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Molecular & Genomic Testing
HIV Reservoir & Virology
Immunology
Sample Processing & Biobanking
Therapeutic Modalities
An immune response to a cell therapy, gene therapy, vaccine, or immunotherapy rarely shows up as a single number. The cells that matter are often a small fraction of the sample, and their surface phenotype does not always predict whether they can proliferate, secrete cytokines, or kill a target. A count of CD8+ T cells, for example, may stay stable while the antigen-specific subset within it shifts toward an exhausted state. Measurement strategies that report phenotype alone can therefore miss the functional change a program most needs to see.
Flow cytometry technology resolves this at the level of the individual cell. Fluidics carry cells single file past the lasers, optics collect scatter and fluorescence, and electronics convert each signal into data, so a cytometer can record dozens of parameters per cell across thousands of cells per second. Identity markers, activation, signaling, and functional readouts are captured in one acquisition. Our flow cytometry services are designed around the biological question your program is asking: which immune compartment the therapeutic acts on, which populations carry the mechanism of action, and which readouts should follow those populations from first preclinical dose into clinical monitoring. Phenotypic panels, complementary functional assays, and an integrated analysis strategy are scoped together so the data answer that question rather than satisfy an assay checklist.
Function measured alongside phenotype.
Molecular and immune endpoints from one aliquot.
Rapid turn-around processing before cells degrade.
Standardized gating across timepoints.
Immunophenotyping alone does not show whether a cell can proliferate, secrete cytokines or kill a target. We pair phenotypic panels with intracellular cytokine staining, antigen-induced proliferation, and cytotoxicity readouts so cell identity and activity can be evaluated in parallel.
Programs that send molecular and cellular work to separate vendors split scarce samples and lose the link between them. We run flow cytometry and dPCR, qPCR, or sequencing from the same sample.
Granulocyte contamination increases after 24 hours in ambient blood, and activated granulocytes can cleave T cell surface receptors and suppress cytokine secretion. Rapid-turnaround PBMC processing avoidsthat shipping artifact before staining begins.
Gating drawn by hand at each visit can introduce variability that looks like biology. Gating strategies are fixed during panel qualification and applied identically at every timepoint, with computational methods such as t-SNE or UMAP available for high-dimensional panels.
Our flow cytometry laboratory is built to detect low-level immune responses: rare antigen-specific T cells, small shifts in exhaustion or activation markers, and functional changes in effector populations that bulk readouts average away. We support cell therapy, gene therapy, immunotherapy, infectious diseases therapy, and vaccine programs, applying the same integrated multi-assay strategy to the immune questions each modality raises.
For mouse and non-human primate studies, we partner with the vivarium of your choice to ensure sample collection plans align with the scoped immune assay testing plan, coordinate sample transfer logistics, and then deliver high-quality results using qualified, SOP-governed assays. , For research studies and clinical trials involving human subjects, our sample chain of custody documentation, assay analytical qualification playbook, assay execution, and data reporting procedures were designed with regulatory standards in mind. For all studies, we work with clients to maximize data collected per sample. Based on the critical questions you need to answer, we can pair flow cytometry with ELISpot, FluoroSpot, secreted multiplex cytokine panels, dPCR, and sequencing services on the same sample, saving both time and sample when volumes are limited. Accelevir is a 100% scientist-run laboratory, with technical specialists and lead scientists across disciplines working as one team from protocol design to final report, so study designs can adapt as the biology evolves.
Immunology assays are analytically qualified, with qualification documentation available to support regulatory filings, and the quality framework is matched to each program’s stage, from research-use work in discovery to clinical testing.
Each service below is tied to the biological question it answers. Most programs combine two or more, because each captures a different property of the same response.
Identification and quantification of immune subsets by surface, cytoplasmic, and nuclear markers using existing multicolor panels for PBMC, T cell, B cell and granulocyte profiling or custom panels designed for your target populations in human, mouse and primate samples.
Detection of cytokines such asIFN-γ, IL-2, TNF-α,IL-17 together with effector molecules such as granzyme B and perforin, following stimulation in the presence of a protein transport inhibitor then fixation and permeabilization.. See CFSE T Cell Proliferation vs. Intracellular Cytokine Staining for how the two readouts differ.
Tracking of CD4+ and CD8+ T cell division with fluorescent dyes such as CFSE or CellTrace after stimulation with antigen, peptide, mitogen or allogeneic cells, reporting activation kinetics by subset.
Flow cytometry readouts of effector cell killing for wild-type and genetically engineered T cells and NK cells against tumor or primary target cells.
PD-1, TIM-3 and LAG-3 alongside activation markers, to follow the functional state of effector populations over time.
Detection of phosphorylated signaling proteins to study intracellular pathway activation across stimulation time courses.
Identification of antigen-specific T cells with MHC class I and class II multimers.
Phenotypic characterization of granulocytic and monocytic myeloid-derived suppressor cells for immuno-oncology studies.
