A bioinformatics approach to identify patients with symptomatic peanut allergy using peptide microarray immunoassay Jing Lin, PhD, Francesca M. Bruni,

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A bioinformatics approach to identify patients with symptomatic peanut allergy using peptide microarray immunoassay Jing Lin, PhD, Francesca M. Bruni,

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Presentation transcript:

A bioinformatics approach to identify patients with symptomatic peanut allergy using peptide microarray immunoassay Jing Lin, PhD, Francesca M. Bruni, MD, Zhiyan Fu, PhD, Jennifer Maloney, MD, Ludmilla Bardina, MSc, Attilio L. Boner, MD, Gustavo Gimenez, BSc, Hugh A. Sampson, MD Journal of Allergy and Clinical Immunology Volume 129, Issue 5, Pages 1321-1328.e5 (May 2012) DOI: 10.1016/j.jaci.2012.02.012 Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 1 Comparison of IgE (A) and IgG4 (B) binding diversity to peanut allergens Ara h 1, Ara h 2, and Ara h 3, and binding diversity to individual allergen Ara h 1, Ara h 2, and Ara h 3 between peanut-allergic and peanut-tolerant groups. Antibody binding diversity was measured as the number of positive peptides (robust Z score > 3) determined by using peptide microarray immunoassay. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 2 Comparison of IgE (above x-axis line) and IgG4 binding (below x-axis line) to peptides of Ara h 1, Ara h 2, and Ara h 3 between peanut-allergic (red lines) and peanut-tolerant (blue lines) groups. The bottom x-axis shows the overlapping peptides, and the top x-axis shows the corresponding amino acid number of the peptide. The y-axis shows the percentage of patients within each group showing positive binding to each peptide. IgE-binding regions/epitopes identified by using TileMap and the key peptide biomarkers identified by using machine learning methods are indicated with red circles and asterisks, respectively. The previously identified epitopes and immunodominant epitopes are indicated with gray and blue diamonds, respectively. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 3 Decision tree built for classifying peanut-allergic and peanut-tolerant individuals. Sixty-two individuals were sorted from root (top circle) to leaf nodes (rectangles), based on their IgE reaction to a panel of peanut peptide biomarkers defined at each node (circle), which represent the splitting points. The peptides selected for each splitting point are listed under the circles, and the splitting threshold (Z score) appears in the circle. At each splitting point, individuals with IgE reactions to the selected peptide at or above the threshold are assigned to the right branch and below the threshold to the left. The value on the branch shows the number of individuals passing through. The percentage value under the leaf nodes represents the calculated accuracy. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 4 Comparison of the diagnostic performance of different allergy tests and analysis methods in predicting the outcome of DBPCFC. The area under the ROC curve indicates how well a test method can distinguish between 2 diagnostic groups (peanut allergic vs peanut tolerant). The diagonal line indicates a completely random guess. Both IgE binding diversity (expressed as the number of positive peptides) and intensity (express as Z score) were measured by using peptide microarray. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E1 Heatmap visualizing IgE (A) and IgG4 (B) binding to all individual peptides from peanut-tolerant and peanut-allergic subjects. Peanut-tolerant subjects were divided into outgrown patients (n = 13) and sensitized patients who never had clinical reactions to peanut (n = 18). Data are presented as Z scores by using TIGR Multiexperiment Viewer. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E2 Results from peptide inhibition assay. A, IgE reactions from the control array, which was immunolabeled with the serum pool without any added inhibiting peptide. B, IgE reactions from the arrays that were immunolabeled with the serum pool preincubated with several inhibiting peptides (indicated with red squares). Data are presented as Z scores by using TIGR Multiexperiment Viewer. Results were combined from replicate arrays and only IgE reactions to the targeted peptides and 4 neighboring peptides are shown. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E3 A serum dilution experiment comparing the sensitivity of Alexa and Dendrimer detection systems. Data are presented as Z scores by using TIGR Multiexperiment Viewer. The “IgE level” was calculated on the basis of milk sIgE level of the serum pool (850 kUA/L, as measured by using UniCAP) and the dilution factor. Note that there is an additional dilution (1:12,500) for Dendrimer detection systems. NC, Nonatopic control. Journal of Allergy and Clinical Immunology 2012 129, 1321-1328.e5DOI: (10.1016/j.jaci.2012.02.012) Copyright © 2012 American Academy of Allergy, Asthma & Immunology Terms and Conditions