For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
21
views
15
references
 Top references
cited by
4
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    2
    shares
      214
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template

      research-article

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          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.

          Related collections

          Most cited references15

          • Record: found
          • Abstract: found
          • Article: not found

          Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing.

          S Boyd, E. Marshall, J Merker … (2009)
          The complex repertoire of immune receptors generated by B and T cells enables recognition of diverse threats to the host organism. In this work, we show that massively parallel DNA sequencing of rearranged immune receptor loci can provide direct detection and tracking of immune diversity and expanded clonal lymphocyte populations in physiological and pathological contexts. DNA was isolated from blood and tissue samples, a series of redundant primers was used to amplify diverse DNA rearrangements, and the resulting mixtures of barcoded amplicons were sequenced using long-read ultra deep sequencing. Individual DNA molecules were then characterized on the basis of DNA segments that had been joined to make a functional (or nonfunctional) immune effector. Current experimental designs can accommodate up to 150 samples in a single sequence run, with the depth of sequencing sufficient to identify stable and dynamic aspects of the immune repertoire in both normal and diseased circumstances. These data provide a high-resolution picture of immune spectra in normal individuals and in patients with hematological malignancies, illuminating, in the latter case, both the initial behavior of clonal tumor populations and the later suppression or re-emergence of such populations after treatment.
          Article 0 comments Cited 130 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            High-throughput immunoglobulin repertoire analysis distinguishes between human IgM memory and switched memory B-cell populations.

            Yu‐Chang Wu, David Kipling, Hui Leong … (2010)
            B-cell receptor (BCR) diversity is achieved centrally by rearrangement of Variable, Diversity, and Joining genes, and peripherally by somatic hypermutation and class-switching of the rearranged genes. Peripheral B-cell populations are subject to both negative and positive selection events in the course of their development that have the potential to shape the BCR repertoire. The origin of IgM(+)IgD(+)CD27(+) (IgM memory) cells is controversial. It has been suggested that they may be a prediversified, antigen-independent, population of cells or that they are a population of cells that develop in response to T-independent antigens. Most recently, it was suggested that the majority of IgM memory cells are directly related to switched memory cells and are early emigrants from the germinal center reaction. Advances in sequencing technology have enabled us to undertake large scale IGH repertoire analysis of transitional, naive, IgM memory and switched memory B-cell populations. We find that the memory B-cell repertoires differ from the transitional and naive repertoires, and that the IgM memory repertoire is distinct from that of class-switched memory. Thus we conclude that a large proportion of IgM memory cells develop in response to different stimuli than for class-switched memory cell development.
            Article 0 comments Cited 113 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: found
              Is Open Access

              Vaccination-induced changes in human B-cell repertoire and pneumococcal IgM and IgA antibody at different ages

              Alexander Ademokun, Yu‐Chang Wu, Victoria Martin … (2011)
              It is well known that older people are more susceptible to morbidity and mortality from infectious diseases, particularly from pulmonary diseases such as pneumococcal pneumonia where vaccines do not provide efficient protection as in younger populations. We have previously shown that the B-cell repertoire in the old is reduced and hypothesise that this may contribute to the impaired humoral responses of the elderly. Here, we investigated the repertoire and antibody responses to winter vaccination in two age groups, aged 18–49 and 65–89. We found that the serum IgM and IgA pneumococcal responses were significantly impaired in the older group, with no difference in IgG levels. IGHM spectratype analysis seems to be the most promising in terms of its predictive ability for vaccine responses. Spectratypes showed a clear change in the repertoire at day 7 after vaccination, with a return to the baseline levels at day 28. The changes at day 7 reflected expansion of IGH sequences that have smaller, more hydrophilic, CDR3 regions, and these changes were attenuated in the older group. The older group was more likely to have spectratypes indicative of a reduced diversity at day 0 and day 28. On average, the baseline repertoire in the older group was comprised of larger CDR3 regions than in the younger group. In conclusion, IgA and IgM responses are significantly impaired in the elderly pneumococcal response and are likely key mediators of protection. Hydrophilicity and/or small size of the IGH CDR3 appear to be important in these responses.
              Article 0 comments Cited 54 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Miri Michaeli
                Michal Barak
                Lena Hazanov
                Hila Noga
                Ramit Mehr
                Journal
                Journal ID (nlm-ta): J Clin Bioinforma
                Journal ID (iso-abbrev): J Clin Bioinforma
                Title: Journal of Clinical Bioinformatics
                Publisher: BioMed Central
                ISSN (Electronic): 2043-9113
                Publication date Collection: 2013
                Publication date (Electronic): 27 August 2013
                Volume: 3
                Page: 15
                Affiliations
                [1 ]The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
                Article
                Publisher ID: 2043-9113-3-15
                DOI: 10.1186/2043-9113-3-15
                PMC ID: 3846367
                PubMed ID: 23977981
                SO-VID: fbb9d9d5-b598-45a9-9204-c820944f071b
                Copyright © Copyright © 2013 Michaeli et al.; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 22 May 2013
                Date accepted : 22 August 2013
                Categories
                Subject: Methodology

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Keywords: immunoglobulin,b cells,high-throughput sequencing,insertions-deletions,repertoire,lineage tree,somatic hyper-mutation
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology
                Keywords: immunoglobulin, b cells, high-throughput sequencing, insertions-deletions, repertoire, lineage tree, somatic hyper-mutation

                Comments

                Comment on this article

                scite_

                Similar content214

                See all similar

                Cited by3

                See all cited by

                Most referenced authors355

                See all reference authors