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Immunogenomics in health and disease

Guest editor: Robert Holt

Our understanding of how the human immune system functions in health and disease is broadening as never before due to the intersection of immunology with high-throughput technologies, and the emergence of the immunogenomics field. To capture the advances in this exciting area Genome Medicine is pleased to present a special issue focused on Immunogenomics in health and disease.

This collection of articles has not been sponsored and articles have undergone the journal’s standard peer-review process. The Guest editor declares no competing interests.

  1. Research

    The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p

    IL-4-driven alternative macrophage activation and proliferation are characteristic features of both antihelminthic immune responses and wound healing in contrast to classical macrophage activation, which prima...

    Zsolt Czimmerer, Tamas Varga, Mate Kiss, Cesaré Ovando Vázquez, Quang Minh Doan-Xuan, Dominik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna S. Nagy, Bence Daniel, Szilard Poliska, Attila Horvath, Gergely Nagy, Eva Varallyay, Matthew N. Poy, Judith E. Allen…

    Genome Medicine 2016 8:63

    Published on: 31 May 2016

  2. Research

    Lower IgG somatic hypermutation rates during acute dengue virus infection is compatible with a germinal center-independent B cell response

    The study of human B cell response to dengue virus (DENV) infection is critical to understand serotype-specific protection and the cross-reactive sub-neutralizing response. Whereas the first is beneficial and ...

    Elizabeth Ernestina Godoy-Lozano, Juan Téllez-Sosa, Gilberto Sánchez-González, Hugo Sámano-Sánchez, Andrés Aguilar-Salgado, Aarón Salinas-Rodríguez, Bernardo Cortina-Ceballos, Héctor Vivanco-Cid, Karina Hernández-Flores, Jennifer M. Pfaff, Kristen M. Kahle, Benjamin J. Doranz, Rosa Elena Gómez-Barreto, Humberto Valdovinos-Torres, Irma López-Martínez, Mario H. Rodriguez…

    Genome Medicine 2016 8:23

    Published on: 25 February 2016

  3. Method

    pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

    Cancer immunotherapy has gained significant momentum from recent clinical successes of checkpoint blockade inhibition. Massively parallel sequence analysis suggests a connection between mutational load and res...

    Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis and Malachi Griffith

    Genome Medicine 2016 8:11

    Published on: 29 January 2016

  4. Method

    Designing string-of-beads vaccines with optimal spacers

    String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epito...

    Benjamin Schubert and Oliver Kohlbacher

    Genome Medicine 2016 8:9

    Published on: 26 January 2016

  5. Research

    Targeted high-throughput sequencing for genetic diagnostics of hemophagocytic lymphohistiocytosis

    Hemophagocytic lymphohistiocytosis (HLH) is a rapid-onset, potentially fatal hyperinflammatory syndrome. A prompt molecular diagnosis is crucial for appropriate clinical management. Here, we validated and pros...

    Bianca Tesi, Kristina Lagerstedt-Robinson, Samuel C. C. Chiang, Eya Ben Bdira, Miguel Abboud, Burcu Belen, Omer Devecioglu, Zehra Fadoo, Allen E. J. Yeoh, Hans Christian Erichsen, Merja Möttönen, Himmet Haluk Akar, Johanna Hästbacka, Zuhre Kaya, Susana Nunes, Turkan Patiroglu…

    Genome Medicine 2015 7:130

    Published on: 18 December 2015

  6. Research

    A donor-specific epigenetic classifier for acute graft-versus-host disease severity in hematopoietic stem cell transplantation

    Allogeneic hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematological conditions. Acute graft-versus-host disease (aGVHD) is a prevalent immune-mediated complication followin...

