A statistical approach to determining responses to individual peptides from pooled-peptide ELISpot data

• Published in: Journal of immunological methods Vol. 435; pp. 43 - 49
• Main Authors: Ström, Peter, Støer, Nathalie, Borthwick, Nicola, Dong, Tao, Hanke, Tomáš, Reilly, Marie
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.08.2016
• Subjects: AIDS Vaccines - immunology; Algorithms; Background adjustment; Data Accuracy; ELISpot assay; EM-algorithm; Enzyme-Linked Immunospot Assay - methods; HIV-1 - immunology; Human immunodeficiency virus 1; Humans; immune response; immune system; Internet; Leukocytes, Mononuclear - immunology; Likelihood Functions; Male; Peptide pools; peptides; Peptides - analysis; Peptides - immunology; Poisson Distribution; scientists; statistical analysis; vaccination; vaccines; Peptide pools; Background adjustment; EM-algorithm; ELISpot assay
• ISSN: 0022-1759; 1872-7905
• DOI: 10.1016/j.jim.2016.05.006

To investigate in detail the effect of infection or vaccination on the human immune system, ELISpot assays are used to simultaneously test the immune response to a large number of peptides of interest. Scientists commonly use “peptide pools”, where, instead of an individual peptide, a test well contains a group of peptides. Since the response from a well may be due to any or many of the peptides in the pool, pooled assays usually need to be followed by confirmatory assays of a number of individual peptides. We present a statistical method that enables estimation of individual peptide responses from pool responses using the Expectation Maximization (EM) algorithm for “incomplete data”. We demonstrate the accuracy and precision of these estimates in simulation studies of ELISpot plates with 90 pools of 6 or 7 peptides arranged in three dimensions and three Mock wells for the estimation of background. In analysis of real pooled data from 6 subjects in a HIV-1 vaccine trial, where 199 peptides were arranged in 80 pools if size 9 or 10, our estimates were in very good agreement with the results from individual-peptide confirmatory assays. Compared to the classical approach, we could identify almost all the same peptides with high or moderate response, with less than half the number of confirmatory tests. Our method facilitates efficient use of the information available in pooled ELISpot data to avoid or reduce the need for confirmatory testing. We provide an easy-to-use free online application for implementing the method, where on uploading two spreadsheets with the pool design and pool responses, the user obtains the estimates of the individual peptide responses. •ELISpot assays of peptide pools enable the estimation of responses to individual peptides.•There was good agreement between estimates and confirmatory assays in an application to HIV-1 immunogenicity.•The estimates can inform substantial reductions in the number confirmatory assays.•We provide an easy-to-use free online tool for obtaining the individual-peptide estimates.•The method enables more efficient use of information from pooled ELISpot assay data.