Quantification of residual leukemic cells after therapy using sensitive multiparameter flow cytometry.
Cell cycle distribution, apoptosis and the evaluation of cell transfectants.
Multiparameter cell sorting and immunomagnetic selection to isolate CD4+ and CD8+ T cell subsets, gamma delta T cells, B cells, NK cells, dendritic cells, monocytes and granulocytes for downstream assays. See Cell Subset Isolation.
| Assay | Biological question it answers | Typical starting material | Often paired with |
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Immunophenotyping
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Which immune subsets are present, and how do their frequencies change?
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Whole blood, PBMCs, tissue, CSF, bone marrow, FNA |
dPCR or qPCR from the same aliquot |
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Intracellular cytokine staining |
Which cells produce which cytokines after stimulation, and are they polyfunctional? |
Fresh or cryopreserved PBMCs |
ELISpot or FluoroSpot; Luminex or ELISA
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Proliferation (CFSE, CellTrace)
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Do CD4+ and CD8+ T cells divide in response to antigen?
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Fresh or cryopreserved PBMCs |
ICS |
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Cytotoxicity (calcein-AM) |
Can effector T or NK cells kill their target?
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Effector cells with tumor or primary target cells
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ICS; exhaustion markers
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Exhaustion markers (PD-1, TIM-3, LAG-3)
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Is the effector population losing function over time?
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Fresh or cryopreserved PBMCs
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Cytotoxicity; proliferation
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Multimer staining
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How frequent are T cells specific for a defined antigen?
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Fresh or cryopreserved PBMCs
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ICS; ELISpot
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PhosphoFlow
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Is a signaling pathway activated, and when?
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Whole blood or PBMCs
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Immunophenotyping
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MDSC profiling
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Are suppressive myeloid populations expanding?
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Whole blood, PBMCs, tumor tissue
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Immunophenotyping
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MRD detection
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How many residual leukemic cells remain after therapy?
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Bone marrow aspirates
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dPCR
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Cell sorting
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What does a defined subset show on |
PBMCs, whole blood |
dPCR, qPCR, sequencing, functional |
In a flow laboratory, the panel is the study design. Marker selection starts from the mechanism-of-action question: which cell population the therapeutic should engage, which markers report that engagement, and which functional readout shows whether it changed cell behavior. Fluorochrome assignment then follows antigen density, so dim markers on rare populations are paired with bright fluorochromes and spillover into the channels that carry critical markers is kept low. Panels across the industry range from 3 to 30 colors, and the right panel is the smallest one that resolves the populations your question depends on.
Flow cytometry assay development proceeds through custom panel design and optimization, then in-depth fit-for-purpose panel qualificationsas the program advances. Inter- and intra-assay variability studies and mock runs are completed before study samples arrive, so the panel that reads the first timepoint is the panel that reads the last.
For CAR-T, CAR-NK and engineered TIL therapies, potency is a functional property: whether the product’s cells recognize the target, secrete effector cytokines, and kill. Our flow cytometry solutions for cell therapy measure that function directly, with ICS for IFN-γ, TNF-α, IL-2 and granzyme B, calcein-AM cytotoxicity against target cells, and proliferation in response to antigen. Exhaustion markers such as PD-1, TIM-3 and LAG-3 add the state of the effector population, which may help explain a functional change that phenotype alone would not predict.
In addition, immuno flow cytometry for cell therapy can follow CAR expression and the persistence of product cells in study participantsamples, and pairs with dPCR for vector copy number from the same PBMC aliquot. Learn more in Flow Cytometry for Cell Therapy Potency: Moving From Phenotype to Function.
Flow cytometry for clinical trials adds variables that a single preclinical study does not: collection at several sites, shipping, and months or years between the first and last timepoint. A flow cytometry CRO or contract lab should be judged on how it controls each of these before the first participantsample arrives.
We address them in three ways. Rapid-turnaround PBMC processing limits the granulocyte contamination and receptor cleavage that develop in ambient blood after 24 hours, as described in The 24-Hour Cliff. As a central laboratory for multi-site studies, we harmonize PBMC isolation across collection sites, an approach covered in Harmonizing PBMC Isolation Across Multi-Center Clinical Trials. Fixed gating strategies keep clinical trial flow cytometry data comparable from baseline through long-term follow-up.
When researchers compare flow cytometry companies, contract labs, or academic flow laboratories, the most useful information is specific to the study: how fresh samples are handled on receipt, whether the gating strategy is fixed before clinical samples arrive, whether molecular and immune readouts can come from the same aliquot, and what qualification documentation will be available to support regulatory filings. The answers matter more than instrument counts, because they determine whether a change in the data truly reflects the biology.
