SBIR-STTR Award

There is an urgent need of bioinformatic tools for mining glycan array data in order to accurately and statistically study the interactions between cell-surface glycans and glycan-binding proteins. We propose here to develop a software and hardware integrated system for the interpretation of glycan array data. The problem with existing glycan array data mining tools is that they give binding information only for simplistic substructures of glycans and not complex binding determinants, and also that they are not automated. To solve this problem, Z Biotech, LLC (a glycan array provider) will team with Dr. Brian Haab's lab in Van Andel Research Institute (a software provider) to develop and improve a robust glycan array data mining tool; MotifFinder. Z Biotech has invented a robust glycan array platform having the advantage to display glycans on solid surfaces in a multivalent form. The glycan arrays Z Biotech provides have superior performance with the criteria for a high-quality microarray, which is suitable for generation of glycan array data for evaluation of a bioinformatic tool like MotifFinder. In addition, The Haab research group has been leading developments in glycan-array bioinformatics. They were the first to publish an algorithm for the analysis of glycan-array data in 2010, and subsequently have contributed many innovations. The proposed research strategy has been supported by a preliminary experimental investigation under collaboration between the two glycoscience groups. In Phase I, the specific aims are (1) development of a catch-all 212 Glycan Array as a primary array for software testing, (2) manufacture individual glycan array subarrays and run assays used for testing software, and (3) optimize and validate software for the automated interpretation of glycan-array data. These are realistic goals within the SBIR program scope, and the resultant glycan array packages with hardware and software will have a broad impact on glycobiology research, glycan-related biomarker characterization, and new drug development targeting glycans.

Public Health Relevance Statement:
Project Narrative Glycan array is a vital tool for studying carbohydrate-protein interactions, biomarker discovery, and potentially drug screening and there is need for a bioinformatics tool for interpretation of glycan array data. The goal of this SBIR project is to develop a robust bioinformatics tool for the analysis of glycan array data. The resulting bioinformatic tools will also deepen our understanding of how glycans contribute to diseases, such as cancers and infectious diseases.

Project Terms:
Algorithms; Animals; Epitopes; Binding Determinants; Antigenic Determinants; Automation; Biological Assay; Biologic Assays; Bioassay; Assay; Biotechnology; Biotech; Malignant Neoplasms; neoplasm/cancer; malignancy; Malignant Tumor; Cancers; plasmalemma; Plasma Membrane; Cytoplasmic Membrane; Cell membrane; Systematics; Classification; Infectious Disorder; Infectious Diseases; Infectious Disease Pathway; Communicable Diseases; Communities; Disorder; Disease; Mucopolysaccharides; Glycosaminoglycans; Sphingoglycolipids; Asialogangliosides; Glycosphingolipids; Goals; Heparan Sulfate; Heparitin Sulfate; Modern Man; Human; Laboratories; Lectin; Libraries; Mannopyranoside; Mannopyranose; D-Mannose; Mannose; Manuals; Mining; Mucus Glycoprotein; Mucins; Names; Plants; Glycans; Polysaccharides; Problem Solving; Publishing; Research; Research Institute; Researchers; Investigators; Research Personnel; Running; Software; Computer software; Specificity; Statistical Study; statistics; Systems Analyses; Systems Analysis; Testing; Vaccines; Work; Generations; base; macromolecule; improved; Surface; Solid; Phase; Biological; Evaluation; Intuition; Individual; Binding Proteins; bound protein; Protein Binding; Ligand Binding Protein Gene; Ligand Binding Protein; cancer immunotherapy; immunotherapy of cancer; immunotherapy for cancer; anticancer immunotherapy; anti-cancer immunotherapy; Collaborations; Therapeutic; tool; programs; Investigation; Complex; Event; System; Services; Performance; receptor; Receptor Protein; success; microbial; Structure; Categories; new technology; novel technologies; Cell surface; Sampling; drug development; Provider; Bioinformatics; Bio-Informatics; Molecular Interaction; Binding; datamining; data mining; Biological Testing; Data; Glycobiology; Protein-Carbohydrate Interaction; Protein Analysis; Small Business Innovation Research Grant; Small Business Innovation Research; SBIR; Validation; Characteristics; Process; Development; developmental; Output; pathogen; innovation; innovative; innovate; novel therapeutics; novel therapy; novel drugs; novel drug treatments; next generation therapeutics; new therapy; new therapeutics; new drugs; new drug treatments; commercial application; Biological Markers; biomarker; biologic marker; bio-markers; Algorithmic Analysis; Analysis of Algorithms; Analyses of Algorithms; Algorithmic Analyses; biomarker discovery; Structural Protein; Drug Screening; bioinformatics tool; bio-informatics tool

