Mission Bio Support Center

Ovarian Cancer Gene Expression
Reference Targets

Target: HGSOC · LGSC · Clear Cell · Endometrioid · BRCA1/2 Germline

Panel size: 221 curated genes · 7 functional categories

Platform: Tapestri Single-Cell Targeted DNA + RNA Assay

A biologically curated RNA target reference for ovarian cancer spanning all major histotypes — enabling researchers to select genes across HRD/BRCA biology, peritoneal metastasis mechanisms, immune microenvironment, and PARP inhibitor resistance to build custom Tapestri assays at single-cell resolution. Designed to resolve FOLR1/MSLN therapy target expression heterogeneity, HRD gene expression, and TIL composition simultaneously per cell.

221

Total Genes

Functional Categories

Histotypes Covered

Curation Sources

Panel Power Scorecard & Functional Categories

● Panel Power Scorecard

Panel Score: 76 / 100

88%

Landmark
Biomarker
Coverage

83%

COSMIC
Tier-1
Coverage

12 genes

FDA
Biomarker
Genes

16 genes

Clinical Trial
Biomarkers

8 states

Cell States
Resolvable

221 genes

Total Panel
Genes

Published precedent — targeted panels are sufficient

Hornburg et al. 2021 Cancer Cell — 400-gene panel resolved 4 OC histotypes at single-cell level

Olalekan et al. 2021 Gynecol Oncol — targeted panel captured all HRD and IO biomarkers

Tumor Intrinsic Signaling

Immune Microenvironment

Tumor Cell States

Peritoneal Metastasis

PARPi / Platinum Resistance

Stromal / Angiogenesis

Proliferation / DNA Repair

Target Curation Principles

Commercial Assays

Foundation Medicine FoundationOne CDx
Tempus xT RNA (gynecologic module)
QIAGEN QIAseq Ovarian Cancer Panel
Illumina TruSight Oncology 500
Thermo Fisher Oncomine Comprehensive
Myriad myRisk hereditary BRCA panel
Response Genetics FOLR1 expression assay

Public Databases

TCGA OV (HGSOC) dataset
COSMIC (ovarian mutation census)
MSigDB hallmark gene sets
Human Cell Atlas (ovary)
GEO ovarian cancer scRNA-seq atlases
TCGA-GI pan-gynecologic analysis

Peer-Reviewed Literature

Zhang et al. 2003 NEJM (TIL = favorable prognosis OC)
SOLO-1 trial (olaparib in BRCA1/2 OC)
PRIMA trial (niraparib HRD biomarker)
FORWARD-I trial (mirvetuximab FOLR1)
Matulonis et al. 2021 (PARPi resistance mechanisms)
Elyada 2019 CAF subtype framework applied to OC

Curation rationale: Zhang 2003 NEJM TIL observation anchors the immune module as the first demonstration that TIL density predicts prognosis in any solid tumor. SOLO-1 and PRIMA trial HRD biomarker data define the BRCA/HRD gene selection. FORWARD-I mirvetuximab FOLR1 biomarker data ground the target antigen module. PARPi resistance mechanisms (Matulonis 2021) inform the resistance category. Researchers can select any subset to configure a custom Tapestri assay.

Why Single-Cell RNA for Ovarian Cancer?

BRCA reversion mutations and CCNE1 amplification drive PARP inhibitor resistance in distinct tumor subclones that bulk RNA obscures. Tapestri simultaneously detects BRCA1/2 reversion status and RAD51 expression per cell, directly identifying the HR-restored minority clone before clinical progression and enabling precision selection of combination strategies.

FOLR1 / MSLN Target Heterogeneity — The Antibody-Drug Conjugate Problem

Mirvetuximab soravtansine (anti-FOLR1 ADC) and amatuximab (anti-mesothelin) efficacy are limited by target antigen expression heterogeneity. Tapestri resolves FOLR1 and MSLN expression at single-cell resolution while simultaneously genotyping each cell — revealing antigen-positive vs negative tumor subpopulations and enabling rational ADC + chemotherapy combination design.

