Graph‐based deconvolution analysis of multiplex sandwich microarray immunoassays: applications for environmental monitoring

Abstract

The sandwich microarray immunoassay (SMI) is a powerful technique for the analysis and characterization of environmental samples, from the identification of microorganisms to specific bioanalytes. As the number of antibodies increases, however, unspecific binding and cross-reactivity can become a problem. To cope with such difficulties, we present here the concept of antibody graph associated to a sandwich antibody microarray. Antibody graphs give valuable information about the antibody cross-reactivity network and all the players involved in the sandwich format: capturing and tracer antibodies, the antigenic sample and the degree of cross-reactivity between antibodies. Making use of the information contained in the antibody graph, we have developed a deconvolution method that disentangles the antibody cross-reactivity events and gives qualitative information about the composition of the experimental sample under study. We have validated the method by using a 66 antibody-containing microarray to describe known antigenic mixtures as well as natural environmental samples characterized by 16S-RNA gene phylogenetic analysis. The application of our antibody graph and deconvolution method allowed us to discriminate between true specific antigen-antibody reactions and spurious signals on a microarray designed for environmental monitoring.

Graph Based Study of Allergen Cross-Reactivity of Plant Lipid Transfer Proteins (LTPs) Using Microarray in a Multicenter Study

“…In the context of graph theory, graphs, also known as networks [7], [10], represent relationships between objects and have been used to obtain reliable information from many different biological systems [11]–[16], including a network that has been established for human diseases [17]. In particular, the graph theory has recently been used to describe cross-reactions between antibodies in a sandwich microarray immunoassay [17], and we use it in a similar way here to study allergen cross-reactivity.…”

“…In particular, the graph theory has recently been used to describe cross-reactions between antibodies in a sandwich microarray immunoassay [17], and we use it in a similar way here to study allergen cross-reactivity.…”

The Involvement of Thaumatin-Like Proteins in Plant Food Cross-Reactivity: A Multicenter Study Using a Specific Protein Microarray

“…In the graphs used in this work, nodes represent allergens, and links (which are undirected and weighted) represent the co-sensitization of sera for pairs of allergens. Recently, these graphs have been used to describe the cross-reactions in an antibody microarray immunoassay in a sandwich format [15], and, in fact, there is an extensive literature about their usefulness for analyzing biological systems [16], [17], [18], [19], [20]. In our particular case, we have focused on developing the potential of graph theory for analyzing TLP microarrays and for applying them in the field.…”

Prokaryotic communities and operating metabolisms in the surface and the permafrost of Deception Island (Antarctica)

“…LDChip300, initially designed for life detection in planetary exploration (Parro et al ., 2005; 2008; 2011a), contains more than 300 antibodies developed against bacterial strains from almost all known phyla, crude extracts from environmental samples, biological polymers, proteins and peptides involved in selected metabolic pathways, cell wall components, etc. (Parro et al ., 2008; 2011b,c; Rivas et al ., 2008; 2011). By analysing the microbiology and the biomarker profiling associated to different depths and water content, our research may contribute the understanding of the ecology and the evolution of permanently frozen soils on Earth, from recent ones like this of Deception Island, to ancient ones like that of the Antarctica's Dry Valleys.…”