Immunogenetic Management Software: a New Tool for Visualization and Analysis of Complex Immunogenetic Datasets

Overview

Journal Immunogenetics

Specialties Allergy & Immunology
Genetics

Date 2011 Nov 15

PMID 22080300

Citations 8

Authors

Z P Johnson

R D Eady

S F Ahmad

S Agravat

T Morris

J Else

S M Lank

R W Wiseman

D H OConnor

M C T Penedo

C P Larsen

L S Kean

Affiliations

Soon will be listed here.

Abstract

Here we describe the Immunogenetic Management Software (IMS) system, a novel web-based application that permits multiplexed analysis of complex immunogenetic traits that are necessary for the accurate planning and execution of experiments involving large animal models, including nonhuman primates. IMS is capable of housing complex pedigree relationships, microsatellite-based MHC typing data, as well as MHC pyrosequencing expression analysis of class I alleles. It includes a novel, automated MHC haplotype naming algorithm and has accomplished an innovative visualization protocol that allows users to view multiple familial and MHC haplotype relationships through a single, interactive graphical interface. Detailed DNA and RNA-based data can also be queried and analyzed in a highly accessible fashion, and flexible search capabilities allow experimental choices to be made based on multiple, individualized and expandable immunogenetic factors. This web application is implemented in Java, MySQL, Tomcat, and Apache, with supported browsers including Internet Explorer and Firefox on Windows and Safari on Mac OS. The software is freely available for distribution to noncommercial users by contacting Leslie.kean@emory.edu. A demonstration site for the software is available at http://typing.emory.edu/typing_demo , user name: imsdemo7@gmail.com and password: imsdemo.

Citing Articles

Evidence for persistence of the SHIV reservoir early after MHC haploidentical hematopoietic stem cell transplantation.

Colonna L, Peterson C, Schell J, Carlson J, Tkachev V, Brown M Nat Commun. 2018; 9(1):4438.

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Combined OX40L and mTOR blockade controls effector T cell activation while preserving T reconstitution after transplant.

Tkachev V, Furlan S, Watkins B, Hunt D, Zheng H, Panoskaltsis-Mortari A Sci Transl Med. 2017; 9(408).

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Advances in targeting co-inhibitory and co-stimulatory pathways in transplantation settings: the Yin to the Yang of cancer immunotherapy.

Kean L, Turka L, Blazar B Immunol Rev. 2017; 276(1):192-212.

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Transcriptome analysis of GVHD reveals aurora kinase A as a targetable pathway for disease prevention.

Furlan S, Watkins B, Tkachev V, Flynn R, Cooley S, Ramakrishnan S Sci Transl Med. 2015; 7(315):315ra191.

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Immunogenetic characterization of a captive colony of sooty mangabeys (Cercocebus atys) used for SIV research.

Smith G, Bauer L, Crane M, Johnson Z J Med Primatol. 2015; 44(2):76-88.

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References

Doxiadis G, Otting N, de Groot N, Bontrop R . Differential evolutionary MHC class II strategies in humans and rhesus macaques: relevance for biomedical studies. Immunol Rev. 2002; 183:76-85. DOI: 10.1034/j.1600-065x.2001.1830106.x. View

Bontrop R . Comparative genetics of MHC polymorphisms in different primate species: duplications and deletions. Hum Immunol. 2006; 67(6):388-97. DOI: 10.1016/j.humimm.2006.03.007. View

Karl J, Wiseman R, OConnor D . Cost-effective sequence-based nonhuman primate MHC class I genotyping from RNA. Methods. 2009; 49(1):11-7. PMC: 2732760. DOI: 10.1016/j.ymeth.2009.05.002. View

Kean L, Gangappa S, Pearson T, Larsen C . Transplant tolerance in non-human primates: progress, current challenges and unmet needs. Am J Transplant. 2006; 6(5 Pt 1):884-93. DOI: 10.1111/j.1600-6143.2006.01260.x. View

Otting N, Heijmans C, Noort R, de Groot N, Doxiadis G, van Rood J . Unparalleled complexity of the MHC class I region in rhesus macaques. Proc Natl Acad Sci U S A. 2005; 102(5):1626-31. PMC: 545086. DOI: 10.1073/pnas.0409084102. View

