Biomarkers

64 values

NormalisationSearchJev query reader

Turns the extractor's biomarker_name into the names pathologists use (ERBB2 → HER2, BCR-ABL1 → BCR::ABL1). Keys at the end of the table are names the list does not know; they pass through unchanged.

Key	Search aliases	Extracted names (rows)	Alteration types	Rows
PD-L1	pd-l1, pdl1, pd l1, pd-l-1, cd274	PD-L1 ×37	overexpression ×37	37
HER2	her2, her-2, her 2, erbb2, her2/neu	ERBB2 ×31, HER2 ×10	overexpression ×40, mutation ×1	41
EGFR	egfr	EGFR ×20	mutation ×19, wild-type-required ×1	20
ALK	alk, anaplastic lymphoma kinase	ALK ×14	fusion ×14	14
ROS1	ros1, ros-1	ROS1 ×3	fusion ×3	3
BRAF	braf	BRAF ×26	mutation ×25, fusion ×1	26
KRAS	kras	KRAS ×2	mutation ×2	2
NRAS	nras	–	–	0
RAS	ras, kras/nras	RAS ×6	wild-type-required ×6	6
MET	met, c-met, cmet, met exon 14, metex14, met ex14	MET ×2	mutation ×2	2
RET	ret	RET ×5	fusion ×3, mutation ×2	5
NTRK	ntrk, ntrk1, ntrk2, ntrk3, trk	NTRK1/NTRK2/NTRK3 ×3	fusion ×3	3
FGFR	fgfr	FGFR2 ×2, FGFR3 ×1	fusion ×2, mutation ×1	3
IDH1/2 `IDH`	idh, idh1/2	IDH1 ×2, IDH1/IDH2 ×2, IDH2 ×2	mutation ×6	6
BRCA1/2 `BRCA`	brca, brca1, brca2, brca1/2, gbrca, sbrca	BRCA1/2 ×6, BRCA1/BRCA2 ×3	mutation ×9	9
HRD	hrd, homologous recombination deficiency, hrd positive, genomic instability	HRD ×1	signature ×1	1
HRR genes `HRR`	hrr, homologous recombination repair	–	–	0
MMR/MSI	mmr, dmmr, pmmr, msi, msi-h, msi high	MMR ×14	loss ×12, wild-type-required ×2	14
TMB	tmb, tumour mutational burden, tumor mutational burden	–	–	0
PIK3CA	pik3ca	PIK3CA ×2	mutation ×2	2
AKT1/PIK3CA/PTEN `AKT`	akt, akt1, pten	PIK3CA/AKT1/PTEN ×1	mutation ×1	1
ESR1	esr1	ESR1 ×3	mutation ×3	3
Hormone receptor `HR`	hr, hr+, hormone receptor, hormone receptors, er, pr	HR ×12, ER ×3	overexpression ×15	15
Androgen receptor `AR`	androgen receptor	–	–	0
CLDN18.2	cldn18.2, cldn18, claudin, claudin 18.2, claudin-18.2	CLDN18.2 ×1	overexpression ×1	1
FRα	fra, frα, fr alpha, folr1, folate receptor, folate receptor alpha	FOLR1 ×1	overexpression ×1	1
TROP2	trop2, trop-2	–	–	0
DLL3	dll3	–	–	0
NRG1	nrg1	–	–	0
del(5q)	del(5q), del 5q, del5q, 5q deletion, 5q-	del(5q) ×2	loss ×1, wild-type-required ×1	2
TP53/del(17p) `TP53`	tp53, 17p, del17p, del(17p)	TP53 ×2	mutation ×2	2
IGHV	ighv	–	–	0
FLT3	flt3	FLT3 ×7	mutation ×7	7
NPM1	npm1	–	–	0
KMT2A	kmt2a, mll	–	–	0
BCR::ABL1	bcr-abl, bcr-abl1, bcr::abl1, bcr abl, philadelphia, ph+	BCR::ABL1 ×22, ABL1 ×4, BCR-ABL ×4, none ×2, BCR-ABL1 ×1	fusion ×29, mutation ×4	33
PML::RARA	pml-rara, pml::rara, t(15;17)	none ×2, PML/RARA ×2	fusion ×4	4
JAK2	jak2	–	–	0
KIT	kit, c-kit, cd117, kit d816v	KIT ×2	overexpression ×2	2
PDGFR	pdgfr	PDGFR ×1, PDGFRA ×1	fusion ×1, mutation ×1	2
FIP1L1::PDGFRA	fip1l1, fip1l1-pdgfra	FIP1L1-PDGFRA ×1	fusion ×1	1
CD19	cd19	CD19 ×6	overexpression ×6	6
CD20	cd20	CD20 ×4	overexpression ×4	4
CD22	cd22	CD22 ×2	overexpression ×2	2
CD30	cd30	CD30 ×5	overexpression ×5	5
CD33	cd33	CD33 ×1	overexpression ×1	1
CD38	cd38	–	–	0
CD79b	cd79b	–	–	0
CD123	cd123	–	–	0
BCMA	bcma	–	–	0
GPRC5D	gprc5d	–	–	0
HLA-A*02:01	hla-a02:01, hla-a2, hla-a02, hla	HLA-A*02:01 ×1	overexpression ×1	1
AFP	afp, alpha fetoprotein, alpha-fetoprotein	AFP ×1	overexpression ×1	1
EpCAM	epcam	EpCAM ×1	overexpression ×1	1
PSMA	psma	PSMA ×1	overexpression ×1	1
MRD	mrd, minimal residual disease, measurable residual disease	–	–	0
EBV	ebv, epstein-barr virus, epstein barr virus, eber	EBV ×1	overexpression ×1	1
Somatostatin receptor `SSTR`	sstr, somatostatin receptor	SSTR ×1	overexpression ×1	1
CD117	–	–	–	0
17p/TP53 not in the list	–	17p/TP53 ×1	wild-type-required ×1	1
EGFR/ALK not in the list	–	EGFR/ALK ×9	wild-type-required ×9	9
EGFR/ALK/ROS1 not in the list	–	EGFR/ALK/ROS1 ×1	wild-type-required ×1	1
EGFR/ALK/ROS1/RET not in the list	–	EGFR/ALK/ROS1/RET ×1	wild-type-required ×1	1
ER/PR/HER2 not in the list	–	ER/PR/HER2 ×1	wild-type-required ×1	1