Cell & Gene Therapy

An engineered cell has to be characterized at more than one molecular level. GenXMap combines genomic, transcriptomic and proteomic profiling with targeted sequencing, single-cell and spatial approaches to determine what an engineered product is, how it behaves, and how consistently that profile is maintained across development and manufacturing.

The Potency & Identity Package

A designed programme rather than an analysis order: GenXMap defines the molecular layers needed for your development question, analyses the engineered product, and integrates the results into a single characterization framework.

• Genomic profilingWGS or WES to characterize mutations, genomic alterations and broader genomic changes
• Targeted sequencingvalidation and quantification of specific edits, mutations, transgenes or engineered sequences
• Vector and transgene analysisconstruct-aware analysis of vector sequences, transgene expression and engineered regions
• Integration-site analysischaracterization of vector integration sites and their distribution across the cell population
• Bulk RNA sequencinganalysis of transgene expression and host-cell transcriptional programmes associated with cellular state and potency
• Proteomicsmass-spectrometry-based protein profiling, including TIMS-TOF MS, to characterize protein-level changes associated with engineered-cell state and function
• Single-cell analysisresolving population heterogeneity, identifying subpopulations and tracking molecular changes across passages or conditions
• Spatial transcriptomicswhere relevant, resolving molecular responses within tissue or cellular environments
• cfDNA / cfRNA profilingmonitoring cell- or treatment-associated molecular signals in relevant biological matrices
• Multiomics integrationconnecting genomic, transcriptomic and proteomic signals rather than interpreting each layer independently

The work starts before the bench: which molecular layers are needed to answer the development question, which reference should be used for the construct, how genomic and transcriptomic measurements should be integrated, and which comparisons are required to distinguish biological variation from process-related changes.

The questions we take on

• Does the engineered cell carry the intended edit or construct?
• Is the expected transgene expressed, and how does engineering affect the host-cell programme?
• What genomic alterations are present, and which require targeted validation?
• Where has the vector integrated, and how is the integration pattern distributed across the population?
• Is the cell population homogeneous, or are distinct subpopulations emerging?
• Does the molecular profile associated with potency remain consistent across batches?
• How does the molecular profile change during engineering, expansion or successive passages?
• Can genomic, transcriptomic and proteomic signals be connected to define a coherent product signature?
• Which molecular features distinguish an intended biological effect from unwanted or process-related changes?

From Engineering to Product Characterization

GenXMap can analyse the molecular trajectory of an engineered cell product across development:

Engineering → expansion → passage → process development → final product

Comparing these stages can reveal changes in population composition, gene expression, genomic profile and protein state that may otherwise remain hidden when only the final product is measured.

Batch Comparison & Process Monitoring

A molecular signature is useful only if it can be compared consistently.

GenXMap applies the same analytical framework across batches, passages or process conditions to distinguish:

• expected biological variation
• emerging subpopulations
• batch-to-batch molecular differences
• process-associated changes
• persistent product characteristics

The objective is not simply to describe each batch independently, but to determine which molecular features remain consistent and which change during development or manufacturing.

Multiomics Integration

Different molecular layers answer different questions.

• DNA defines the genomic context.
• RNA captures transcriptional state.
• Protein reflects downstream molecular phenotype.
• Single-cell and spatial data identify where those signals originate.
• cfDNA and cfRNA can extend monitoring beyond the cellular product.

GenXMap integrates these layers around the biological question rather than treating each dataset as a separate analysis.

Working to a Development Milestone

Cell and gene therapy programmes progress through defined development stages: engineering, process development, potency assessment, comparability, tech transfer and, where relevant, IND-enabling work.

GenXMap designs the analytical strategy around the milestone, defining the required samples, molecular layers, comparisons and validation steps before the study begins.

What the report contains

A complete record of the analysis: study design, sample information, methods, tool versions, parameters, QC metrics and statistical results.

Results are reported at the appropriate molecular level, from variants and integration sites to gene expression, protein profiles, cellular populations and integrated signatures.

Every analytical decision is documented and traceable.

Built to be reviewed, challenged and reproduced by an independent scientific team.

From Data to Biological Evidence

The laboratory work can be performed through OMICS4, GenXMap's wet-lab platform, or the analysis can start with data generated elsewhere.

GenXMap can analyse existing WGS, WES, targeted sequencing, RNA-seq, proteomics, single-cell, spatial or liquid-biopsy datasets and integrate them within the same analytical framework.

What determines the analysis is the biological question, the study design and the available metadata — not where the data were generated.

Case studies for this industry are in preparation: get in touch to discuss a project directly.