    Dirk S. Paul, Allison Jones, Rob S. Sellar, Neema P. Mayor, Andrew Feber, Amy P. Webster, Neuza Afonso, Ruhena Sergeant, Richard M. Szydlo, Jane F. Apperley, Martin Widschwendter, Stephen Mackinnon, Steven G. E. Marsh, J. Alejandro Madrigal, Vardhman K. Rakyan, Karl S. Peggs…

    Genome Medicine 2015 7:128

    Published on: 15 December 2015

  7. Method

    Profiling tissue-resident T cell repertoires by RNA sequencing

    Deep sequencing of recombined T cell receptor (TCR) genes and transcripts has provided a view of T cell repertoire diversity at an unprecedented resolution. Beyond profiling peripheral blood, analysis of tissu...

    Scott D. Brown, Lisa A. Raeburn and Robert A. Holt

    Genome Medicine 2015 7:125

    Published on: 30 November 2015

  8. Research

    Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain

    Despite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against...

    Bernardo Cortina-Ceballos, Elizabeth Ernestina Godoy-Lozano, Juan Téllez-Sosa, Marbella Ovilla-Muñoz, Hugo Sámano-Sánchez, Andrés Aguilar-Salgado, Rosa Elena Gómez-Barreto, Humberto Valdovinos-Torres, Irma López-Martínez, Rodrigo Aparicio-Antonio, Mario H. Rodríguez and Jesús Martínez-Barnetche

    Genome Medicine 2015 7:124

    Published on: 25 November 2015

  9. Research

    Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci

    The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementar...

    Jared Dean, Ryan O. Emerson, Marissa Vignali, Anna M. Sherwood, Mark J. Rieder, Christopher S. Carlson and Harlan S. Robins

    Genome Medicine 2015 7:123

    Published on: 23 November 2015

  10. Research

    Identification of global regulators of T-helper cell lineage specification

    Activation and differentiation of T-helper (Th) cells into Th1 and Th2 types is a complex process orchestrated by distinct gene activation programs engaging a number of genes. This process is crucial for a rob...

    Kartiek Kanduri, Subhash Tripathi, Antti Larjo, Henrik Mannerström, Ubaid Ullah, Riikka Lund, R. David Hawkins, Bing Ren, Harri Lähdesmäki and Riitta Lahesmaa

    Genome Medicine 2015 7:122

    Published on: 20 November 2015

  11. Database

    TCLP: an online cancer cell line catalogue integrating HLA type, predicted neo-epitopes, virus and gene expression

    Human cancer cell lines are an important resource for research and drug development. However, the available annotations of cell lines are sparse, incomplete, and distributed in multiple repositories. Re-analyz...

    Jelle Scholtalbers, Sebastian Boegel, Thomas Bukur, Marius Byl, Sebastian Goerges, Patrick Sorn, Martin Loewer, Ugur Sahin and John C. Castle

    Genome Medicine 2015 7:118

    Published on: 20 November 2015

  12. Editorial

    Immunogenomics: a foundation for intelligent immune design

    The complexity of the immune system is now being interrogated using methodologies that generate extensive multi-dimensional data. Effective collection, integration and interpretation of these data remain diffi...

    Robert A. Holt

    Genome Medicine 2015 7:116

    Published on: 19 November 2015

  13. Comment

    Integrating tumor microenvironment with cancer molecular classifications

    The composition of the tumor microenvironment is associated with a patient's prognosis and can be therapeutically targeted. A link between the cellular composition and genomic features of the tumor and its res...

    Etienne Becht, Aurélien de Reyniès and Wolf H. Fridman

    Genome Medicine 2015 7:115

    Published on: 14 November 2015

  14. Research

    DNA methylation loci associated with atopy and high serum IgE: a genome-wide application of recursive Random Forest feature selection

    The prevalence of allergic diseases are increasing worldwide, emphasizing the need to elucidate their pathogeneses. The aims of this study were to use a two-stage design to identify DNA methylation levels at c...

    Todd M. Everson, Genevieve Lyons, Hongmei Zhang, Nelís Soto-Ramírez, Gabrielle A. Lockett, Veeresh K. Patil, Simon K. Merid, Cilla Sӧderhӓll, Erik Melén, John W. Holloway, S. Hasan Arshad and Wilfried Karmaus

    Genome Medicine 2015 7:89

    Published on: 21 August 2015