening gene targets suitable as diagnostic tools for radiation exposure scenarios, while at the same time meeting comparable microarray quality criteria. For developing new clinical diagnostic tools, a two-stage study design was employed in five projects. At first, pooled and not individual RNA samples were hybridized on microarrays for screening purposes. Potential gene candidates were selected based on their fold-change only. This was followed by a validation/quantification step using individual RNA samples and quantitative RT-PCR. Quality criteria from the screening approach with pooled RNA samples were compared with published data from the MicroArray Quality Control (MAQC) consortium that hybridized each reference RNA sample separately and established quality criteria for microarrays. When comparing both approaches, only insignificant differences for quality criteria such as false positives, sensitivity, specificity, and overall agreement were found. However, material, costs, and time were drastically reduced when hybridizing pooled RNA and gene targets applicable for clinical diagnostic purposes could be successfully selected. In search of new diagnostic tools for radiation exposure scenarios, the two stage study design using either pooled or individual RNA samples on microarrays shows comparable quality criteria, but the RNA pooling approach saves unique material, costs, and efforts and successfully selects gene targets that can be used for the desired diagnostic purposes.