28 Jan 2021

Introducing the IGX Platform 3.0

With version 3.0, ENPICOM introduces new applications specifically developed for antibody discovery, revamped receptor profiling workflows, vastly improved metadata importing, the new MiXCR App, and more!

We are proud to announce the release of the Antibody Discovery Module (ADM), which extends the functionality of the IGX Platform and empowers life scientists to identify better and more diverse antibody candidates. The IGX Platform 3.0 brings a set of specialized Apps for antibody discovery, high-throughput receptor profiling, expanded tools for metadata importing, a new MiXCR App, and significant user interface and experience enhancements. Discover the new features below.

Introducing the Antibody Discovery Module

Antibody discovery is a quest for developable molecules with superior properties. The integrated analysis of sequence and assay data in this process requires diverse expertise, including immunology, protein biology, and bioinformatics. Based on the input from over 50 organizations, ENPICOM developed an end-to-end solution to accelerate the candidate selection process.

We are kickstarting the ADM with two Apps: IGX-Cluster and IGX-Branch. These Apps were specifically designed to quickly go from thousands of candidate sequences, to a selection of just those few needle-in-a-haystack antibodies worth following up on. The ADM caters to a variety of discovery workflows: it enables scientists to gather crucial insights that guide antibody candidate selection using Sanger or NGS data, or a combination of both. These complementary data sets can be combined by grouping them in IGX-Cluster. The resulting clusters – containing information from both data types – are visualized in IGX-Branch, producing phylogenetic trees that can be explored interactively. The trees can be further annotated by overlaying experimental metadata and sequences can be viewed in a multiple-sequence alignment. This enables the discovery of new candidate sequences – with potentially more favorable properties – from the broad NGS candidate pool, by leveraging the information provided by well-characterized Sanger clones present in the same cluster.

 

 

See the ADM in action

On February 18, we will present the ADM’s capabilities and answer any questions you may have in a live webcast. Save your seat today!

If you can’t make it on the 18th, don’t worry! You will receive a recording of the presentation shortly after the live event.

Group sequences with the new IGX-Cluster App

IGX-Cluster groups sequences based on user-defined parameters such as CDR3 similarity, gene usage, and CDR3 length. It can effortlessly 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 IGX-Branch, this provides the ideal setup for important discovery tasks like antibody candidate selection and hit expansion.

Key features:

  • It runs safely in the cloud. You can continue your work while we cluster millions of sequences.
  • It has flexible configuration options. You can customize the cluster definition to your liking by setting similarity thresholds separately for each chain (heavy, lambda, or kappa), and adding V- and J-gene family and CDR3 amino acid length restrictions for clustering.
  • It supports paired chains. You can include heavy and light chain information in your cluster definition if available to increase clustering accuracy.

Prioritize clusters and go for next-generation phylogeny with IGX-Branch

IGX-Branch is a two-stage rocket. First, an intuitive overview makes it easy to prioritize clusters based on their size and to compute phylogenetic trees for clusters of interest. Second, the powerful interactive tree visualization links visual variables such as node color, shape, and size to available assay data, providing a versatile system to discover promising antibody candidates for follow-up analysis.

Key features:

  • It’s interactive. You can hide specific branches, zoom and drag the tree to quickly navigate and focus on your branches of interest.
  • It’s informative. You can link assay data directly to clones and explore up to 6 antibody characteristics in a single visualization, by associating these characteristics to the color, shape and size of nodes in the tree.
  • It’s thorough. You can easily visualize the sequence alignment between clones of interest and make a fully informed decision on your candidates of interest.

High-throughput receptor profiling with support for Sanger data

We’ve completely revamped our profiling workflows, which means you can now easily configure and analyze multiple samples at once using IGX-Profile. In addition, we now support data generated with Sanger protocols, next to our existing support for NGS data. You can upload Sanger data in AB1 or FASTA formats and annotate important regions in receptor sequences such as frameworks and CDRs. For data generated from sorted single-cells using Sanger protocols, we create Single-cell Collections which 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.

Interactive metadata importer

Whether you answer immunological questions, develop therapeutic antibodies or TCR-based therapies, a tight integration of sequencing data and associated metadata is key. From this release onward, you can import metadata annotations through a brand-new, intuitive user interface and even extract metadata from file names. 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: they allow you to easily find specific samples or sequences and can be used in visualizations to stratify plots or add additional layers of information.

New MiXCR App

The MiXCR pipeline is a widely used open-source tool for annotation and quantification of receptor sequences. Next to the existing support for the MiXCR output format, we now provide MiXCR as an App on the IGX Platform. Much like IGX-Profile, the MiXCR app also benefits from the same, intuitive high-throughput interface, which makes configuring and running multiple clone annotation jobs a breeze. Our collaboration with MiLaboratories enables organizations to run their MiXCR workflows in the intuitive and accessible environment of the IGX Platform, while at the same time benefitting from its powerful data management, analysis, and visualization options.

See the IGX Platform in action

The IGX Platform 3.0 is setting a new standard for antibody discovery. Be sure to join our live broadcast on February 18 to learn how to efficiently use all available information to rationally select the best candidate.