Genedata Biologics

Genedata Biologics™ enables an efficient and flexible optimization and engineering of both antibodies and proteins, including novel molecule formats such as bispecific antibodies, fusion proteins, and Fc-engineered molecules. The system supports a variety of engineering strategies, including affinity maturation (e.g., by PCR), germlining, humanization, murinization, antibody reformatting (e.g., scFv to Fab to IgG), isotype switching, and directed engineering (e.g., removal of glycosylation sites). Genedata Biologics stores all engineered biomolecules and their underlying molecular ancestry.

Tools for automatic in silico construction, registration, and annotation of engineered molecule sequences and relevant plasmid maps make manual sequence handling unnecessary. Genedata Biologics provides a central and structured registry for all vectors encoding the engineered protein variants. Integrated tools analyze sequence and assay data to systematically assess engineered molecule variants, enabling the identification of residues that are critical for achieving the desired properties of the engineered molecules.

Key Features

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.

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).

Bulk Cloning & Molecule Re-formatting
Alleviating bottlenecks in molecular biology via in silico cloning tools

Genedata Biologics provides specialized tools for automation and scale-up of vector design. This is particularly useful if larger sets of inserts or variable regions, such as those derived from high-throughput antibody screening campaigns, need to be cloned into a backbone vector to produce full-sized IgG molecules. The system provides flexible tools for automating the bulk generation of new antibody and non-antibody vector maps and encoded protein molecules, based on selected backbone vectors and desired cloning strategies (e.g., Gateway Cloning). Specific functionalities enable automated antibody re-formatting (scFv or Fab to IgG) and isotype switching. The system also enables rapid expression vector optimization by simultaneously cloning inserts into different backbone vectors carrying different combinations of modules of interest (e.g., cleavage sites, tags, leader peptides). All resulting vectors are auto-referenced to the proteins they encode. Auto-generated expression vectors are centrally stored in a common vector repository and can be queried according to their specific properties such as used promoters, leader peptides, resistance cassettes, tags, Kozak, isotype, and constant region sequences.

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).