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Genomics-Driven Immunoproteomics: An Integrative Platform to Uncover Important Biomarkers for Human Diseases

  • Raghavendra Giri
  • Veneta Qendro
  • Pooja Rani
  • Carren Jepchumba
  • Grace Bugos
  • Volker Stadler
  • David K. HanEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2024)

Abstract

Genomics-driven immunoproteomics (GDI) is a platform that helps identify antigenic protein targets of mutations and other deoxyribonucleic acid (DNA) variations that are commonly associated with pathological states. This platform utilizes data generated from deep sequencing of exomic DNA or ribonucleic acid (RNA) as input to synthesize mutant peptides into microarrays, which then can be used to detect antigenic proteins that invoke immune response in patients. The technology has been used to detect antigenic targets of multiple sclerosis, an autoimmune disease [1], and cancer to identify mutant proteins that invoke immune response in breast cancer patients [2]. This technology has many potential applications to select genomic changes that are specifically recognized by the immune system in a rapid and efficient manner.

Key words

Immunoproteomics Biomarker Cancer diagnostic test Autoimmune antigens Cancer antigens Neo-antigens Integrative platform 

References

  1. 1.
    Qendro V, Lundgren DH, Palczewski S et al (2017) Discovery of putative breast cancer antigens using an integrative platform of genomics-driven immunoproteomics. Proteomics 17:1600318CrossRefGoogle Scholar
  2. 2.
    Qendro V, Bugos GA, Lundgren DH et al (2017) Integrative proteomics, genomics, and translational immunology approaches reveal mutated forms of Proteolipid Protein 1 (PLP1) and mutant-specific immune response in multiple sclerosis. Proteomics 17:1600322CrossRefGoogle Scholar
  3. 3.
    Readhead B, Haure-Mirande J-V, Funk CC et al (2018) Multiscale analysis of independent Alzheimer’s cohorts finds disruption of molecular, genetic, and clinical networks by human herpesvirus. Neuron 99:64–82.e7CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Raghavendra Giri
    • 1
  • Veneta Qendro
    • 1
  • Pooja Rani
    • 1
  • Carren Jepchumba
    • 1
  • Grace Bugos
    • 1
  • Volker Stadler
    • 2
  • David K. Han
    • 1
    Email author
  1. 1.Center for Vascular Biology, Department of Cell BiologyUniversity Connecticut School of MedicineFarmingtonUSA
  2. 2.PEPperPrint, GmBHHeidelbergGermany

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