What is PAM50 for breast cancer?

PAM50 is a list of 50 genes that classify breast cancers into one of five intrinsic subtypes from formalin-fixed, paraffin-embedded tissues by real time polymerase chain reaction (RT-PCR).

Initially developed on microarray data, PAM50 is being successfully used in digital multiplexed gene expression platforms such as NanoString nCounter®, which is the basis for the Prosigna® test. The latter includes the PAM50 assay in combination with a clinical factor (i.e. tumor size) and has been approved for the risk of distant relapse estimation in postmenopausal women with hormone receptor-positive, node negative or node positive early stage breast cancer patients; and is a daily-used tool assessing the indication of adjuvant chemotherapy.

Here is the full list of PAM50.

Input	Match type	Approved symbol	Approved name	HGNC ID	Location
ACTR3B	Approved symbol	ACTR3B	actin related protein 3B	HGNC:17256	7q36.1-q36.2
ANLN	Approved symbol	ANLN	anillin actin binding protein	HGNC:14082	7p14.2
BAG1	Approved symbol	BAG1	BAG cochaperone 1	HGNC:937	9p13.3
BCL2	Approved symbol	BCL2	BCL2 apoptosis regulator	HGNC:990	18q21.33
BIRC5	Approved symbol	BIRC5	baculoviral IAP repeat containing 5	HGNC:593	17q25.3
BLVRA	Approved symbol	BLVRA	biliverdin reductase A	HGNC:1062	7p13
CCNB1	Approved symbol	CCNB1	cyclin B1	HGNC:1579	5q13.2
CCNE1	Approved symbol	CCNE1	cyclin E1	HGNC:1589	19q12
CDC20	Approved symbol	CDC20	cell division cycle 20	HGNC:1723	1p34.2
CDC6	Approved symbol	CDC6	cell division cycle 6	HGNC:1744	17q21.2
CDH3	Approved symbol	CDH3	cadherin 3	HGNC:1762	16q22.1
CENPF	Approved symbol	CENPF	centromere protein F	HGNC:1857	1q41
CEP55	Approved symbol	CEP55	centrosomal protein 55	HGNC:1161	10q23.33
CXXC5	Approved symbol	CXXC5	CXXC finger protein 5	HGNC:26943	5q31.2
EGFR	Approved symbol	EGFR	epidermal growth factor receptor	HGNC:3236	7p11.2
ERBB2	Approved symbol	ERBB2	erb-b2 receptor tyrosine kinase 2	HGNC:3430	17q12
ESR1	Approved symbol	ESR1	estrogen receptor 1	HGNC:3467	6q25.1-q25.2
EXO1	Approved symbol	EXO1	exonuclease 1	HGNC:3511	1q43
FGFR4	Approved symbol	FGFR4	fibroblast growth factor receptor 4	HGNC:3691	5q35.2
FOXA1	Approved symbol	FOXA1	forkhead box A1	HGNC:5021	14q21.1
FOXC1	Approved symbol	FOXC1	forkhead box C1	HGNC:3800	6p25.3
GPR160	Approved symbol	GPR160	G protein-coupled receptor 160	HGNC:23693	3q26.2
GRB7	Approved symbol	GRB7	growth factor receptor bound protein 7	HGNC:4567	17q12
KIF2C	Approved symbol	KIF2C	kinesin family member 2C	HGNC:6393	1p34.1
KRT14	Approved symbol	KRT14	keratin 14	HGNC:6416	17q21.2
KRT17	Approved symbol	KRT17	keratin 17	HGNC:6427	17q21.2
KRT5	Approved symbol	KRT5	keratin 5	HGNC:6442	12q13.13
MAPT	Approved symbol	MAPT	microtubule associated protein tau	HGNC:6893	17q21.31
MDM2	Approved symbol	MDM2	MDM2 proto-oncogene	HGNC:6973	12q15
MELK	Approved symbol	MELK	maternal embryonic leucine zipper kinase	HGNC:16870	9p13.2
MIA	Approved symbol	MIA	MIA SH3 domain containing	HGNC:7076	19q13.2
MKI67	Approved symbol	MKI67	marker of proliferation Ki-67	HGNC:7107	10q26.2
MLPH	Approved symbol	MLPH	melanophilin	HGNC:29643	2q37.3
MMP11	Approved symbol	MMP11	matrix metallopeptidase 11	HGNC:7157	22q11.23
MYBL2	Approved symbol	MYBL2	MYB proto-oncogene like 2	HGNC:7548	20q13.12
MYC	Approved symbol	MYC	MYC proto-oncogene, bHLH transcription factor	HGNC:7553	8q24.21
NAT1	Approved symbol	NAT1	N-acetyltransferase 1	HGNC:7645	8p22
NDC80	Approved symbol	NDC80	NDC80 kinetochore complex component	HGNC:16909	18p11.32
NUF2	Approved symbol	NUF2	NUF2 component of NDC80 kinetochore complex	HGNC:14621	1q23.3
ORC6L	Previous symbol	ORC6	origin recognition complex subunit 6	HGNC:17151	16q11.2
PGR	Approved symbol	PGR	progesterone receptor	HGNC:8910	11q22.1
PHGDH	Approved symbol	PHGDH	phosphoglycerate dehydrogenase	HGNC:8923	1p12
PTTG1	Approved symbol	PTTG1	PTTG1 regulator of sister chromatid separation, securin	HGNC:9690	5q33.3
RRM2	Approved symbol	RRM2	ribonucleotide reductase regulatory subunit M2	HGNC:10452	2p25.1
SFRP1	Approved symbol	SFRP1	secreted frizzled related protein 1	HGNC:10776	8p11.21
SLC39A6	Approved symbol	SLC39A6	solute carrier family 39 member 6	HGNC:18607	18q12.2
TMEM45B	Approved symbol	TMEM45B	transmembrane protein 45B	HGNC:25194	11q24.3
TYMS	Approved symbol	TYMS	thymidylate synthetase	HGNC:12441	18p11.32
UBE2C	Approved symbol	UBE2C	ubiquitin conjugating enzyme E2 C	HGNC:15937	20q13.12
UBE2T	Approved symbol	UBE2T	ubiquitin conjugating enzyme E2 T	HGNC:25009	1q32.1

One response to “What is PAM50 for breast cancer?”

Machine Learning Project 3 – Comparison of Five Machine Learning Methods in Subtyping Breast Cancer Tumors Based on Gene Expression of Biomarkers (R version) – NoteForDataScience

March 26, 2022 at 7:50 pm

[…] can find that I retrieved the gene expression profiles for PAM50 genes (What is PAM50 for breast cancer?) rather than the three biomakers because PAM50 genes are more informative and accurate to classify […]

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