Good contract science starts from what the sample can support. When PBMC or biopsy volumes are limited, our contract analytical services pair molecular readouts (dPCR, qPCR, targeted short- and long-read sequencing) with flow cytometry, ELISpot, FluoroSpot, cytokine multiplex, cytotoxicity and proliferation assays from the same small-volume sample. dPCR provides absolute quantification of low-copy targets without a standard curve. In a gene therapy program, for example, vector genome copy number by dPCR and immune subset dynamics by flow cytometry can be measured from one PBMC aliquot, so transgene levels and immune activation describe the same cells. Because sample preparation, flow cytometry and molecular testing happen in one contract laboratory under one quality system, there is no handoff between vendors. See Integrated Molecular + Immune Endpoints.
Our scientists review the biological question, the immune compartments of interest, sample types and program stage.
Existing panels are selected or custom panels designed, with markers matched to the mechanism-of-action question.
Panels are optimized and qualified, including inter- and intra-assay variability studies and mock runs, and the gating strategy is fixed.
Samples are received with chain-of-custody documentation, then processed by PBMC isolation, subset enrichment or tissue dissociation.
Cells are stained with fluorescently labeled antibodies and acquired.
Data are gated with the fixed strategy and delivered as gated data files with optional statistical reporting and customized interpretive reports.
Our flow cytometry testing services accept whole blood, fresh or cryopreserved PBMCs, cell lines, dissociated tumor tissue, lymphoid tissues, cerebrospinal fluid, bone marrow aspirates and fine-needle aspirates. Panels are available for human, mouse, and non-human primate samples. MNCscan be cryopreserved and biobanked for longitudinal studies or downstream functional assays in the same laboratory that runs the flow cytometry service.
Contract flow cytometry services support studies across immuno-oncology, infectious disease and virology, vaccine development, cell therapy, gene therapy, autoimmune disease and immunogenicity. Biomarker flow cytometry testing services support mechanism-of-action confirmation, biomarker discovery and pharmacodynamic monitoring within each of these. Each study type asks a different question of the assay.
Immuno-oncology and checkpoint inhibitor studies ask whether effector populations expand, stay functional or become exhausted. Vaccine studies ask whether antigen-specific T cells appear and which cytokines they produce. Cell therapy programs ask whether product cells persist and remain potent. Gene therapy programs ask whether immune responses arise against the capsid or the transgene product, and how those responses track with vector levels. Across preclinical studies, Phase 1 through Phase 3 clinical trials, and long-term patient follow-up, the panel and gating strategy can carry forward so results stay comparable as the program advances.
Flow cytometry measures phenotype, activation state and functional activity at single-cell resolution. To understand the full immune response, each limit below is paired with a complementary assay in our lab, often run from the same collection.
Flow cytometry measures cytokines inside cells, not circulating levels in plasma or serum. Our Luminex and ELISA cytokine multiplex panels measure soluble cytokines and chemokines, which may precede cellular shifts and inform safety signals such as cytokine release syndrome.
ICS reports cytokine-producing cells after stimulation; ELISpot and FluoroSpot count individual secreting cells and may be better suited to rare antigen-specific responses.
Flow cytometry does not measure vector genome copy number or transgene DNA and RNA. Digital PCR from the same aliquot fills that gap.
Flow cytometry does not measure anti-drug or neutralizing antibodies. ADA and nAb immunogenicity testing addresses the humoral side of the anti-drug immune response.
A change in a population’s frequency or function describes the immune response. By itself, it is not a measure of clinical benefit.
Blood-based studies usually send fresh whole blood for rapid-turnaround processing or cryopreserved PBMCs. Tissue, cerebrospinal fluid, bone marrow and fine-needle aspirates are also accepted. We support human, mouse, and non-human primate studies.
FACS, or fluorescence-activated cell sorting, is a form of flow cytometry that physically separates cells into collection tubes, while analytical flow cytometry measures cells without sorting them. Both cell sorting instruments and bead-based immunomagnetic selection approaches enable our team to isolate a defined cell subset for downstream dPCR, sequencing, or functional assays.
The gating strategy is locked before the first studysample is tested and is not redrawn by hand between visits. Every sample, from every site, passes through the same sequence of debris exclusion, singlet discrimination, viability gating and marker-based gates, so a population reported at the final timepoint is defined exactly as it was at baseline.
You receive the gated results and the raw FCS files behind them, so your own team can reanalyze any population. Statistical reporting, data visualization, and customized interpretive reportscan be added when a study needs them.
Yes, Accelevir is a CAP-accredited, CLIA-certified laboratory.
Turnaround is set during project scoping, because it depends on panel complexity, whether the panel is new or already qualified, sample volume and how your study batches samples across timepoints. When you share your sample schedule and panel requirements, our scientists will define a timeline that fits your study design.
The right flow cytometry design depends on what you bring: your therapeutic’s mechanism and the populations it should engage, your sample types, volumes and species, your collection schedule across sites and timepoints, and the endpoint your next milestone depends on. Share those with our scientists, and we will scope the panels, functional assays, and paired molecular readouts your study needs.
Accelevir Diagnostics, LLC is a CAP-accredited, CLIA-certified laboratory. Services are provided for research use in support of clinical and preclinical studies and are not intended for diagnostic, therapeutic, prognostic, or patient-management use.
