A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling

• Published in: Journal of immunological methods Vol. 395; no. 1-2; pp. 1 - 13
• Main Authors: Imholte, Greg C., Sauteraud, Renan, Korber, Bette, Bailer, Robert T., Turk, Ellen T., Shen, Xiaoying, Tomaras, Georgia D., Mascola, John R., Koup, Richard A., Montefiori, David C., Gottardo, Raphael
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 30.09.2013
• Subjects: AIDS Vaccines - immunology; analytical methods; Antibodies; antibody microarrays; Antibody Specificity; clinical trials; Clinical Trials as Topic - statistics & numerical data; data collection; Data Interpretation, Statistical; Epitope Mapping - statistics & numerical data; Epitopes - metabolism; HIV Antibodies - biosynthesis; HIV Antibodies - metabolism; HIV Antigens - metabolism; HIV-1 - immunology; Human immunodeficiency virus 1; Humans; Immunologic Techniques - methods; Immunologic Techniques - statistics & numerical data; Normalization; Peptide microarrays; peptides; Positivity calls; Protein Array Analysis - methods; Protein Array Analysis - statistics & numerical data; Protein Interaction Mapping - statistics & numerical data; ROC Curve; Software; vaccines; Visualization; Peptide microarrays; Antibodies; Visualization; Positivity calls; Normalization; Software
• ISSN: 0022-1759; 1872-7905; 1872-7905
• DOI: 10.1016/j.jim.2013.06.001

We present an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization. Current techniques for the normalization of such data sets do not account for non-specific binding activity. A novel normalization technique based on peptide sequence information quickly and effectively reduced systematic biases. We also employed a sliding mean window technique that borrows strength from peptides sharing similar sequences, resulting in reduced signal variability. A smoothed signal aided in the detection of weak antibody binding hotspots. A new principled FDR method of setting positivity thresholds struck a balance between sensitivity and specificity. In addition, we demonstrate the utility and importance of using baseline control measurements when making subject-specific positivity calls. Data sets from two human clinical trials of candidate HIV-1 vaccines were used to validate the effectiveness of our overall computational framework.