Larsen C, Page A, Linzie K, Russell M, Deane T, Stempora L . An MHC-defined primate model reveals significant rejection of bone marrow after mixed chimerism induction despite full MHC matching. Am J Transplant. 2010; 10(11):2396-409. PMC: 2980834. DOI: 10.1111/j.1600-6143.2010.03272.x. View

Petersdorf E, Malkki M, Gooley T, Martin P, Guo Z . MHC haplotype matching for unrelated hematopoietic cell transplantation. PLoS Med. 2007; 4(1):e8. PMC: 1796628. DOI: 10.1371/journal.pmed.0040008. View

Kenyon N, Chatzipetrou M, Masetti M, Ranuncoli A, Oliveira M, Wagner J . Long-term survival and function of intrahepatic islet allografts in rhesus monkeys treated with humanized anti-CD154. Proc Natl Acad Sci U S A. 1999; 96(14):8132-7. PMC: 22200. DOI: 10.1073/pnas.96.14.8132. View

Malkki M, Gooley T, Horowitz M, Absi L, Christiansen F, Cornelissen J . Mapping MHC-resident transplantation determinants. Biol Blood Marrow Transplant. 2007; 13(8):986-95. PMC: 3182140. DOI: 10.1016/j.bbmt.2007.05.007. View

10.

Wiseman R, Karl J, Bimber B, OLeary C, Lank S, Tuscher J . Major histocompatibility complex genotyping with massively parallel pyrosequencing. Nat Med. 2009; 15(11):1322-6. PMC: 2824247. DOI: 10.1038/nm.2038. View

11.

Thomas J, Eckhoff D, Contreras J, Lobashevsky A, Hubbard W, Moore J . Durable donor-specific T and B cell tolerance in rhesus macaques induced with peritransplantation anti-CD3 immunotoxin and deoxyspergualin: absence of chronic allograft nephropathy. Transplantation. 2000; 69(12):2497-503. DOI: 10.1097/00007890-200006270-00007. View

12.

Gruen J, Weissman S . Evolving views of the major histocompatibility complex. Blood. 1997; 90(11):4252-65. View

13.

Sawai E, Khan I, Montbriand P, Peterlin B, Cheng-Mayer C, Luciw P . Activation of PAK by HIV and SIV Nef: importance for AIDS in rhesus macaques. Curr Biol. 1996; 6(11):1519-27. DOI: 10.1016/s0960-9822(96)00757-9. View

14.

Lechler R, Sykes M, Thomson A, Turka L . Organ transplantation--how much of the promise has been realized?. Nat Med. 2005; 11(6):605-13. DOI: 10.1038/nm1251. View

15.

Stephens M, Donnelly P . A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet. 2003; 73(5):1162-9. PMC: 1180495. DOI: 10.1086/379378. View

16.

Barouch D, Craiu A, Kuroda M, Schmitz J, Zheng X, Santra S . Augmentation of immune responses to HIV-1 and simian immunodeficiency virus DNA vaccines by IL-2/Ig plasmid administration in rhesus monkeys. Proc Natl Acad Sci U S A. 2000; 97(8):4192-7. PMC: 18194. DOI: 10.1073/pnas.050417697. View

17.

Wu X, Anderson J, Campbell E, Joseph A, Hope T . Proteasome inhibitors uncouple rhesus TRIM5alpha restriction of HIV-1 reverse transcription and infection. Proc Natl Acad Sci U S A. 2006; 103(19):7465-70. PMC: 1464362. DOI: 10.1073/pnas.0510483103. View

18.

Rosner C, Kruse P, Lubke T, Walter L . Erratum to: rhesus macaque MHC class I molecules show differential subcellular localizations. Immunogenetics. 2010; 62(6):409-18. PMC: 3128699. DOI: 10.1007/s00251-010-0447-y. View

19.

Browning S, Browning B . Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet. 2007; 81(5):1084-97. PMC: 2265661. DOI: 10.1086/521987. View

20.

Penedo M, Bontrop R, Heijmans C, Otting N, Noort R, Rouweler A . Microsatellite typing of the rhesus macaque MHC region. Immunogenetics. 2005; 57(3-4):198-209. DOI: 10.1007/s00251-005-0787-1. View