RNA TargetsSolid Tumor · BreastResearch Use Only
Breast Cancer Gene Expression
Reference Targets
Reference Targets
A biologically curated RNA target reference for breast cancer spanning all four major molecular subtypes — enabling researchers to select genes across receptor signaling, HRD, immune biology, and lineage plasticity to build custom Tapestri assays. Designed to resolve ESR1 resistance mutations, HER2 heterogeneity, and TNBC CSC hierarchies at single-cell resolution.
290
Total Genes
7
Functional Categories
4
Molecular Subtypes
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 90 / 100
91%
Landmark
Biomarker
Coverage
Biomarker
Coverage
87%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
19 genes
FDA
Biomarker
Genes
Biomarker
Genes
22 genes
Clinical Trial
Biomarkers
Biomarkers
9 states
Cell States
Resolvable
Resolvable
290 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Pal et al. 2021 Nature — targeted scRNA resolved all 10 BC subtypes with <400 genes
Azizi et al. 2018 Cell — 500-gene panel fully characterized BC immune microenvironment
Pal et al. 2021 EMBO J — targeted scRNA resolved all 10 BC subtypes with <400 genes
61
Hormone Receptor & HER2
39
DNA Damage / HRD
59
Immune Microenvironment
44
Stromal / Angiogenesis
34
Proliferation / Cell Cycle
27
AR / Metabolism
36
Cell State / Lineage
2
Target Curation Principles
Commercial Assays
- Foundation Medicine FoundationOne CDx
- Tempus xT RNA (breast module)
- QIAGEN QIAseq Breast Cancer Panel
- Illumina TruSight Oncology 500
- Thermo Fisher Oncomine Breast
- IDT xGen Breast Panel
- NeoGenomics BRCA/HER2 assays
Public Databases
- TCGA BRCA dataset & METABRIC
- COSMIC breast mutation census
- MSigDB hallmark gene sets
- Human Cell Atlas (breast)
- GEO scRNA-seq breast cancer datasets
- cBioPortal TCGA-BRCA cohort
Peer-Reviewed Literature
- PAM50 intrinsic subtype classifier
- Lehmann et al. 2011 JCI (TNBC subtypes)
- KEYNOTE-522 (pCR + PD-L1 in TNBC)
- OlympiA trial (olaparib in BRCA1/2 BC)
- MONARCH-2/3 (CDK4/6i + fulvestrant)
- ESR1 mutation endocrine resistance reviews
Why Single-Cell RNA for Breast Cancer?
ESR1 resistance mutations and HER2 copy number heterogeneity emerge in distinct tumor subclones that bulk RNA obscures. Tapestri simultaneously links each cell’s ESR1/PIK3CA/BRCA1 mutation status to its transcriptional subtype, directly revealing the endocrine-resistant minority population before clinical progression.
Four Subtypes + CDK4/6 Resistance Covered
HR+ (ESR1/CDK4-6), HER2+ (trastuzumab/T-DXd), TNBC (atezolizumab/sacituzumab/olaparib), and CSC (ALDH1A1/CD44/CD24). CDK4/6 inhibitor resistance (RB1 loss, CCNE1 amp., ESR1 mut.) covered with 30+ dedicated DDR and cell cycle genes.
