EPIphany—A Platform for Analysis and Visualization of Peptide Immunoarray Data

Abstract

Antibodies are critical effector molecules of the humoral immune system. Upon infection or vaccination, populations of antibodies are generated which bind to various regions of the invading pathogen or exogenous agent. Defining the reactivity and breadth of this antibody response provides an understanding of the antigenic determinants and enables the rational development and assessment of vaccine candidates. High-resolution analysis of these populations typically requires advanced techniques such as B cell receptor repertoire sequencing, mass spectrometry of isolated immunoglobulins, or phage display libraries that are dependent upon equipment and expertise which are prohibitive for many labs. High-density peptide microarrays representing diverse populations of putative linear epitopes (immunoarrays) are an effective alternative for high-throughput examination of antibody reactivity and diversity. While a promising technology, widespread adoption of immunoarrays has been limited by the need for, and relative absence of, user-friendly tools for consideration and visualization of the emerging data. To address this limitation, we developed EPIphany, a software platform with a simple web-based user interface, aimed at biological users, that provides access to important analysis parameters, data normalization options, and a variety of unique data visualization options. This platform provides researchers the greatest opportunity to extract biologically meaningful information from the immunoarray data, thereby facilitating the discovery and development of novel immuno-therapeutics.

High-resolution analysis of long-term serum antibodies in humans following convalescence of SARS-CoV-2 infection

“…Images were scanned at 10 µm resolution and data acquired using GenePix software (version 6.0). Data was analyzed with the web-based service EPIphany ( https://epiphany.usask.ca/epiphany/ 34 ). Briefly, background-corrected foreground was used to extract spot signal intensity and no normalization was applied.…”

MARTin—an open-source platform for microarray analysis

“…In addition, a versatile solution for custom printing formats or data acquisition array types is entirely missing. Beyond the quantification of microarray data, a multitude of analysis algorithms has been devised to automatically derive results through data aggregation (Renard et al, 2011;Parker Cates et al, 2021;Cathryn et al, 2022). To make algorithms such as these viable for mass data processing a certain degree of output-data standardization has to be met.…”