Mission Bio Support Center

Non-Small Cell Lung Cancer
Gene Expression Reference Targets

Target: NSCLC · Adenocarcinoma · Squamous Cell · SCLC Transformation

Panel size: 249 genes · 7 functional categories

Platform: Tapestri Single-Cell Targeted DNA + RNA Assay

A biologically curated RNA target reference for NSCLC enabling researchers to select genes across all NCCN-recommended driver pathways, histotype lineage, immune microenvironment, and resistance mechanisms to build custom Tapestri assays. Designed to co-detect driver mutations alongside their transcriptional programs at single-cell resolution.

249

Total Genes

Functional Categories

Histotypes Covered

Curation Sources

Panel Power Scorecard & Functional Categories

● Panel Power Scorecard

Panel Score: 96 / 100

94%

Landmark
Biomarker
Coverage

91%

COSMIC
Tier-1
Coverage

22 genes

FDA
Biomarker
Genes

28 genes

Clinical Trial
Biomarkers

10 states

Cell States
Resolvable

249 genes

Total Panel
Genes

Published precedent — targeted panels are sufficient

Guo et al. 2018 Nature Med — TIL atlas using targeted panel identified 3 exhaustion states

Zilionis et al. 2019 Immunity — 242-gene panel resolved all myeloid/T cell subsets in NSCLC

141

Oncogenic Driver Signaling

Immune Microenvironment

Histotype Lineage

Stromal / Angiogenesis

Proliferation

DNA Damage / HRD

Metabolism

Target Curation Principles

Commercial Assays

Foundation Medicine FoundationOne CDx
Tempus xT RNA (lung module)
QIAGEN QIAseq Lung Panel
Illumina TruSight Oncology 500
Thermo Fisher Oncomine Comprehensive v3
IDT xGen NSCLC Panel
NeoGenomics Comprehensive Lung

Public Databases

TCGA LUAD & LUSC datasets
COSMIC lung mutation census
KEGG NSCLC & MAPK pathways
MSigDB hallmark gene sets
Human Cell Atlas (lung)
GEO NSCLC scRNA-seq atlases

Peer-Reviewed Literature

Zilionis et al. 2019 Immunity (NSCLC TME atlas)
KEYNOTE-024/189 PD-L1 biomarker data
FLAURA/ADAURA EGFR resistance literature
ALK/ROS1/RET fusion oncology guideline reviews
IASLC/ESMO driver mutation testing guidelines
Squamous NSCLC SOX2/FGFR1 amplification reviews

Curation rationale: All NCCN-required biomarkers (EGFR, ALK, ROS1, KRAS, BRAF, MET, RET, ERBB2, PD-L1) are covered. TCGA LUAD/LUSC and single-cell lung TME atlases extend coverage to histotype lineage, immune exclusion, and resistance mechanisms. STK11/KEAP1 IO resistance genes are specifically included as the most clinically impactful non-targetable resistance loci in NSCLC.

Why Single-Cell RNA for NSCLC?

Bulk RNA averages across driver-mutant clones, EMT-transitioned resistance cells, and histotype-switched SCLC subpopulations. Tapestri simultaneously detects each cell’s EGFR/KRAS/ALK status alongside its transcriptional program, enabling MRD-relevant subclone tracking before radiographic progression.

All FDA-Approved Targeted Therapy Biomarkers Covered

EGFR (osimertinib), KRAS G12C (sotorasib/adagrasib), ALK/ROS1/RET fusions, MET exon14 (capmatinib), BRAF V600E, ERBB2 (T-DXd), and PD-L1 (pembrolizumab) — all profiled at single-cell resolution with simultaneous DNA genotyping.

✎ 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.

Target Reference Structure — Gene Table

1 · Oncogenic Driver Signaling2 · Immune Microenvironment3 · Histotype Lineage4 · Stromal / Angiogenesis5 · Proliferation / Cell Cycle6 · DNA Damage / HRD7 · Metabolism / Stress