3
Target Reference Structure — Gene Table
1 · Hormone Receptor & HER22 · DNA Damage / HRD3 · Immune Microenvironment4 · Stromal / Angiogenesis5 · Proliferation / Cell Cycle6 · AR / Metabolism7 · Cell State / Lineage
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · Hormone Receptor & HER2 Signaling · 61 genes | ||||
| ER/PR/HER2/PI3K | ESR1, PGR, ERBB2, ERBB3, EGFR, FOXA1, GATA3, XBP1, TFF1, TFF3, CCND1, CDK4, CDK6, RB1, PIK3CA, PTEN, AKT1, MTOR, FBXW7, FGFR1, FGFR2, NRG1, NCOA3 (23) + 38 accessory | ER/PR/HER2 subtype; endocrine/CDK4-6/HER2 targets | ESR1 mut. = endocrine resistance; HER2 amp. = trastuzumab/T-DXd; PIK3CA = alpelisib; CDK4/6 = palbociclib | Resolve ESR1-mut resistant clones; co-detect PIK3CA + ER expression |
| 2 · DNA Damage / HRD · 39 genes | ||||
| BRCA / HRD / DDR | BRCA1, BRCA2, PALB2, RAD51, ATM, ATR, CHEK1, CHEK2, TP53, BARD1, NBN, BRIP1, FANCA, FANCD2, RAD51C, PARP1, MLH1, MSH2, MSH6, PMS2, POLE (21) + 18 accessory | HR repair; HRD; PARP inhibitor | BRCA1/2 = olaparib/talazoparib; HRD score guides therapy; TP53 >80% TNBC; ATM mut. | Link BRCA expression to HRD genotype per cell |
| 3 · Immune Microenvironment · 59 genes | ||||
| TIL / Checkpoint / Myeloid | CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, FOXP3, TCF7, B2M, HLA-A, CD68, CD163, TREM2, SPP1, CXCL9, ARG1, IDO1, MS4A1, CD19, NCAM1, NKG7, LILRA4, C1QA (29) + 30 accessory | CTL; checkpoint; TAM; NK; TLS | TIL density predicts pCR in TNBC; PD-L1 = atezolizumab; TREM2+ TAMs = exclusion; TLS = IO response | Resolve TIL states; classify TAM subtypes; identify TLS |
| 4 · Stromal / Angiogenesis · 44 genes | ||||
| CAF / Vasculature | ACTA2, FAP, PDGFRA, PDGFRB, POSTN, LRRC15, MYH11, CXCL12, VEGFA, KDR, ANGPT1, PECAM1, COL1A1, MMP2, FN1, SPARC, CTGF, THY1, TGFB1 (19) + 25 accessory | CAF; vasculature; ECM | myoCAF = paclitaxel resistance; iCAF = immune exclusion; bevacizumab + chemo in mBC | Classify CAF subtypes; resolve perivascular niche |
| 5 · Proliferation / Cell Cycle · 34 genes | ||||
| Proliferation | MKI67, TOP2A, AURKA, AURKB, CCNB1, CDK2, E2F1, FOXM1, TYMS, MCM2, PLK1, BUB1, UBE2C (13) + 21 accessory | Mitotic progression; proliferation | Ki-67 = PAM50 grade; TOP2A = anthracycline; TYMS = capecitabine; FOXM1 drives CDK4/6i resistance | Score S-phase vs G2/M vs quiescent cells |
| 6 · AR / Metabolism · 27 genes | ||||
| AR / Lipid | AR, FASN, ACACA, SLC2A1, LDHA, HK2, CA9, HIF1A, BNIP3, SRD5A1, NRG1 (11) + 16 accessory | AR; lipid; Warburg | AR in LAR TNBC = enzalutamide; FASN = lipid synthesis; HIF1A = hypoxic resistance | Identify AR+ TNBC cells; map metabolic state |
| 7 · Cell State / Lineage Plasticity · 36 genes | ||||
| Luminal/Basal/CSC | FOXA1, GATA3, ESR1, KRT8, KRT18, KRT5, KRT14, CDH1, CDH2, VIM, SNAI2, ZEB2, TWIST1, SOX9, ALDH1A1, CD44, CD24, EPCAM, MUC1 (19) + 17 accessory | Luminal vs basal vs mesenchymal identity | Plasticity drives TNBC heterogeneity; CDH1 loss = lobular BC; claudin-low = stem-like | Resolve cell-state hierarchy; track cadherin switch |
Total: 290 genesCat 1: 61 · Cat 2: 39 · Cat 3: 59 · Cat 4: 44 · Cat 5: 34 · Cat 6: 27 · Cat 7: 36
ⓘ Select genes appear in more than one functional category reflecting their multi-role biology. The total above counts unique genes; per-category counts include all category-relevant entries.