Software Development for Immune Repertoire RNA-seq (IR-Seq) Processing and Analysis

University of Texas at Austin
Wright State University
ImmuDX LLC.

Using V(D)J recombination, the human immune system generates hundreds of millions of B T cells that each bear a unique antigen receptor gene. This so called “antibody repertoire” forms a safety net that protects each individual against pathogens. Antibody repertoire is able to further diversify upon antigen stimulation through somatic hypermutation (SHM), which randomly mutates the antibody genes. The RNA-sequencing (RNA-seq) techniques has shown to be highly effective in studying antibody repertoire and the related techniques are specifically named IR-Seq.

Figure 1 shows the four major stages in IR-Seq: Reads processing, Sequence Annotation, Lineage Formation, and Sequence/lineage-Level analyses. Each stage has several key modules that can be implemented with different algorithms as shown the bullets in Figure 1, which make the whole pipeline is highly versatile and complex.

Currently, the collaboration team consists of the Jiang Lab in the Biomedical Engineering Department at University of Texas at Austin, the Data Intensive Analysis and Computing (DIAC) lab in the Computer Science and Engineering Department at Wright State University, and the ImmuDX LLC. The alpha-version of the software suite has implemented most of the modules in Figure 1 and has been actively used in immune systems research conducted by the Jiang Lab.

Software Tools Under Development:

· Barcode-marked RNA-seq processing pipeline (C++ version)

· CLOT lineage tree generation algorithms from RNA sequences (C++ version)

· CLOT lineage tree visual analysis tool (Java)

· Extensible and scalable RNA-seq pipeline cloud services

· Parallel sequence clustering (Scala/Spark)

Key Personnel:

· Ning Jiang, Jiang Lab, Department of Biomedical Engineering, University of Texas at Austin

· Keke Chen, Data Intensive Analysis and Computing Lab, Department of Computer Science and Engineering, Wright State University

· Jun Xiao, ImmuDX, LLC.