The IDMS lab offers consultation with designing robust, tailored assay solutions to support any immunology research project. From basic science experiments to clinical trial research correlatives, we help identify fundamental assay design requirements and goals, coordinate study-specific biospecimen collection protocols, and define assays to evaluate immune responses. Our multidisciplinary team specializes in custom assay development services as well as in transferring assays previously developed by your team. We will help identify sample requirements and configure reagents, controls, data analysis, estimated timelines and costs. We have extensive expertise performing complex immune assays and will focus on optimizing and validating assays to maximizing data quality and reproducibility, while minimizing timelines and cost.

To prepare samples for our downstream assays, our team offers comprehensive biospecimen processing services for the isolation of serum, plasma, mononuclear cells, and other mammalian cell types from peripheral blood and tissue biopsies. Once processed, we provide short term (up to 4 weeks) storage to facilitate downstream analysis by our team. Additionally, we provide reliable sample data management, aliquoting and shipment of any remaining or unused samples to other MSKCC labs or non-MSKCC entities. We also collaborate with MSKCC’s Human Oncology Tissue Bank (HOTB) for secure long-term storage of samples.

Our integrated flow cytometry team has pioneered the development of extensive immunophenotyping analysis to enable in-depth monitoring of all leukocyte types (Figure 1). We utilize a 5-laser Cytek Aurora spectral flow cytometer to perform multi-parametric single cell analysis of heterogeneous samples and provide comprehensive phenotyping of immune populations and cellular signatures. Our lab has integrated extensive immunophenotyping panels into several comprehensive immune analysis pipelines, that includes optimized sample processing SOPs and an efficient data processing pipeline to facilitate analysis of complex cytometry datasets. We have extensive experience with all aspects of the spectral flow cytometry workflow, and we routinely process over 2000 samples per year with a turnaround time of 2-4 weeks from sample-to-data. Our immunophenotyping services include routine basic data analysis, and our team can also assist with additional expert data analysis (see below: Data Management and Analysis).

IDMS Immunophenotyping Panels

Pan-leukocyte panel

CAR-T cell screening panel

T cell exhaustion and activation (“ExAct) panel

B cell panel

Dendritic cell panel

NK cell panel

Unconventional T cells and iNKT cells panel

Acute Myeloid Leukemia (AML) panel

Custom panel design

In addition to our standard immunophenotyping panels, we can help with the design and development of customized flow cytometry panels. We have unique and extensive experience in making custom alterations to our existing panels or designing new immunophenotyping panels to fit your needs. New panels are created and optimized using an iterative design and testing process we routinely utilize within the IDMS Lab.

Our experienced team can design tailored immune activation assays for the in vitro functional characterization of immune cells. Depending on the type of assay, the IDMS Lab has various platforms to measure the functional readout.

Flow Cytometric Measurement of Transcription Factors or Cytokines

The IDMS team has developed customized methods for the measurement of intracellular transcription factor and cytokine levels via flow cytometry. This method is ideal for assays that need to assess function in conjunction with cell surface marker expression profiles.

IDMS Intracellular Panels

Transcription factor panel

Cytokine panel

Single Cell Cytokine Secretion via IsoPlexis

The IsoPlexis platform, a proteomic 32-plex antibody barcoded chip analysis technology, provides functional phenotypic analysis of single cells. The platform evaluates viable cell subsets by polyfunctional profiling (the ability of cells to secrete ≥2 cytokines) and determines their polyfunctional strength index (PSI). This method is ideal for the assessment of single cells that don’t require immune complex formation.

Measurement of Cytokines by Olink

The Olink technology platform can measure bulk secreted biomarker output from cell supernatants or lysates. This method is ideal for cell culture assays that involve the analysis of a uniform cell type. For more details about the platform (see below: Soluble Biomarker and Cytokine Profiling).

The IDMS team offers complex cell sorting services for the separation and single cell sorting of specific immune populations. Our assays are customized for various downstream applications and analysis.

Fluorescence-Activated Cell Sorting

We utilize a 3-laser FACSMelody cell sorter that is capable of 4-way sorting based on up to 9 fluorescent parameters. The instrument is enclosed in a BSL2 biosafety cabinet to ensure sterile and safe sorting of live cell populations.  

Magnetic Cell Sorting

Where flow cytometry-based sorting is not appropriate, we offer magnetic enrichment of viable immune populations for a range of downstream assays, such as nucleic acid isolation, or downstream functional assays.  

The IDMS team utilizes the Olink proteomics platform for the large-scale testing of disease-related biomarkers. The method employs proximity extension assay (PEA) technology and relies on dual antibody recognition incorporating several innovative QC steps that result in an extremely robust assay. This highly multiplexed and high throughput technology allows the simultaneous measurement of 92 disease-related cytokines, chemokines, growth factors, circulating immune co-stimulatory and inhibitory molecules within 1 ul of any biological sample, including serum and plasma.

The IDMS team measures the levels of several antibody-based drugs, including ATG, Daratumumab, Emapalumab. In addition, we collaborate with Lab Medicine’s mass spectrometry team for the measurement of Fludarabine, Busulfan, Clofarabine, Melphalan. Using the measurements, our team can assist in calculating AUC values based on pre-existing PK/PD models.

The IDMS data analysis team has developed customized methods for high throughput data processing and analysis. Our efficient data analysis pipelines are aimed to facilitate statistical analysis and interpretation of complex immunological datasets, including flow cytometry and Olink data, and employ various data visualization methods. We utilize algorithms for community clustering, dimensionality reduction, and association analytics to characterize relationships between the research and clinical datapoints. The data analysis team works closely with investigators to determine the biological relevance of statistical results and provides custom tailored figures for publication and presentation.