The implementation is open-source and available on. In summary, IMDA reduces the effort usually required for immune repertoire data analysis by providing an automated workflow for processing raw NGS data into immune repertoires and subsequent analysis. IMDA further supports the detection of sample swaps and cross-sample contamination that potentially occurred during sample preparation. The provided output directly facilitates the interpretation of input data and includes information about clonality, diversity, clonotype overlap as well as similarity, and V(D)J gene segment usage. The IMDA workflow focus on quality control and ease of use for non-computer scientists. IMDA constructs TCR and IG repertoire data from raw NGS reads and facilitates descriptive data analysis and comparison of immune repertoires. IMDA further generates an output file including key figures for all samples, designed to serve as input for machine learning frameworks to find models for differentiating between specific traits of samples. IMDA reports all relevant information in a compact summary containing visualizations, calculations, and sample details, all of which serve for a more detailed overview. These include commonly used clonality and diversity measures, as well as indicators for V(D)J gene segment usage and between sample similarity. It provides methods for automated pre-processing of barcoded and UMI tagged immune repertoire NGS data, facilitates the assembly of clonotypes and calculates key figures for describing the immune repertoire.
William robinson immune repertoire capture software#
IMDA unites the functionality from carefully selected immune repertoire analysis software tools and covers the whole spectrum from initial quality control up to the comparison of multiple immune repertoires. ImmunoDataAnalyzer (IMDA) is a pipeline we have developed for automatizing the analysis of immunological NGS data. Accurate processing, evaluation and visualization of immune repertoire NGS data is important for better understanding immune responses and immunological behavior. A main objective is the analysis of the V(D)J recombination defining the structure and specificity of the immune repertoire. Research in the field of T cell receptor (TCR) and immunoglobulin (IG) repertoires aids in understanding immunological diseases. Among others NGS enables the in-depth analysis of immune repertoires.
Zimmerman professor of neurology and neurological sciences and pediatrics at Stanford, and Stanford researchers Robert Axtell Jeremy Sokolove Yann Chong Tan and Guy Cavet.Next-generation sequencing (NGS) is nowadays the most used high-throughput technology for DNA sequencing. The co-founders of the company are Lawrence Steinman, the George A. Initial investors into the firm include Mission Bay Capital. "The technology is, therefore, a highly prolific engine for the discovery and development of therapeutic antibodies, vaccines, diagnostics, and research reagents," Robinson said in a statement.įinancial and other terms of the deal were not disclosed.Ītreca, based in San Carlos, Calif., was founded in 2010. The technology was developed in the laboratories of William Robinson, an associate professor of medicine in the Division of Immunology and Rheumatology at Stanford, and leverages next-generation sequencing to identify new antibodies that have utility themselves and that define targets of functional immune response. NEW YORK (GenomeWeb News) – Atreca today announced it has licensed immune repertoire capture technology from Stanford University, which the biopharmaceutical company will develop for a broad range of applications. Advances in Clinical Genomics Profiling.
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