TY - JOUR
T1 - VDJML
T2 - A file format with tools for capturing the results of inferring immune receptor rearrangements
AU - Toby, Inimary T.
AU - Levin, Mikhail K.
AU - Salinas, Edward A.
AU - Christley, Scott
AU - Bhattacharya, Sanchita
AU - Breden, Felix
AU - Buntzman, Adam
AU - Corrie, Brian
AU - Fonner, John
AU - Gupta, Namita T.
AU - Hershberg, Uri
AU - Marthandan, Nishanth
AU - Rosenfeld, Aaron
AU - Rounds, William
AU - Rubelt, Florian
AU - Scarborough, Walter
AU - Scott, Jamie K.
AU - Uduman, Mohamed
AU - Vander Heiden, Jason A.
AU - Scheuermann, Richard H.
AU - Monson, Nancy
AU - Kleinstein, Steven H.
AU - Cowell, Lindsay G.
N1 - Publisher Copyright:
© 2016 The Author(s).
PY - 2016/10/6
Y1 - 2016/10/6
N2 - 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.
AB - 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.
KW - Antigen receptor repertoire
KW - C++
KW - Data sharing
KW - Data standards
KW - Immune repertoire
KW - Python
KW - Repertoire profiling
KW - XML
UR - http://www.scopus.com/inward/record.url?scp=84990817455&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84990817455&partnerID=8YFLogxK
U2 - 10.1186/s12859-016-1214-3
DO - 10.1186/s12859-016-1214-3
M3 - Article
C2 - 27766961
AN - SCOPUS:84990817455
SN - 1471-2105
VL - 17
JO - BMC bioinformatics
JF - BMC bioinformatics
M1 - 333
ER -