Genedata Biologics

Genedata Biologics enables wholly automated antibody discovery processes. Shown is a direct two-way integration with Kymab’s high-throughput B-cell selection and screening robotics. Genedata Biologics is the data backbone that manages all sample and microtiter plate information and captures assay data in a fully automated manner (integration via RESTful Webservices, fully barcoded process).

Genedata Biologics® processes and stores data derived from diverse discovery technologies, including phage display, yeast display, B-cell cloning, or hybridoma. Designed to support automated and high-throughput screening processes, the system includes built-in tools for plate management and isolate tracking, and supports plate barcoding, plate reformatting and re-arraying, as well as hit selection and cherry picking.

By directly interacting with colony pickers, liquid handling systems, screening readers, and other automation equipment, Genedata Biologics greatly facilitates automated laboratory processes. The system captures diverse screening readouts based on assay type and antigen as well as applied screening technology (e.g., ELISA, FACS, Biacore, FMAT). All screened molecules are automatically annotated based on their underlying DNA sequences, including CDR and Framework structure, post-translational modifications, or chemical liability motifs. Integrated tools enable hit selection based on the isolates’ assay signals and their sequences.

Downstream antibody reformatting is supported by tools for bulk in silico construct and plasmid design (e.g., for bulk “Fab-to-IgG” conversions) for subsequent DNA synthesis and protein expression. Genedata Biologics can be configured to work with diverse native or synthetic libraries and flexibly supports various molecule formats including IgG, Fab, scFv, bispecific, and other next-generation antibodies.

Key Features

Screening Isolate Tracking & Plate Management
Supporting laboratory logistics and plate-based sample handling

Genedata Biologics provides integrated screening isolate tracking tools to support microtiter plate-based screening, affinity maturation, and engineering campaigns. Isolate tracking is tightly integrated with the system’s plate management and laboratory instrument integration infrastructure. Genedata Biologics supports registration and barcoding of all microtiter plates (MTPs) types, either directly from agar plates produced by colony picking devices or by re-arraying or re-formatting from existing plates. The system directly interacts with laboratory equipment such as colony pickers, liquid handling systems, and pipetting robots. Supporting all plate formats including 96-, 384-, and 1536-well formats, Genedata Biologics can be configured to handle different plate layouts for different purposes (e.g., reserving specific wells for negative, blank, or stimulator controls).  Pre-configured arraying protocols streamline laboratory operations and automatically record plate genealogy and plate isolates (e.g., re-arraying according to defined filling patterns, or reformatting from four 96-well plates to one 384-well plate). All isolate tracking is supported by a central and automated bookkeeping mechanism that registers all master and daughter plates with their isolates (e.g., assay plates, sequencing plates), minimizing laborious and error-prone manual interactions. Plate barcoding facilitates inventory management of master plates and isolates. The system also supports low- and medium- throughput processes, and manual workflows (e.g., clone re-streaking).

High-throughput Antibody Screening
Supporting fully barcoded and automated discovery processes

Genedata Biologics has been designed to support fully automated high-throughput antibody screening and engineering processes. The system’s tight integration with robotics systems for plate management, liquid handling, and screening readers enables fully automated and truly high-throughput processes. Genedata Biologics helps to eliminate bottlenecks by supporting all steps in the discovery process, from streaking on agar, colony picking, plating, plate barcoding, and generation of master-, culture-, assay-, and re-array plates, to downstream interactions with pipetting instruments and reader equipment. Automation support can be configured to work with high-throughput phage or yeast display technologies, B-cell cloning or hybridoma processes, and other antibody discovery technologies. The system is fully scalable and can process hundreds of thousands of screening isolates at a time. Bulk upload facilities enable the simultaneous import and processing of relevant assay and sequence data. The system’s two-way integration with laboratory instruments facilitates data exchange and instrument operation, such as through the system’s ability to process and interpret instrument output files, and by producing instrument control files.

Integrated Assay Data Management & Hit Selection
Identifying the most promising screening hits

Genedata Biologics comes with a database for the storage of all relevant biologics screening assay data. Assay data can be imported in bulk via standard templates, which is particularly useful for data derived from high-throughput, plate-based campaigns. The system can be flexibly configured to process and store assay data derived from different assay types (e.g., ELISA, FACS, FMAT, Biacore), different antigens (e.g. human and murine or coated antigen variants), different plate formats (e.g., 96-, 384-, 1536-well plates, flexible filling patterns), and different pre-processing steps (e.g., S/B or more complex data aggregation involving positive and negative controls). Aggregated assay data is stored in a shared database and automatically referenced against appropriate screening isolates using the Genedata Biologics isolate tracking mechanism. Integrated barcoding helps to track relevant microtiter plates and required assay reagents (e.g., antigens, panning outputs). All assay data for a given isolate can be queried and is automatically reported. Integrated tools for hit selection allow the identification of the best hits based on multiple criteria (e.g., cross-assay analyses combining ELISA and FACS readouts, and HCDR3 sequence properties). The system also supports hit list management.

Library Management & V-Region Discovery
Flexible platform for supporting diverse antibody discovery technologies

Genedata Biologics is technology-agnostic, supporting all major antibody discovery technologies and documenting all relevant experimental protocols, parameters, and results. For phage display approaches the system enables registration of the applied selection techniques (e.g., immunotube or cell-based), panning strategy, input and output titers, and hit rates, and combines this with all library-relevant information. Panning and selection outputs are tracked and documented together with relevant antigens (e.g., human, murine, rat; coated/truncated versions) and selection strategies. Genedata Biologics is agnostic to the applied discovery technology and can work with various display systems (e.g., yeast display), as well as animal-based antibody discovery technologies (e.g., hybridoma, B-cells, SLAM). The Genedata Biologics platform provides a structured way to store, reference, and query all critical experimental parameters. This also includes sophisticated antigen management and specialized functions to register focused maturation libraries.

Integrated Vector Management
Management of constructs, plasmids, and other molecular biology data

Genedata Biologics comes with a built-in database for backbone vectors, cloning and expression constructs, and corresponding vectors maps. All vectors are centrally stored, together with their DNA sequences and annotations, such as promoters, leader peptides, resistance cassette, and cloning strategy. Vectors may encode therapeutic antibodies, proteins, or tool proteins, such as antigens or drug targets. A vector registration engine checks for vector uniqueness to avoid entry duplication. All vector sequences, annotations, and references are managed within a single system. Vectors can be organized and queried according to various criteria such as encoded proteins, contact person, or relevant project. The system stores vectors according to encoded protein ancestries, which makes it easy to link vectors that are used in a specific scientific context, e.g., molecular biology efforts organized by related proteins such as full-length wild-type proteins, catalytic domain expressions, truncations, and mutated variants. Typical applications for tool proteins and reagents include assay development for MTS/HTS, structural biology and X-ray studies, and co-crystallization studies with antibodies or small-molecule compounds. Genedata Biologics supports DNA synthesis workflows by performing automated quality checks to ensure correctness of the encoded protein after codon-optimization. The system includes explicit data organization models for multi-vector expression systems, which is of critical importance when working with multi-chain proteins such as antibodies (e.g., IgGs, bispecifics).