Enpicom sets a new standard for B cell receptor repertoire analysis

The Dutch bioinformatics software engineering company ENPICOM announced that they have finalized development and released an expanded version of their ImmunoGenomiX (IGX) platform to support discovery and development of novel immunotherapies, patient stratification for, and treatment monitoring of immunotherapies. IGX now also accepts B cell receptor (BCR) in addition to T cell receptor (TCR) sequencing data. Head-to-head benchmarking studies versus world’s most popular tool, pRESTO, show superiority on several levels.

The improvements in high-throughput sequencing (HTS) technology provide unprecedented opportunities to explore the enormous diversity of the immune repertoire by deep sequencing T cell receptors and B cell receptors. However, an efficient, integrated, easy-to-use and accurate analytical tool required to process the huge amounts of immunosequencing data has so far been lacking.

With the IGX platform, ENPICOM is on a mission to provide the immunotherapy community with a best-in-class solution to analyze T cell and B cell receptor (TCR/BCR) immunosequencing data. The base module of the IGX platform to perform T cell receptor repertoire analysis, IGX Explore, was launched in August this year. The current functional expansion of IGX Explore adds support for the identification and quantification of B cell receptors (BCRs) from HTS data. Dr. Nicola Bonzanni, ENPICOM’s Chief Scientific Officer, commented: “As BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e. antibody) gene somatic hypermutations, the development of a state-of-the-art solution for Ig/BCR sequence analysis offered more extensive challenges for our bioinformatics and software engineering teams. It is with great pleasure that we announce the timely release of the next version of IGX Explore and that our benchmarking studies showed even better performance than expected.”

Dr. Bonzanni continues: “We benchmarked the performance of IGX Explore for BCRs using both synthetic and experimental datasets. IGX Explore shows superior performance for critical metrics such as correctly identified CDR3 sequences and V/J gene identification. Specifically, we compared IGX Explore with pRESTO (Vander Heiden, et al. 2014), the world’s most popular BCR sequencing analysis tool. On synthetic data, we show that IGX Explore achieves consistent and highly precise performance across all commonly used read lengths, and outperforms pRESTO at short reads lengths in particular, as visualized in the graphs below.

Furthermore, using an independently published experimental dataset (Meng W, et al. 2017), we showed that IGX Explore is able to recapitulate the reference immune repertoire composition with high accuracy. Finally, IGX Explore outperforms pRESTO with regards to speed and scalability”.

As announced before, the ImmunoGenomiX (IGX) platform will be modularly expanded to become a comprehensive end-to-end immunosequencing data analysis platform designed to analyze, monitor, and compare immune repertoires in the context of immunotherapy development and at all stages of treatment and disease over time. Starting from high-throughput sequencing data, it will deliver an easy-to-read report appropriate for the specific application, be it research, diagnosis, patient stratification, or treatment monitoring. The IGX platform will allow customers to select their own sample preparation protocols and the HTS technology of choice. It requires no programming skills as the interface is intuitive and flexible.

The complete base module, IGX Explore, is now available and can perform clonality analysis of both TCR and BCR repertoires starting from raw sequencing data, report back the number of individual TCR/BCR clones and interactively visualize them in a user-friendly way. With IGX Explore, immunotherapy companies can boost their target discovery, research and drug development processes. Tailored software extensions to answer specific research or clinical questions can be custom-built in collaboration with ENPICOM’s team of immunologists and bioinformaticians.

Using a recently published and independent benchmark, ENPICOM showed in August that IGX Explore offered superior accuracy on TCRs and the current benchmark studies complement this picture for BCRs. More information about these benchmark studies can be found at the company’s website and will be published in a white paper shortly.

Source: ENPICOM