title: Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays.
abstract: The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development has created a need for tools to aid in the analysis and archival storage of the large amounts of data generated. We have developed a comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software applications developed in our laboratory specifically for this purpose. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis. Hierarchical clustering analysis is a powerful means of assessing relatedness within groups of tumors, based on their immunostaining with a panel of antibodies. Other analyses, such as generation of survival curves, construction of Cox regression models, or assessment of intra- or interobserver variation, can also be done readily on the reformatted data. Finally, the immunoprofile of a specific case can be rapidly retrieved from the archives and reviewed through the use of Stainfinder, a novel web-based program that creates a direct link between the clustered data and a digital image database. An on-line demonstration of this system is available at http://genome-www.stanford.edu/TMA/explore.shtml.
authors.affiliation: Department of Biochemistry, Stanford University Medical Center, California 94305, USA.
authors.forename: Chih Long
authors.initials: CL
authors.lastname: Liu
authors.forename: Wijan
authors.initials: W
authors.lastname: Prapong
authors.forename: Yasodha
authors.initials: Y
authors.lastname: Natkunam
authors.forename: Ash
authors.initials: A
authors.lastname: Alizadeh
authors.forename: Kelli
authors.initials: K
authors.lastname: Montgomery
authors.forename: C Blake
authors.initials: CB
authors.lastname: Gilks
authors.forename: Matt
authors.initials: M
authors.lastname: van de Rijn
mesh_terms: D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods*; D016247:Information Storage and Retrieval; D020407:Internet; D009363:Neoplasm Proteins / Q000276:immunology / Q000378:metabolism; D009369:Neoplasms / Q000145:classification / Q000378:metabolism*; D012984:Software
chemical_list: D009363:Neoplasm Proteins