Molecular profiling — one tumor, many lenses
Molecular profiling examines a tumor through DNA, RNA, protein, tissue location, functional experiments, and repeated measurements. Each lens answers a different question. Agreement can strengthen an interpretation; it does not automatically establish drug response or clinical eligibility.
For the learning map, use Understand multi-omics. This directory is the assay-by-assay reference within that path.
The six layers
| Lesson | The question | Main limit |
|---|---|---|
| 1. DNA — the blueprint | What sequence and copy changes are present? | A change does not establish its downstream consequence |
| 2. RNA — the activity layer | What messages and cell programs were captured? | Composition, preparation, and background affect interpretation |
| 3. Protein — expression and activation | What is made, where is it, and what is activated? | Abundance and signaling are different from dependence |
| 4. Spatial biology | Where are cancer cells, immune cells, and targets? | Location alone does not establish recognition or killing |
| 5. Functional response | What happens under a defined perturbation? | A model's response may not translate to the clinical setting |
| 6. ctDNA and MRD | What tumor-derived signal is detectable in blood over time? | Detection depends on shedding, assay sensitivity, and sampling |
Current test status, tissue allocation and patient results have their own linked owners below.
Start with the tissue mixture
A biopsy includes malignant cells and normal neighbors. Epithelial identifies the lining/gland cell family, malignant identifies cancer, and luminal-progenitor-like describes a reference-like expression state. Those words cannot substitute for each other.
Bulk RNA and protein combine contributions from that mixture. Single-cell/nucleus methods help assign signals, while spatial methods retain location. Every comparison still needs the right cell group, specimen, preparation, and reference. See cell identity and RNA counts.
Applied to Diana
Use the molecular profile for current integrated findings and the specimen map for collection and assay attribution. Research measurements do not automatically establish clinical function or treatment eligibility.
Continue by question
- “How can both BRCA1 copies be disabled?” → Copies and alleles → Splicing and repair → HRD and PARP.
- “What does high expression actually prove?” → RNA counts → Protein → Comparisons and evidence.
- “Does an immune-rich sample mean tumor recognition?” → Recognition → Measuring T-cell engagement.
- “How do repair, recycling, and growth signaling interact?” → PARP, recycling, and cell survival.
- “What remains useful in the earlier EVEE pathway course?” → Historical hypotheses and current qualifications. General pathway biology remains useful; old variant calls and confounded RNA ranks do not establish Diana's dependencies.
- “How should I read a new assay report?” → Reading a tumor report.
Current records and operational questions
- Molecular profile — the current integrated patient findings.
- Specimen-to-sample map — collection dates and assay attribution, including unresolved provenance.
- Test tracker — completed, missing, and pending results.
- Tissue and data — available material and custody.
- October 4 reports — the supplied research evidence.
- Omics methods and reproducibility — analysis workflows and data questions.
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