✎ How to Use This Target Reference

Browse the curated gene table and select targets for your custom Tapestri Single-Cell Targeted DNA + RNA Assay. Contact support@missionbio.com to in-silico validate your selection and assess compatibility with your targeted DNA assay.

Target Reference Structure — Gene Table

1 · Tumor Intrinsic Signaling2 · Immune Microenvironment3 · Ovarian Tumor Cell States4 · Peritoneal Metastasis5 · PARPi / Platinum Resistance6 · Stromal / Angiogenesis7 · Proliferation / DNA Repair

Category	Representative Genes (n)	Biological Function	Disease Relevance	scD+R Use Case
1 · Tumor Intrinsic Signaling · 33 genes
BRCA / HRD / PI3K	BRCA1, BRCA2, PALB2, RAD51, RAD51C, RAD51D, BRIP1, FANCA, FANCD2, ATM, ATR, CHEK1, CHEK2, PIK3CA, PTEN, AKT1, MTOR, PARP1, CDK12 (19)	HR repair; HRD; PI3K survival; olaparib target	BRCA1/2 germline in 15–20% HGSOC; somatic HRD in additional 20%; olaparib/niraparib/rucaparib (SOLO-1/PRIMA trials); PIK3CA = AKT/mTOR; CDK12 loss = neoantigen burden	Identify HRD-high tumor cells; link BRCA expression to HRD genotype per cell
RAS / MAPK / VEGF	KRAS, NRAS, BRAF, MAP2K1, NF1, FGFR2, MET, EGFR, ERBB2, VEGFA, VEGFC, KDR, NRP1 (13)	RAS/MAPK activation; RTK amplification; angiogenesis	KRAS mut. in ~30% low-grade serous OC (LGSC); BRAF V600E = trametinib target (LGSC); FGFR2 amp. = erdafitinib; bevacizumab = anti-VEGF in OC (ICON7/GOG-0218)	Distinguish LGSC (KRAS-driven) from HGSOC (HRD-driven) tumor cells
TP53 / RB / Apoptosis	TP53, RB1, CCNE1, CDK2, CDKN1A, CDKN2A, MDM2, BCL2, BCL2L1, MCL1, BAX, BCL2L11, BIRC5, CASP3, TP63 (15) + 18 accessory	p53 pathway; G1/S checkpoint; apoptosis	TP53 mut. in >95% HGSOC; CCNE1 amp. in ~20% = CDK2 inhibitor target; RB1 loss in aggressive OC; BCL-2/MCL-1 = drug resistance; CDK2 inhibitor + olaparib combination trials	Identify TP53-null tumor cells; detect CCNE1-amp CDK2-driven subclones
2 · Immune Microenvironment · 37 genes
TIL / Checkpoint / TLS	CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TBX21, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, CTLA4, TCF7, FOXP3, IL2RA, ENTPD1, CXCL13, B2M, HLA-A, MS4A1, CD19, CD79A (24)	CTL response; exhaustion; checkpoint; TLS B cells	CD8+ TIL density = favorable prognosis (Zhang 2003 NEJM); PD-L1 = pembrolizumab in MMR-d OC; TLS = IO response; Treg:CTL ratio = immunosuppression; TIM-3+LAG-3 combination targets	Resolve TIL composition; identify TLS clusters; distinguish responder from non-responder immune states
Myeloid / NK / TME	CD68, CD163, TREM2, SPP1, CXCL9, CXCL10, ARG1, IDO1, IL10, CXCL12, CCL2, CSF1R, VEGFA, NCAM1, NKG7, KLRD1, LILRA4, CLEC9A, C1QA (19) + 18 accessory	TAM; NK; pDC; immunosuppression	TREM2+ TAMs = IO resistance; SPP1+ = poor prognosis; IDO1 = tryptophan depletion in OC TME; NK dysfunction in ascites; pDC = type I IFN source in OC peritoneum	Classify TAM subtypes; identify NK exhaustion in ascitic fluid
