title: A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling.
abstract: 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.
authors.affiliation: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, M2-C200, PO Box 19024, Seattle, WA 98109-1024, United States. gimholte@uw.edu
authors.forename: Greg C
authors.initials: GC
authors.lastname: Imholte
authors.forename: Renan
authors.initials: R
authors.lastname: Sauteraud
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
authors.forename: Robert T
authors.initials: RT
authors.lastname: Bailer
authors.forename: Ellen T
authors.initials: ET
authors.lastname: Turk
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Shen
authors.forename: Georgia D
authors.initials: GD
authors.lastname: Tomaras
authors.forename: John R
authors.initials: JR
authors.lastname: Mascola
authors.forename: Richard A
authors.initials: RA
authors.lastname: Koup
authors.forename: David C
authors.initials: DC
authors.lastname: Montefiori
authors.forename: Raphael
authors.initials: R
authors.lastname: Gottardo
mesh_terms: D016915:AIDS Vaccines / Q000276:immunology*; D000918:Antibody Specificity; D002986:Clinical Trials as Topic / Q000706:statistics & numerical data; D003627:Data Interpretation, Statistical; D018604:Epitope Mapping / Q000706:statistics & numerical data; D000939:Epitopes / Q000378:metabolism; D015483:HIV Antibodies / Q000096:biosynthesis / Q000378:metabolism*; D015488:HIV Antigens / Q000378:metabolism; D015497:HIV-1 / Q000276:immunology; D006801:Humans; D007158:Immunologic Techniques / Q000379:methods / Q000706:statistics & numerical data; D040081:Protein Array Analysis / Q000379:methods* / Q000706:statistics & numerical data; D025941:Protein Interaction Mapping / Q000706:statistics & numerical data; D012372:ROC Curve
chemical_list: D016915:AIDS Vaccines; D000939:Epitopes; D015483:HIV Antibodies; D015488:HIV Antigens
keywords: Antibodies; Normalization; Peptide microarrays; Positivity calls; Software; Visualization