High-throughput interrogation of immune responses using the Human Immune Profiling Pipeline

Guanning Wang, Olga Lyudovyk, Justin Y. Kim, Ya Hui Lin, Yuval Elhanati, Divij Mathew, E. John Wherry, Ramin S. Herati, Allison R. Greenplate, Benjamin Greenbaum, Santosha A. Vardhana, Alexander C. Huang

Research output: Contribution to journalArticlepeer-review


The current abundance of immunotherapy clinical trials presents an opportunity to learn about the underlying mechanisms and pharmacodynamic effects of novel drugs on the human immune system. Here, we present a protocol to study how these immune responses impact clinical outcomes using large-scale high-throughput immune profiling of clinical cohorts. We describe the Human Immune Profiling Pipeline, which comprises an end-to-end solution from flow cytometry results to computational approaches and unsupervised patient clustering based on lymphocyte landscape. For complete details on the use and execution of this protocol, please refer to Lyudovyk et al. (2022).1

Original languageEnglish
Article number102289
JournalSTAR Protocols
Issue number2
StatePublished - 16 Jun 2023
Externally publishedYes


  • Flow Cytometry/Mass Cytometry
  • Health Sciences
  • Immunology


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