VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
Author
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.
Affiliation
Univ Arizona, Sch Med, Dept ImmunobiolIssue Date
2016-10-06Keywords
Repertoire profilingImmune repertoire
Antigen receptor repertoire
Data standards
Data sharing
Python
C plus
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BIOMED CENTRAL LTDCitation
VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements 2016, 17 (S13) BMC BioinformaticsJournal
BMC BioinformaticsRights
© 2016 The Author(s). Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License.Collection Information
This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.Abstract
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.ISSN
1471-2105PubMed ID
27766961Version
Final published versionSponsors
Burroughs Welcome Fund Career Award; NIAID [AI097403]; Bioinformatics Support Contract (BISC) [HHSN272201200028C]; National Institute of Allergy and Infectious Diseases grant [U19 AI090019, R01 AI104739]; PhRMA foundation pre-doctoral informatics fellowship; National Library of Medicine of the National Institutes of Health [T15 LM07056]ae974a485f413a2113503eed53cd6c53
10.1186/s12859-016-1214-3
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