New module: The Antibody Discovery Module (ADM)
The Antibody Discovery Module (ADM) is comprised of two new analysis applications tailored to a variety of antibody discovery workflows: IGX-Cluster and IGX-Branch. These Apps were developed to make the most of both Sanger and NGS data. By clustering both data types in IGX-Cluster, and combining them into singular visualizations in IGX-Branch, interactive phylogenetic trees can be explored for clusters that contain sequences from both samples. This enables the discovery of new candidate sequences from NGS data – with potentially more favorable properties – that are present in the vicinity of well-characterized Sanger clones. Together with the new ADM, the IGX Platform provides an end-to-end solution to identify better and more diverse antibody candidates in a more efficient way.
New App: IGX-Cluster
IGX-Cluster groups sequences based on user-defined parameters such as CDR3 similarity, gene usage, and CDR3 length. It allows to perform large clustering tasks in the cloud and supports a wide variety of workflows. IGX-Cluster can be used to group together samples from different sequencing technologies, such as Sanger and NGS. Together with the IGX-Branch functionalities, this provides an efficient setup for tasks like antibody candidate selection and hit expansion.
New App: IGX-Branch
IGX-Branch provides interactive visualizations to prioritize clusters and pick antibody candidates for follow-up analysis.
It works in two steps:
- An intuitive overview makes it easy to prioritize clusters based on their size and content and compute phylogenetic trees for clusters of interest.
- An interactive phylogenetic tree visualization links visual variables such as node color, shape, and size to available assay data, allowing for informed selection of antibody candidates.
New feature: High-throughput receptor profiling with support for Sanger data
Our revamped profiling workflows allow to easily configure and analyze multiple samples at once using IGX-Profile. In addition to NGS data, the IGX Platform now supports data generated with Sanger protocols. You can upload Sanger data in AB1 or FASTA format and annotate important regions in receptor sequences such as frameworks and CDRs. For data generated from sorted single cells using Sanger protocols, the IGX Platform creates Single-cell Collections that automatically keep track of which chains are paired. These sequences can be annotated with assay data and analyzed in IGX-Cluster and IGX-Branch, providing a versatile system for many essential antibody discovery tasks.
New feature: Interactive metadata importing
From this release onward, you can import metadata annotations through a brand-new, intuitive user interface and even extract metadata from other tags (e.g., filenames). As before, the information is added in the form of tags and can be associated to any data level: collections, cells, or sequences. These tags and their data can then be used throughout the entire platform to find specific samples or sequences, stratify plots, or add additional layers of information.
New App: MiXCR
The MiXCR pipeline is a widely used open-source tool for the annotation and quantification of receptor sequences. Next to the existing support for the MiXCR output format, IGX Platform now includes a MiXCR App. Like IGX-Profile, the MiXCR App comes with an intuitive high-throughput interface to allow for easy clone configuration and annotation.
- Extract information from file and collection names. Information can now be extracted from file and collection names and added as a new tag by using the new “Extract” pane of our tagger. Select Files or Collections, click the “Add Tag” button in the bottom bar and navigate to “Extract” to give it a try.
- Quick filter on the Files page. We have added a Quick Filter at the top of your File Browser so you can quickly find the files you’re looking for and start your analysis.
- Top bar App navigation. We have added breadcrumb trails to the top bar to facilitate navigation through our Apps.