TY - JOUR
T1 - Automated analysis of immunoglobulin genes from high-throughput sequencing
T2 - Life without a template
AU - Michaeli, Miri
AU - Barak, Michal
AU - Hazanov, Lena
AU - Noga, Hila
AU - Mehr, Ramit
N1 - Copyright:
Copyright 2014 Elsevier B.V., All rights reserved.
PY - 2013/8/27
Y1 - 2013/8/27
N2 - Background: Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. The introduction of high throughput sequencing has generated unprecedented amounts of repertoire and mutation data from immunoglobulin genes. However, common analysis programs are not appropriate for pre-processing and analyzing these data due to the lack of a template or reference for the whole gene.Results: We present here the automated analysis pipeline we created for this purpose, which integrates various software packages of our own development and others', and demonstrate its performance.Conclusions: Our analysis pipeline presented here is highly modular, and makes it possible to analyze the data resulting from high-throughput sequencing of immunoglobulin genes, in spite of the lack of a template gene. An executable version of the Automation program (and its source code) is freely available for downloading from our website: http://immsilico2.lnx.biu.ac.il/Software.html.
AB - Background: Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. The introduction of high throughput sequencing has generated unprecedented amounts of repertoire and mutation data from immunoglobulin genes. However, common analysis programs are not appropriate for pre-processing and analyzing these data due to the lack of a template or reference for the whole gene.Results: We present here the automated analysis pipeline we created for this purpose, which integrates various software packages of our own development and others', and demonstrate its performance.Conclusions: Our analysis pipeline presented here is highly modular, and makes it possible to analyze the data resulting from high-throughput sequencing of immunoglobulin genes, in spite of the lack of a template gene. An executable version of the Automation program (and its source code) is freely available for downloading from our website: http://immsilico2.lnx.biu.ac.il/Software.html.
KW - B cells
KW - High-throughput sequencing
KW - Immunoglobulin
KW - Insertions-deletions
KW - Lineage tree
KW - Repertoire
KW - Somatic hyper-mutation
UR - http://www.scopus.com/inward/record.url?scp=84896362591&partnerID=8YFLogxK
U2 - 10.1186/2043-9113-3-15
DO - 10.1186/2043-9113-3-15
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C2 - 23977981
SN - 2043-9113
VL - 3
JO - Journal of Clinical Bioinformatics
JF - Journal of Clinical Bioinformatics
IS - 1
M1 - 15
ER -