title: Processing and analysis of serum antibody binding signals from Printed Glycan Arrays for diagnostic and prognostic applications.
abstract: Procedures for data preprocessing, quality control, data analysis, evaluation and visualization of the new high-throughput biomarker platform based on printed glycan arrays (PGA) are presented in this paper. PGAs are similar in concept to DNA arrays but contain deposits of various carbohydrate structures (glycans) instead of spotted DNAs. PGA biomarker discovery for the early detection, diagnosis and prognosis of human malignancies and viral diseases is based on the response of the immune system as measured by the level of binding of anti-glycan antibodies from human serum to the glycans on the array. Procedures related to PGA data processing are herein demonstrated in a pilot study of cases representing 50 sera from patients with malignant mesothelioma and a control sample of 65 sera from high risk subjects exposed to asbestos without symptoms of disease.
authors: Department of Computer Science, San Diego State University, San Diego, CA 92182, USA. marko@cs.sdsu.edu
authors: Marko I
authors: MI
authors: Vuskovic
authors: Hongyu
authors: H
authors: Xu
authors: Nicolai V
authors: NV
authors: Bovin
authors: Harvey I
authors: HI
authors: Pass
authors: Margaret E
authors: ME
authors: Huflejt
mesh_terms: D000906:Antibodies / Q000097:blood*; D001194:Asbestos / Q000633:toxicity; D015415:Biomarkers / Q000097:blood; D016022:Case-Control Studies; D006801:Humans; D008654:Mesothelioma / Q000175:diagnosis / Q000209:etiology / Q000401:mortality; D046228:Microarray Analysis / Q000379:methods*; D011134:Polysaccharides / Q000737:chemistry* / Q000276:immunology; D011237:Predictive Value of Tests; D016019:Survival Analysis
chemical_list: D000906:Antibodies; D015415:Biomarkers; D011134:Polysaccharides; D001194:Asbestos