Transcriptomic biomarker services for oncology clinical trials
Explicyte supports transcriptomic biomarker studies in baseline and on-treatment tumor samples, integrating gene-expression data with treatment, response and outcome metadata to identify predictive, pharmacodynamic and resistance-associated signatures.
Since 2018, we have supported translational biomarker programs with comprehensive cancer centers and industry sponsors, delivering interpretable datasets and publication-ready figures to inform biomarker strategy and go/no-go decisions.
biomarker findings published from patient & trials samples
From patient selection to in-human mechanism of action
What transcriptomics answers on trial samples
Predictive biomarkers & patient stratification
Predict who benefits. Profile pretreatment biopsies by bulk, single-cell or spatial transcriptomics to identify and test gene-expression signatures, immune-contexture scores and cell-state markers associated with response.
Resistance mechanisms:
Primary & acquired resistance
Explain why patients fail. Compare responders and non-responders, including extreme phenotypes where appropriate, to identify cellular programs, microenvironment states and escape pathways associated with resistance.
Pharmacodynamics &
drug-induced remodeling
Show your drug at work in patients. Paired pre- and on-treatment biopsies read at single-cell and spatial resolution to map how the investigational agent remodels the tumor and its microenvironment — pathway modulation, immune activation, and the biology behind the response.
Transcriptomic platforms for clinical biomarker analysis
The right resolution for your clinical question
High-plex single-cell spatial transcriptomics
Xenium
What it answers on trial samples. Where responding and resisting cells sit in the tissue — cell-type identity, neighborhoods, and microenvironment context read at single-cell resolution.
Best when. Tissue architecture and cell-neighborhood organization drive the response question.
Whole-transcriptome spatial transcriptomics
Visium HD
What it answers on trial samples. Unbiased spatial discovery across the whole section — signatures of response and resistance mapped to tissue geography without a fixed gene list.
Best when. You need spatial context and the biology to look for isn't yet nailed down.
High-throughput single-cell RNA-seq
Chromium X
What it answers on trial samples. Which cell populations expand, exhaust, or activate on treatment — cell-state resolution of pharmacodynamic remodeling in tumor and peripheral samples.
Best when. Cellular heterogeneity and immune dynamics drive the response question, or when spatial context isn't required.
Region-of-interest digital spatial profiling
GeoMx DSP
What it answers on trial samples. Tumor-versus-stroma and pathology-defined compartment comparisons — targeted spatial contrasts that isolate where the biology sits.
Best when. The biomarker question is compartment-level rather than single-cell, or when tissue is limited and ROI selection maximizes signal per section.
10x Genomics' next-generation spatial platform
Atera (starting Q4 2026)
Status. Explicyte has ordered an instrument and will begin Atera services in Q4 2026 – Q1 2027, extending our 10x-certified spatial toolkit as the platform reaches production.
Plan ahead. For trials sampling from 2027, we can scope Atera into the biomarker plan today and confirm timing once your protocol locks.
Whole-transcriptome cohort profiling
Bulk RNA-seq
What it answers on trial samples. Broad signatures of response and resistance across a full trial arm, at the lowest cost per sample.
Best when. Broad signal across many patients matters more than cellular or spatial resolution — including as a low-cost first pass before a focused single-cell or spatial follow-up.
representative EVIDENCE
Published transcriptomic biomarkers from clinical cohorts
A dedicated infrastructure to support clinical trials
How we secure your biomarker program in trials
Sample management
- Robust quality system: sample and metadata registration with full traceability.
- Standardized processing & QC: for FFPE and fresh/frozen biopsies — reduced variability, better inputs.
- Safe storage & sample return.
Expertise & technologies
- Track record in biomarker study design, reducing sample use and optimizing turnaround and cost.
- 10x Genomics Certified Service Provider across Chromium X, Visium HD, and Xenium.
- Platform-agnostic — bulk RNA-seq and GeoMx DSP fit alongside the 10x stack.
Actionable data
- In-house data science team — processing, QC and downstream analysis across bulk, single-cell and spatial datasets.
- Clinical metadata integration — response, resistance, pharmacodynamic and outcome analyses.
- Publication-ready outputs — figures, interpretation and Materials & Methods content.
contact our team
Discuss your trial and request a quote
Whether you're designing the transcriptomic biomarker plan for an upcoming trial or analyzing samples already collected, we'll scope the right readouts, endpoints, and reporting — from patient selection to on-treatment mechanism of action.
Answers about clinical trial biomarker services
Frequently asked questions
What transcriptomic biomarker services do you provide for oncology trials?
Single-cell, spatial, and bulk transcriptomic analysis of trial biopsies to discover and test biomarkers of response and resistance, and to read pharmacodynamics and mechanism of action in patients — from study design through analyzed, publication-ready datasets.
How is this different from your target discovery service?
Target discovery nominates and ranks novel therapeutic targets from archival FFPE cohorts. This service discovers biomarkers — of response, resistance, and drug activity — in the clinical samples generated by a trial. Different question, different sample context. See our FFPE transcriptomics for target identification page for the discovery workflow.
Can you work with an extreme-responder or outlier design?
Yes. High-contrast comparisons of exceptional responders against rapid progressors are an efficient way to surface strong biomarker candidates from a small number of samples, which we then test in a larger set.
Can you analyze paired pre- and on-treatment biopsies?
Yes. Within-patient, longitudinal analysis is central to reading pharmacodynamics — what the drug switches on or off and how the microenvironment evolves on treatment.
Which transcriptomic platform will you use?
We’re platform-agnostic and 10x Genomics-certified. We recommend bulk, single-cell, or spatial based on the biological question and the tissue you can spare; platform specifics live on our MultiOmics pages.
What sample types and amounts do you need?
FFPE and fresh/frozen tumor biopsies, and matched peripheral samples where relevant. We design workflows that limit sample consumption and advise on inputs and handling up front. For blood-based readouts, see our peripheral biomarker services.
Can transcriptomic hits be confirmed at the protein or tissue level?
Yes. Candidate markers can be taken to multiplex IF/IHC under our ISO-certified pathology workflows for orthogonal, spatially resolved confirmation.
Can you integrate clinical metadata and outcomes?
When available, we integrate clinical and pathological variables for subgroup and enrichment analyses, keeping all data de-identified.
What do deliverables look like?
Deliverables are defined according to the selected platform and analysis scope and can include QC outputs, processed expression data, differential-expression and pathway analyses, cell-type or spatial analyses where applicable, integration with clinical metadata, publication-ready figures and biological interpretation.