Cancer Molecular Profile

Tumor molecular profiles for various cancer types

About

This cancer-molecular-profile repository lists tumor molecular profiles for various cancer types, including rare fractions.

We create the list of gene variants and biomarkers by referring to public databases as follows:

• COSMIC
• GDC Data Portal (TCGA)
• My Cancer Genome

To make the list more objective, we also referred to literature, especially comprehensive papers summarizing NGS analysis, searched by PubMed for each cancer type. We reflected these in the list of gene variants and biomarkers.

We define the following two sections as molecular profiles for each tumor type:

• Representative Gene Variants or Biomarkers: Frequently present in the specified tumor type and significant for the specific molecular subtype of it
• Other Gene Variants or Biomarkers: Present in some of the specified tumor types and characterize the molecular subtype

Profiles

Total: 114 cases

Tissue	Subtype	Representative Gene Variants or Biomarkers	Other Gene Variants or Biomarkers
Adrenal Gland	Pheochromocytoma	SDHB loss	TP53 truncation, ATRX truncation, HRAS p.Q61X
Adrenal Gland	Pheochromocytoma	RET p.C634R p.M918T	TP53 truncation, ATRX truncation
Biliary Tract	Cholangiocarcinoma	KRAS p.G12X, TP53 truncation	BAP1 truncation, CDKN2A loss, CDKN2B loss, MTAP loss, ARID1A truncation
Biliary Tract	Cholangiocarcinoma	ERBB2 amplification, TP53 truncation	BAP1 truncation, CDKN2A loss, CDKN2B loss, MTAP loss, ARID1A truncation
Biliary Tract	Cholangiocarcinoma	FGFR2-BICC1 fusion, TP53 truncation	BAP1 truncation, CDKN2A loss, CDKN2B loss, MTAP loss, ARID1A truncation
Biliary Tract	Cholangiocarcinoma	IDH1 p.R132C, TP53 truncation	CDKN2A loss, CDKN2B loss, MTAP loss, ARID1A truncation, BAP1 loss
Biliary Tract	Cholangiocarcinoma	IDH2 p.R172G/K/M/S/W, TP53 truncation	BAP1 truncation loss, CDKN2A loss, CDKN2B loss, MTAP loss, ARID1A truncation
Biliary Tract	Gallbladder Cancer	KRAS p.G12X, TP53 truncation, CDKN2A loss, CDKN2B loss, SMAD4 loss truncation	ARID1A truncation, CCNE1 amplification, PIK3CA p.E542K p.E545K p.H1047R
Biliary Tract	Gallbladder Cancer	ERBB2 amplification p.S310F/Y, TP53 truncation, CDKN2A loss, CDKN2B loss, SMAD4 loss truncation	ARID1A truncation, CCNE1 amplification, PIK3CA p.E542K p.E545K p.H1047R
Biliary Tract	Gallbladder Cancer	ERBB2 amplification p.S310F/Y, MDM2 amplification, CDKN2A loss, CDKN2B loss, SMAD4 loss truncation	ARID1A truncation, CCNE1 amplification, PIK3CA p.E542K p.E545K p.H1047R
Bladder	Urothelial Carcinoma	CDKN2A loss, CDKN2B loss	TP53 truncation, TERT c.-124C>T, PIK3CA p.E545K p.H1047R, ARID1A truncation, RB1 truncation, BRAF p.V600E/K
Bladder	Urothelial Carcinoma	FGFR3-TACC3 fusion	TP53 truncation, TERT c.-124C>T, PIK3CA p.E545K p.H1047R, ARID1A truncation, RB1 truncation, BRAF p.V600E/K
Bladder	Urothelial Carcinoma	FGFR3 p.S249C p.R248C	TP53 truncation, TERT c.-124C>T, PIK3CA p.E545K p.H1047R, ARID1A truncation, RB1 truncation, BRAF p.V600E/K
Bone	Osteosarcoma	TP53 loss, RB1 loss	BRCA1 truncation, PTEN truncation, MYC amplification, CCNE1 amplification, CDKN2A loss, CDKN2B loss
Bowel	Colorectal Adenocarcinoma	MLH1 truncation, TMB-High, MSI-High, APC truncation, SMAD4 truncation, TP53 truncation	BRAF p.V600E/K
Bowel	Colorectal Adenocarcinoma	APC truncation, KRAS p.G12X, SMAD4 truncation, TP53 truncation	EGFR amplification, ERBB2 amplification p.R678Q, PTEN truncation
Bowel	Colorectal Adenocarcinoma	PMS2 truncation, TMB-High, MSI-High, APC truncation, SMAD4 truncation, TP53 truncation	BRAF p.V600E/K
Bowel	Colorectal Adenocarcinoma	MSH2 truncation, TMB-High, MSI-High, APC truncation, SMAD4 truncation, TP53 truncation	BRAF p.V600E/K
Bowel	Colorectal Adenocarcinoma	APC truncation, NRAS p.Q61X, SMAD4 truncation, TP53 truncation	EGFR amplification, ERBB2 amplification p.R678Q, PTEN truncation
Bowel	Colorectal Adenocarcinoma	MSH6 truncation, TMB-High, MSI-High, APC truncation, SMAD4 truncation, TP53 truncation	BRAF p.V600E/K
