Gene Expression Detection Assay for Cancer Clinical Use

Narrandes, Shavira; Xu, Wayne

Minute tissue samples (typically 0.6 mm in diameter) from up to 1000 different tissues can be analyzed on one microscope glass slide. Since all tissue samples are simultaneously analyzed with the same set of reagents, standardization, speed of processing, and cost are all efficient so that normalization to account for technical experimental variances between samples need not be extensively performed. 67, 68, 70 The tissue sections can first be analyzed via H and E staining or immunofluorescent ISH. An automated scanning system can be purchased to scan and analyze the prepared TMA slides. As the tests carried out on a TMA may vary depending on one's experimental design and purpose, a different combination of gene detection and analysis may be performed. Autoradiography or immunohistochemistry may be applied for detection followed by fluorescent microscopy or imaging by an array scanner may be used for the assessment of fluorescent levels in a TMA. 69 For example, one can use digital imaging scanning and processing technologies and Microsoft Access and Excel as databases, then compare their results to clinical data. 68 As various techniques exist to visualize TMAs, numerous data analysis and normalization methods have been developed. The Tissue Array Management and Evaluation Environment (TAMEE) web-based database application that stores experimental parameters, TMA images, and evaluation results is available for TMA data analysis and management for the whole TMA workflow. 72 The Tissue Array Co-Occurrence Matrix Analysis (TACOMA) uses local inter-pixel relationships to quantify cellular phenotypes to recognize specific staining patterns and output a score of categorization. 73