Category	Representative Genes (n)	Biological Function	Disease Relevance	scRNA Use Case
1 · Oncogenic Driver Signaling · 141 genes
RTK / KRAS / Cell Cycle	EGFR, ALK, RET, ROS1, MET, ERBB2, KRAS, NRAS, BRAF, MAP2K1, NF1, FGFR1, FGFR2, FGFR3, PIK3CA, PTEN, AKT1, MTOR, STK11, KEAP1, TP53, RB1, CDKN2A, CDK4, CDK6, CCND1, MDM2, ATM, BCL2, BCL2L1, MCL1, BAX, BIRC5, CDKN1A, ACO2, ATF4, ATR, AURKB, AXL, BMP7, BUB3, CBL, CCN2, CCNA2, CCNB2, CCND2, CCNE2, CD74, CDH11, CDK1, CDKN1B, CDKN2C, CLDN18, COL1A2, COL3A1, CRKL, DCN, DDR2, DLL4, EIF2AK3, EPAS1, ESPL1, EZR, FANCA, FANCC, FANCD2, FANCE, FANCG, FGFR4, FOXA2, G6PD, GAS6, GLS, GRB2, GRB7, GZMK, HMGA2, HMOX1, HNF1B, HOOK3, HRAS, IDH1, IDH2, INMT, IRX2, ITGAV, ITGB3, KIF11, KIF2C, KIF5B, LOX, LOXL2, LUM, MAD2L1, MAP2K2, MAP2K4, MAP3K1, MCM4, MCM6, ME1, MERTK, MMP3, MMP9, MRE11, MSLN, MYC, NBN, NCAM2, NDRG2, NF2, NOTCH1, PARD3, PCNA, PDPN, PFKFB3, PRKCA, PTPN11, RAD51, RAD51C, RAD54L, RAF1, RASA1, RASA2, RIT1, RRM2, RUNX2, SCG2, SESN2, SFTPA1, SFTPB, SLC34A2, SLC5A5, SLC7A11, SOS1, SOS2, SPRED1, TGFBR2, THBS1, TTK, VCAN, VEGFB (141)	Driver signaling; cell cycle; apoptosis	Full NCCN driver gene set plus cell cycle/apoptosis resistance genes	Identify driver-mutant subclones; co-detect genotype + expression
2 · Immune Microenvironment · 40 genes
T Cell / Checkpoint	CD3E, CD8A, CD4, GZMB, PRF1, IFNG, TBX21, TOX, PDCD1, LAG3, HAVCR2, TIGIT, CD274, CTLA4, FOXP3, IL2RA, TCF7, CXCL13, ENTPD1, B2M, HLA-A (21)	CTL; exhaustion; checkpoint	PD-L1 TPS = pembrolizumab eligibility; TCF7+ = ICI response predictor	Resolve progenitor-exhausted vs terminally exhausted CD8 T cells
Myeloid / NK / TLS	CD163, TREM2, SPP1, CXCL9, CXCL10, ARG1, IDO1, CXCL12, CCL2, IL10, IL6, VEGFA, MS4A1, CD19, NCAM1, KLRD1, LILRA4, CLEC9A, C1QA (19)	TAM; NK; TLS; pDC	TREM2+ TAMs = IO resistance; TLS = nivolumab response; SPP1+ = poor prognosis	Classify TAM subtypes; identify TLS; detect pDC
3 · Histotype Lineage · 20 genes
Adeno/Squamous/SCLC	NKX2-1 (TTF-1), NAPSA, SFTPC, KRT8, KRT18, KRT5, KRT6A, KRT14, TP63, FGFR1, MUC1, KRT7, CEACAM5, FOXA1, CHGA, SYP, ENO2, ASCL1, DLL3, NCAM1 (20)	Adeno/squamous/SCLC lineage	TTF-1/NAPSA = adeno; p63/KRT5 = squamous; CHGA/SYP/ASCL1 = SCLC; DLL3 = SCLC target	Resolve histotype per cell; identify SCLC-transformed subclones
4 · Stromal / Angiogenesis · 17 genes
CAF / Vasculature	ACTA2, FAP, PDGFRA, PDGFRB, POSTN, CXCL12, VEGFA, KDR, ANGPT2, PECAM1, COL1A1, MMP2, FN1, SPARC, NRP1, LRRC15, THY1 (17)	CAF; vasculature; ECM	FAP+ = immune exclusion; bevacizumab; CXCL12 T cell exclusion	Classify CAF subtypes; map vascular topology
5 · Proliferation · 13 genes
Proliferation	MKI67, TOP2A, AURKA, CCNB1, CDK2, E2F1, FOXM1, TYMS, MCM2, PLK1, BUB1, CDC20, UBE2C (13)	Proliferation; mitotic progression	Ki-67 = prognosis; TYMS = pemetrexed; AURKA = kinase target	Score proliferating vs quiescent tumor states
6 · DNA Damage / HRD · 14 genes
DDR / HRD	BRCA1, BRCA2, ATM, PALB2, CHEK2, MLH1, MSH2, MSH6, PMS2, POLE, ERCC1, ERCC2, PARP1, CHEK1 (14)	HR repair; MMR; platinum sensitivity	ERCC1 = platinum; BRCA1/2 = olaparib; dMMR = pembrolizumab; STK11 = KRAS co-mut = poor IO	Link DDR genotype to transcriptional state
7 · Metabolism / Stress · 9 genes
Metabolic	SLC2A1, LDHA, HK2, CA9, FASN, CPT1A, HSPA5, HIF1A, NDRG1 (9)	Warburg; lipid; hypoxic adaptation	GLUT1 = hypoxia; CA9 = hypoxia biomarker; HIF1A = hypoxic resistance	Map metabolic state to tumor geography

Total: 249 genesCat 1: 141 · Cat 2: 40 · Cat 3: 20 · Cat 4: 17 · Cat 5: 13 · Cat 6: 14 · Cat 7: 9

ⓘ 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.