SINGLE-CELL TUMOR EVOLUTION
From clonal clues in archived tissue to DNA and RNA in the same cell. Connect the samples you have to the questions that matter.
START WITH THE MATERIALLet the specimen define the starting point.
Traceable scientific evidence
ONE RESEARCH CONTINUUM
Move from specimen to workflow to insight, organizing material, molecular layers and validation into one readable, discussable research path.
Research concept visual · not experimental dataStart with archival FFPE, fresh tissue or existing data, then define material constraints and the study timeline.
Use single-cell CNA profiles to compare clonal composition, shared events and changes across time points.
In suitable fresh tissue, directly pair genetic subclones with expression states from the same cell.
Plan tissue localization, cohort review or functional work around candidate findings and the next testable step.
Not every project requires every layer. Methods, sample requirements and deliverables are agreed around the research question.
TWO METHODS. ONE RESEARCH CONTINUUM.
Two sample pathways, preserving genomic information at single-cell resolution.
ARCHIVAL SINGLE-CELL DNA
Recover single-cell copy-number alteration (CNA) profiles from formalin-fixed, paraffin-embedded (FFPE) tissue and compare clonal structure across time.
Cell 2023 · Archival single-cell DNA
Explore the method
SAME-CELL DNA + RNA
Measure DNA copy number and RNA expression in the same cell, pairing genomic subclones with transcriptional programs in assessed fresh-tissue studies.
Cell 2025 · Paired genotype and phenotype
Explore the method
FIND YOUR STARTING POINT
Start with the specimen and the question, then select the technology.
For primary–recurrence, pre/post-treatment or longitudinal material. Review archive age, tissue availability, tumor content and nuclear quality before scaling a paired cohort.
For subclone phenotypes, gene-dosage associations and origin hypotheses. Agree collection and transport first; archived FFPE is not assumed to support the same-cell DNA+RNA workflow.
With existing scRNA, bulk or spatial data, begin with the question and validation plan. Integrating separate assays does not create directly measured same-cell pairs.
WHY CLONAL RESOLUTION
Single-cell CNA supplies genomic evidence for clone analysis, complementing bulk averages and RNA-based inference.
wellDR-seq retains paired DNA and RNA measurements, allowing transcriptional states to be compared between genomic clones.
Move from clonal structure to candidate genes, spatial localization, cohort replication and functional experiments—not just heatmaps.
BIOINFORMATICS
Clones, cellular states and tissue context.
Different perspectives on your research question.
DNA · CLONAL STRUCTURE
Start with single-cell copy-number profiles to compare subclones, shared events and changes across research time points.
RNA · CELLULAR STATES
Connect cell-type identification with marker expression, composition and differential analysis to study cellular states.
SPACE · TISSUE CONTEXT
Interpret cell types, regional differences and neighborhoods in tissue coordinates, with clonal integration planned around matched material.
NETWORKS · CANDIDATE MECHANISMS
Use cell relationships, communication and regulatory-network analysis to prioritize questions for follow-up mechanistic work.
FROM PUBLICATIONS TO YOUR QUESTION
See what the methods have shown in published studies, then explore how they fit your samples.
View the evidenceCELL 2023 · FIGURE 4
Paired primary and recurrent FFPE samples combine histology, timelines and CNA profiles to investigate persistent subclones.
Read the studyCELL 2025 · FIGURE 5
Same-cell DNA+RNA enables comparison of copy number and expression, supporting candidate mechanisms for follow-up experiments.
Read the studyRESEARCH APPLICATIONS
Connect retrospective cohorts to spatial and functional validation. Exploratory directions require study-specific assessment.
Explore six study directionsCompare clonal composition across time to investigate persistence and treatment-associated selection.
View the study approachRelate candidate clones to tissue regions and neighboring cells, supported by in situ validation.
View the study approachCompare clones across model establishment and perturbation to explore candidate mechanisms—a collaborative study direction.
View the study approachFROM SAMPLE TO INSIGHT
A coordinated process, from collection planning to result interpretation.
Review sample preparationDefine the question, available material and research goals.
Agree on methods, controls, study scope and deliverables.
Prepare and label material using the agreed collection plan.
Check metadata and tissue, cell or nuclear quality.
Review tissue regions for pathology or spatial studies as needed.
Prepare samples and libraries, then sequence using the agreed assay.
Review QC, clones, expression and relevant spatial associations.
Deliver agreed datasets and figures, then discuss interpretation.
THREE LAYERS OF SIGNAL
Move from clonal structure to cellular state and tissue context. Each layer has a defined data basis and a route to the next validation step.
Wang et al., Cell 2023 · Figure 5AUse cell-level DNA copy number as genomic evidence to compare subclones, shared events and evolutionary relationships across time points.
Explore Arc-well evidence
Example: supplied single-cell sequencing material · page 2Study cell identity, expression differences and candidate programs; same-cell DNA + RNA studies can further connect state to clonal identity.
Explore single-cell analysis
Example: supplied spatial transcriptomics material · page 2Return cell types, tissue regions and neighborhoods to spatial coordinates, then plan cross-data integration or in-situ validation around matched material.
Explore spatial analysisFigures illustrate analysis layers, not results from a current project. Applicable data, analysis and validation are agreed per study.
BEYOND A SINGLE ASSAY
Developing reagents, automation modules and data tools around sample preparation, nanowell dispensing and imaging, library construction and analysis.
Explore the development roadmap
LET’S BUILD YOUR STUDY
Bring your sample type, research question and existing data. Let’s find the right starting point.
