Protein Function Microarrays: Design, Use and Bioinformatic Analysis in Cancer Biomarker Discovery and Quantitation

Abstract

Protein microarrays have many potential applications in the systematic, quantitative analysis of protein function, including in biomarker discovery applica- tions. In this chapter, we review available methodologies relevant to this field and describe a simple approach to the design and fabrication of cancer-antigen arrays suitable for cancer biomarker discovery through serological analysis of cancer patients. We consider general issues that arise in antigen content generation, microar- ray fabrication and microarray-based assays and provide practical examples of experimental approaches that address these. We then focus on general issues that arise in raw data extraction, raw data preprocessing and analysis of the resultant preprocessed data to determine its biological significance, and we describe compu- tational approaches to address these that enable quantitative assessment of serologi- cal protein microarray data. We exemplify this overall approach by reference to the creation of a multiplexed cancer-antigen microarray that contains 100 unique, purified, immobilised antigens in a spatially defined array, and we describe specific methods for serological assay and data analysis on such microarrays, including test cases with data originated from a malignant melanoma cohort.