RNA TargetsHematologic OncologyResearch Use Only
Acute Lymphoblastic Leukemia (ALL)
Gene Expression Reference Targets
Gene Expression Reference Targets
A biologically curated RNA target reference for acute lymphoblastic leukemia spanning BCR-ABL1/Ph-like kinase fusions, lymphoid lineage identity, MRD-relevant surface antigens, and immune evasion biology — enabling researchers to configure custom Tapestri assays for precision subtype classification, CAR-T target identification, and relapse mechanism studies.
242
Total Genes
7
Functional Categories
5+
ALL Subtypes Covered
6+
Curation Sources
1
Panel Power Scorecard & Functional Categories
● Panel Power Scorecard
Panel Score: 75 / 100
88%
Landmark
Biomarker
Coverage
Biomarker
Coverage
82%
COSMIC
Tier-1
Coverage
Tier-1
Coverage
11 genes
FDA
Biomarker
Genes
Biomarker
Genes
16 genes
Clinical Trial
Biomarkers
Biomarkers
8 states
Cell States
Resolvable
Resolvable
242 genes
Total Panel
Genes
Genes
Published precedent — targeted panels are sufficient
Maude et al. 2018 NEJM (tisagenlecleucel ALL CAR-T)
Roberts et al. 2014 NEJM (Ph-like ALL kinase fusions)
52
Driver / Fusions
50
Lineage / Subtype
42
CAR-T Antigens
40
Immune Evasion
40
T-ALL / NOTCH1
24
Cell Cycle
20
Epigenetic
2
Background & Curation Principles
Commercial Assays
- FoundationOne Heme (hematologic panel)
- IDT xGen ALL Panel
- QIAGEN QIAseq Myeloid/Lymphoid
- Thermo Fisher Oncomine Myeloid
Public Databases
- COSMIC (ALL mutations)
- ClinVar (ALL germline variants)
- St. Jude PCGP ALL dataset
- ELN ALL guidelines
- Human Cell Atlas (immune)
Peer-Reviewed Literature
- Ph-like ALL kinase fusions (Roberts 2014 NEJM)
- CAR-T CD19/CD22 target biology (Maude 2018 NEJM)
- T-ALL NOTCH1 oncogenesis (Weng 2004 Science)
- ALL MRD and relapse mechanisms (Bhojwani 2020 Blood)
Why Single-Cell RNA for ALL?
ALL is defined by leukemic blast clones with distinct surface antigen expression levels — yet bulk RNA averages CD19-high and CD19-low blasts, masking the antigen-dim subpopulation that escapes CD19-targeted CAR-T therapy. Tapestri co-detects BCR-ABL1 or CRLF2 mutation status alongside CD19/CD22 surface antigen expression level per blast cell, directly enabling pre-CAR-T antigen escape risk assessment at single-cell resolution.
CD19 Antigen Escape — The CAR-T Achilles Heel
30–40% of B-ALL patients relapse after CD19-directed CAR-T therapy due to antigen escape: CD19 isoform switching, lineage switch to AML, or selection of CD19-dim blasts. Panel covers CD19/CD22/CD38/TSLPR antigen expression + lineage identity (PAX5, IKZF1, CEBPA) per cell — identifying antigen-dim populations before therapy that predict escape at relapse.