There is an urgent need of analysis tools for mining glycan array data in order to accurately and statistically study the interactions between cell-surface glycans and glycan-binding proteins. In this SBIR program we propose to develop a software and hardware integrated system for analysis and interpretation of glycan array data. The problem with existing glycan array data mining tools is that they give binding information only for simplistic substructures of glycans and not complex binding determinants, and they lack consistent signal quantification in an automated way. To solve this problem, Z Biotech, LLC (a glycan array provider) is teaming with Dr. Brian Haab's lab at the Van Andel Institute (a software provider) to develop and improve a robust glycan-array data mining tool (MotifFinder) and a glycan-array image analysis program (SignalFinder). Z Biotech has invented a robust glycan array platform having the advantage to display glycans on solid surfaces in a multivalent form. The glycan arrays Z Biotech provides have superior performance with the criteria for a high-quality microarray, which is suitable for generation of glycan array data for evaluation of analysis tools like MotifFinder and SignalFinder. In addition, the Haab research group has been leading developments in glycan-array analysis tools. They were the first to publish an algorithm for the analysis of glycan-array data in 2010, and subsequently have contributed many innovations. In the Phase I project, we developed MotifFinder for fully automating the analysis, including new approaches for identifying subtle patterns and features in the glycan array data. In addition, we developed SignalFinder for the automated image analysis of glycan-array images. This software program addresses the previous bottlenecks and limitations in the array image analysis. It is built on the unique algorithm that has functioned well for the automated analysis of immunofluorescence and microarray images. The goal for the Phase II project is to enhance the ability of the two glycan-array mining tools through testing on glycan arrays with the expanded glycan library. The resultant glycan-array analysis system with hardware and software will have a broad impact on glycobiology research, glycan-related biomarker characterization, and new drug development targeting glycans.

Public Health Relevance Statement:
Project Narrative The glycan array is a vital tool for studying carbohydrate-protein interactions, biomarker discovery, and potentially drug screening, but there is a need for analysis tools for the interpretation of glycan array data. The goal of this SBIR Phase II project is to further develop robust tools for the analysis of glycan array data. The resulting tools will expedite research to deepen our understanding of how glycans contribute to diseases, such as cancers and infectious diseases.

Project Terms:
Algorithms; Animals; Epitopes; Antigenic Determinants; Binding Determinants; Biotechnology; Biotech; Malignant Neoplasms; Cancers; Malignant Tumor; malignancy; neoplasm/cancer; Cell membrane; Cytoplasmic Membrane; Plasma Membrane; plasmalemma; Communicable Diseases; Infectious Disease Pathway; Infectious Diseases; Infectious Disorder; Communities; Data Analyses; Data Analysis; data interpretation; Disease; Disorder; GAG Gene; GAG; Glycopeptides; Glycosaminoglycans; Mucopolysaccharides; Goals; Human; Modern Man; Institutes; Laboratories; Libraries; Mining; Mucins; Mucus Glycoprotein; Names; Plants; Polysaccharides; Glycans; Problem Solving; Publishing; Research; Research Institute; Research Personnel; Investigators; Researchers; Signal Transduction; Cell Communication and Signaling; Cell Signaling; Intracellular Communication and Signaling; Signal Transduction Systems; Signaling; biological signal transduction; Computer software; Software; Software Tools; Computer Software Tools; Statistical Study; statistics; Systems Analysis; Systems Analyses; Testing; Vaccines; Generations; Immunofluorescence Immunologic; Immunofluorescence; Data Set; Dataset; base; macromolecule; improved; Image Analysis; Image Analyses; image evaluation; image interpretation; Surface; Solid; Phase; Variant; Variation; Biological; Evaluation; Binding Proteins; Ligand Binding Protein; Ligand Binding Protein Gene; Protein Binding; bound protein; cancer immunotherapy; anti-cancer immunotherapy; anticancer immunotherapy; immune-based cancer therapies; immunotherapy for cancer; immunotherapy of cancer; Therapeutic; Spottings; Morphology; Shapes; tool; programs; Complex; Event; Pattern; System; Sulfate; Services; Performance; Receptor Protein; receptor; microbial; Structure; novel technologies; new technology; Cell surface; Reporting; Sampling; drug development; Provider; Bio-Informatics; Bioinformatics; Molecular Interaction; Binding; datamining; data mining; Address; Data; Glycobiology; Imaging Instrument; Imaging Tool; Imaging Device; Protein-Carbohydrate Interaction; Protein Analysis; Small Business Innovation Research Grant; SBIR; Small Business Innovation Research; Validation; Characteristics; Development; developmental; Image; imaging; Output; digital; novel strategies; new approaches; novel approaches; novel strategy; pathogen; innovation; innovate; innovative; graphical user interface; Graphical interface; graphic user interface; software user interface; novel therapeutics; new drug treatments; new drugs; new therapeutics; new therapy; next generation therapeutics; novel drug treatments; novel drugs; novel therapy; commercial application; Biological Markers; bio-markers; biologic marker; biomarker; Algorithmic Analysis; Algorithmic Analyses; Analyses of Algorithms; Analysis of Algorithms; biomarker discovery; Structural Protein; Drug Screening; automated image analysis; bioinformatics tool; bio-informatics tool; automated analysis; data tools