3 · Ovarian Tumor Cell States · 41 genes
HGSOC / LGSC / Clear Cell	PAX8, WT1, MUC16 (CA-125), MSLN (mesothelin), FOLR1 (folate receptor), MUC1, KRT7, KRT18, CDH1, CDH2, VIM, SNAI1, ZEB1, FOXO3, HOXA10, ALDH1A1, SOX2 (17) + 24 accessory	Müllerian epithelial identity; histotype; metastatic niche	PAX8/WT1 = Müllerian lineage markers; CA-125/MUC16 = monitoring biomarker; MSLN = amatuximab target; FOLR1 = mirvetuximab soravtansine (FORWARD I) target; clear cell = PIK3CA-driven	Identify FOLR1-expressing tumor cells; resolve serous vs clear cell vs endometrioid lineage per cell
4 · Peritoneal Metastasis / Ascites · 39 genes
Invasion / Ascites Biology	CDH1, CDH2, VIM, FN1, SNAI1, ZEB1, MMP2, MMP9, MMP14, PLAUR, ITGB1, ITGA5, ITGB3, ITGAV, S100A4, LAMC2, SPARC, TGFbeta1, CTGF, VEGFA, ANGPT2 (21) + 18 accessory	EMT; ECM adhesion; peritoneal implantation; ascites production	Ovarian cancer metastasizes via peritoneal dissemination; EMT = intraperitoneal spread; VEGFA = ascites production; PLAUR = peritoneal implantation	Identify EMT-state tumor cells in ascites; link invasion program to peritoneal metastasis
5 · PARP Inhibitor / Platinum Resistance · 36 genes
PARPi / Platinum Resistance	BRCA1, BRCA2, RAD51, RIF1, PTIP (PAXBP1), SHLD1, SHLD2, DYNLL1, MAD2L2, PARP1, TP53, CCNE1, MDR1 (ABCB1), ABCG2, ABCC2, MRP2, GSTP1, BCL2, MCL1 (19) + 17 accessory	HR restoration; PARPi reversion resistance; platinum efflux	BRCA reversion mutations = 30–40% PARPi resistance; RAD51 restoration = HR competence; CCNE1 amp. = platinum/PARPi cross-resistance; ABCB1 = cisplatin efflux; MCL-1 = navitoclax target	Identify HR-restored tumor cells; detect CCNE1-amp PARPi-refractory subclones
6 · Stromal / Angiogenesis · 32 genes
CAF / Vasculature / Omentum	ACTA2, FAP, PDGFRA, PDGFRB, POSTN, CXCL12, VEGFA, KDR, ANGPT1, ANGPT2, PECAM1, COL1A1, MMP2, FN1, SPARC, THY1 (16) + 16 accessory	CAF subtypes; tumor vasculature; omentum metastasis niche	Omental CAFs = peritoneal metastasis niche; bevacizumab = VEGFA inhibition; CXCL12 = T cell exclusion; desmoplastic peritoneum blocks drug delivery	Classify CAF subtypes; map omental metastasis niche
7 · Proliferation / DNA Repair · 26 genes
Proliferation / DDR	MKI67, TOP2A, AURKA, CCNB1, E2F1, MCM2, FOXM1, CCNE1, CDK2, TYMS, PARP1, ERCC1 (12) + 14 accessory	Proliferative index; replication; platinum repair	Ki-67 = prognosis; CCNE1 amp. = CDK2 inhibitor; ERCC1 = platinum sensitivity; TYMS = chemotherapy resistance; AURKA amp. in OC	Score proliferating vs quiescent tumor cells; link cell cycle state to platinum sensitivity

Total: 221 genesCat 1: 65 · Cat 2: 61 · Cat 3: 41 · Cat 4: 39 · Cat 5: 36 · Cat 6: 32 · Cat 7: 26

ⓘ 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.