VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements

• Published in: BMC bioinformatics Vol. 17; no. Suppl 13; p. 333
• Main Authors: Toby, Inimary T., Levin, Mikhail K., Salinas, Edward A., Christley, Scott, Bhattacharya, Sanchita, Breden, Felix, Buntzman, Adam, Corrie, Brian, Fonner, John, Gupta, Namita T., Hershberg, Uri, Marthandan, Nishanth, Rosenfeld, Aaron, Rounds, William, Rubelt, Florian, Scarborough, Walter, Scott, Jamie K., Uduman, Mohamed, Vander Heiden, Jason A., Scheuermann, Richard H., Monson, Nancy, Kleinstein, Steven H., Cowell, Lindsay G.
• Format: Journal Article
• Language: English
• Published: London BioMed Central 06.10.2016; BioMed Central Ltd; Springer Nature B.V
• Subjects: Algorithms; Antibodies; Bioinformatics; Biomedical and Life Sciences; Community involvement; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Genes; Genetic aspects; Genetic recombination; Genomics - methods; Humans; Immune response; Infectious diseases; Information Dissemination; Libraries; Life Sciences; Lymphocytes; Microarrays; Observations; Open standards; Proceedings; Receptors, Immunologic - genetics; Software; Software packages; V(D)J Recombination; Viral antibodies; C++; Data sharing; XML; Antigen receptor repertoire; Data standards; Repertoire profiling; Immune repertoire; Python
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-016-1214-3

Background The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/ . We welcome participation from the community in developing the file format standard, as well as code contributions.