MARCH 31, 2020

IGX Platform 2.0


New feature: Single-cell support


Single-cell sequencing is increasingly applied for the elucidation of paired chain information, essential for the characterization of therapeutic molecules. The analysis of single-cell receptor sequencing data comes with an additional layer of complexity: keeping track of paired chains. The IGX Platform 2.0 supports the storage, annotation, and analysis of paired receptor chains. Users can now easily structure paired receptor data and perform highly customizable searches to explore, prioritize, and select clones.

New App: IGX-Compare


Internal data and public databases of receptor sequences contain a lot of valuable information. Finding your sequences of interest in public databases can be a difficult task due to their size and complexity. Moreover, project data often cannot be used on publicly accessible websites for IP reasons. With IGX-Compare, users can compare any two datasets and easily discover more information about their sequences, for example by matching a single clone against a public database to discover more information. IGX-Compare is also perfectly suited to find common clones between selected datasets, such as multiple patient cohorts.

IGXCompare Clonotypes

New feature: Clonotype grouping


Research groups often have their own definition of a B or T cell clone, depending on the experimental setup or even the biological question that they aim to answer. The IGX Platform 2.0 supports various commonly used clonotype grouping definitions (e.g., CDR3 Amino Acids and CDR3 Nucleotides), making it compatible with a wide variety of use cases.

New analysis: V/J Gene Usage plot


IGX-Explore has a new analysis: the V/J Gene Usage plot, an interactive visualization that allows users to spot preferential use of specific gene segments. Gene segments play a major role in defining antigen recognition, and skewed V/J gene usage can indicate expansion of antigen-specific clones. Using metadata annotations, users can group their samples and quickly compare gene usage across different experimental conditions or patient cohorts.

V/J Gene Frequency plot

New page: Dashboard


Keeping track of the data that is being produced in different projects can be challenging. The new dashboard page in the IGX Platform provides a centralized overview of active analyses and summary statistics of the collections and sequences in your studies, facilitating strategic discussions and reporting.


Improved data format support


We have extended integration capabilities allowing users to organize and analyze all their receptor sequences in a single environment. The IGX Platform 2.0 supports the upload of readily annotated clone tables (e.g., in CSV, TSV format) from common platforms such as Adaptive Biotechnologies and 10x Genomics. This way, users can continue analyzing their data through an intuitive user interface, integrate sequencing data from different technologies in one place, and compare their results with publicly available data using IGX-Compare.

Rich metadata upload


Adding many metadata tags has been significantly improved. We now support the upload of Excel sheets containing metadata, enabling tagging of hundreds of collections at the same time. The first column of the file is used to specify name of the collection; all subsequent columns are used to tag your data.

Better performance


The IGX Platform now supports the management and analysis of hundreds of millions of sequences, which is a must-have when providing a gateway to external Rep-Seq databases. We have made significant changes to the way we store and retrieve data, meaning you quickly get to what you’re looking for.

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