Processing and analysis of serum antibody binding signals from Printed Glycan Arrays for diagnostic and prognostic applications

Authors:
Marko I. Vuskovic;Hongyu Xu;Nicolai V. Bovin;Harvey I. Pass;Margaret E. Huflejt
Affiliations:
Department of Computer Science, College of Science San Diego State University, San Diego, CA 92182, USA.;Transaction Analytics Department, Fair Issac Corporation, San Diego, CA 92130, USA.;Carbohydrate Chemistry Laboratory, Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.;Department of Cardiothoracic Surgery, New York University, School of Medicine, New York, 10016 NY, USA.;Department of Cardiothoracic Surgery, New York University, School of Medicine, New York, 10016 NY, USA
Venue:
International Journal of Bioinformatics Research and Applications
Year:
2011

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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.