3
Target Reference Structure — Gene Table
1 · Driver / Ph / Ph-like Fusions2 · Lymphoid Lineage / Subtype3 · CAR-T Antigens / Surface4 · Immune Evasion / MRD5 · T-ALL / NOTCH1 Axis6 · Cell Cycle / Apoptosis7 · Epigenetic / Splicing
| Category | Representative Genes (n) | Biological Function | Disease Relevance | scD+R Use Case |
|---|---|---|---|---|
| 1 · Driver / BCR-ABL1 / Ph-like Kinase Fusions · 52 genes | ||||
| Driver | BCR, ABL1, JAK2, JAK1, CRLF2, TSLP, ABL2, PDGFRB, CSF1R, EPOR, FLT3, KRAS, NRAS, PTPN11, PIK3CA, PTEN, AKT1, MTOR, MYC, CDKN2A, TP53, RB1 (22) + 30 accessory | BCR-ABL1; Ph-like kinase fusion; RAS/PI3K survival signaling | BCR-ABL1 = imatinib/ponatinib target; CRLF2 = Ph-like (TSLP receptor); JAK2 = ruxolitinib target; FLT3 = ITD (gilteritinib target in ALL) | Co-detect BCR-ABL1 fusion + blast transcriptional identity; identify Ph-like kinase-active subclones |
| 2 · Lymphoid Lineage / Subtype Classification · 50 genes | ||||
| Lineage | PAX5, EBF1, IKZF1, IKZF2, IKZF3, E2A (TCF3), HLF, ZNF384, MEF2D, KMT2A, ETV6, RUNX1, GATA3, LMO2, TAL1, LYL1, NOTCH1, CEBPA, CD34, CD19, CD22, CD10 (MME), CD38, CD58, TSLPR (IL7R) (25) + 25 accessory | B/T lineage identity; molecular subtype classifiers | PAX5/EBF1/IKZF1 = B cell lineage; KMT2A-AFF1 = infant ALL; ETV6-RUNX1 = favorable; IKZF1 del = IKZF1plus/poor prognosis | Classify ALL subtype per blast cell; identify lineage switch (B→myeloid) at relapse |
| 3 · CAR-T Antigens / Surface Target Expression · 42 genes | ||||
| Signaling | CD19, CD22, CD38, CD20 (MS4A1), CD79A, CD79B, CD123, TSLPR, CD33, CD3E, CD7, CD5, THYG, CD1A, CD2, CD4, CD8A, BCL11B, PTPRC (CD45), CD44, CD34, IL7R (22) + 20 accessory | B/T surface antigen expression; CAR-T target density | CD19/CD22 = approved CAR-T targets; CD38 (daratumumab); CD19-dim = escape mechanism; CD22 = salvage after CD19 escape | Quantify CAR-T antigen expression level per blast; identify CD19-dim subpopulation pre-therapy |
| 4 · Immune Evasion / MRD Markers · 40 genes | ||||
| Immune | B2M, HLA-A, HLA-B, HLA-C, CD274, PDCD1, LAG3, HAVCR2, TIGIT, FOXP3, IL2RA, CD3E, CD8A, NKG7, GZMB, CD47, LILRB2, CD200, LGALS9, NECTIN2 (20) + 20 accessory | MHC-I / immune escape; T cell dysfunction; MRD-relevant surface | B2M/HLA-A loss = MHC-I escape (resistance to T cell + CAR-T); CD47 = don't-eat-me signal; CD274 = ICI target | Identify MHC-I-loss subclones at relapse; characterize T cell exhaustion in ALL bone marrow |
| 5 · T-ALL / NOTCH1 / ETP-ALL · 40 genes | ||||
| Resistance | NOTCH1, FBXW7, PTEN, CDKN2A, MYC, LYL1, TAL1, LMO2, TLX1, TLX3, NKX2-1, HOXA9, HOXA10, MEIS1, ETP (IL7R), RUNX1, FLT3, KIT, PTPN2, DNMT3A (20) + 20 accessory | NOTCH1/FBXW7 mutations; ETP-ALL myeloid markers; T-ALL oncogenesis | NOTCH1 = 55% T-ALL (gamma-secretase target); ETP-ALL = HOXA/FLT3/DNMT3A (similar to AML); TLX1/3 = favorable T-ALL | Classify T-ALL molecular subtypes; identify ETP-ALL (mixed myeloid/lymphoid phenotype) |
| 6 · Cell Cycle / Apoptosis / Therapy Resistance · 24 genes | ||||
| Cell Cycle | BCL2, BCL2L1, MCL1, BAX, BCL2L11, BBC3, BIRC5, CDKN1A, MKI67, TOP2A, CDK2, CCNB1, E2F1 (13) + 11 accessory | Apoptosis; venetoclax sensitivity; proliferative index | BCL2 = venetoclax target (ALL combination studies); MCL1 = resistance mechanism; BIRC5 = elevated in relapsed ALL | Identify apoptosis-primed vs -resistant subclones; assess venetoclax combination eligibility |
| 7 · Epigenetic / Splicing / MRD · 20 genes | ||||
| Epigenetic | DNMT3A, TET1, TET2, KDM6A, EZH2, CREBBP, EP300, ASXL1, KMT2A, PHF6, WT1, IKZF1, SRSF2, U2AF1, SF3B1 (15) + 5 accessory | Epigenetic regulators; splicing factor mutations; steroid resistance | CREBBP/EP300 = glucocorticoid resistance; KMT2A = MRD target; IKZF1 deletion = minimal residual disease | Detect MRD-relevant epigenetic mutations; identify steroid-resistant subclones at diagnosis |
Total: 242 genesCat 1: 52 · Cat 2: 50 · Cat 3: 42 · Cat 4: 40 · Cat 5: 40 · Cat 6: 24 · Cat 7: 20
ⓘ 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.