Bowel	Colorectal Adenocarcinoma	EPCAM truncation, APC truncation, KRAS p.G12X, SMAD4 truncation, TP53 truncation	EGFR amplification, ERBB2 amplification p.R678Q
Bowel	Colorectal Adenocarcinoma	MUTYH truncation, APC truncation, KRAS p.G12X, SMAD4 truncation, TP53 truncation	EGFR amplification, ERBB2 amplification p.R678Q
Bowel	Colorectal Adenocarcinoma	APC truncation, BRAF p.V600E/K, SMAD4 truncation, TP53 truncation	EGFR amplification, ERBB2 amplification p.R678Q, PTEN truncation
Brain	Astrocytoma, IDH-mutant	IDH2 p.R172K/S, TP53 truncation	PTEN truncation, BRAF p.V600E, EGFR amplification
Brain	Astrocytoma, IDH-mutant	IDH1 p.R132C/G/H/L/S, TP53 truncation	PTEN truncation, BRAF p.V600E, EGFR amplification
Brain	Atypical Teratoid/Rhabdoid Tumor	SMARCB1 loss	TP53 truncation
Brain	Diffuse Midline Glioma, H3 K27-altered	H3-3A p.K28M, TP53 truncation	PIK3CA p.E542K p.E545K p.H1047R, ATRX truncation
Brain	Glioblastoma, IDH-wildtype	TP53 truncation, EGFR amplification, PTEN truncation	NF1 truncation, RB1 truncation
Brain	Glioblastoma, IDH-wildtype	TERT c.-124C>T, TP53 truncation	PTEN truncation, NF1 truncation, EGFR amplification, RB1 truncation
Brain	Glioblastoma, IDH-wildtype	TP53 truncation, EGFR amplification, PIK3CA p.E542K p.E545K p.H1047R	NF1 truncation, RB1 truncation
Brain	Glioblastoma, IDH-wildtype	TERT c.-124C>T, TP53 truncation	PIK3CA p.E542K p.E545K p.H1047R, BRAF p.V600E, EGFR amplification, RB1 truncation
Brain	Glioblastoma, IDH-wildtype	ATRX truncation, TP53 truncation	PTEN truncation, NF1 truncation, EGFR amplification, RB1 truncation
Brain	Medulloblastoma	CTNNB1 p.S33A/C/F/Y p.S37A/F/Y	TP53 truncation, DDX3X p.T275M p.G302V p.R326C p.R351W p.M380I, KMT2D truncation, CREBBP truncation
Brain	Medulloblastoma	PTCH1 truncation	TP53 truncation, DDX3X p.T275M p.G302V p.R326C p.R351W p.M380I, TERT c.-124C>T, KMT2D truncation, CREBBP truncation
Brain	Oligodendroglioma, IDH-mutant and 1p/19q-codeleted	IDH2 p.R172K/S, 1p loss, 19q loss	TP53 truncation, ARID1A truncation, PIK3CA p.E542K p.E545K p.H1047R, NOTCH1 truncation, CIC p.R1111W p.R1124W/Q truncation
Brain	Oligodendroglioma, IDH-mutant and 1p/19q-codeleted	IDH1 p.R132H/C/G, 1p loss, 19q loss	TP53 truncation, ARID1A truncation, PIK3CA p.E542K p.E545K p.H1047R, NOTCH1 truncation, CIC p.R1111W p.R1124W/Q truncation
Breast	Breast Invasive Ductal Carcinoma	TP53 truncation, BRCA2 truncation, HRD-High	ERBB2 amplification p.S310F, PTEN truncation, KMT2C truncation, RB1 loss
Breast	Breast Invasive Ductal Carcinoma	ESR1 p.Y537S p.D538G amplification, PIK3CA p.E545K p.H1047R	TP53 truncation, MAP3K1 truncation, ERBB2 amplification p.S310F, PTEN truncation, KMT2C truncation, CDKN2A loss, RB1 loss
Breast	Breast Invasive Ductal Carcinoma	TP53 truncation, CHEK2 truncation, HRD-High	ERBB2 amplification p.S310F, PTEN truncation, KMT2C truncation, RB1 loss
Breast	Breast Invasive Ductal Carcinoma	ERBB2 amplification p.S310F, TP53 truncation	FGFR1 amplification, MAP3K1 truncation, PTEN truncation, KMT2C truncation, CDKN2A loss, RB1 loss
Breast	Breast Invasive Ductal Carcinoma	TP53 truncation, BRCA1 truncation, HRD-High	ERBB2 amplification p.S310F, PTEN truncation, KMT2C truncation, RB1 loss
Breast	Breast Invasive Ductal Carcinoma	TP53 truncation, PALB2 truncation, HRD-High	ERBB2 amplification p.S310F, PTEN truncation, KMT2C truncation, RB1 loss
Breast	Breast Invasive Ductal Carcinoma	TP53 truncation, ATM truncation	ERBB2 amplification p.S310F, PTEN truncation, KMT2C truncation, RB1 loss
Breast	Breast Invasive Lobular Carcinoma	CDH1 truncation, PIK3CA p.E545K p.H1047R	TP53 truncation, RUNX1 truncation, TBX3 truncation, PTEN loss
Esophagus	Squamous Cell Carcinoma	TP53 truncation	NOTCH1 truncation, KMT2D truncation, PTEN truncation
Esophagus	Squamous Cell Carcinoma	TP53 truncation	CDKN2A truncation, KMT2D truncation, PTEN truncation
Esophagus	Squamous Cell Carcinoma	TP53 truncation	NFE2L2 p.R34G/L p.E79K/Q, KMT2D truncation, PTEN truncation
Kidney	Renal Cell Carcinoma	VHL truncation loss	TP53 truncation
Kidney	Wilms Tumor	WT1 loss	TP53 truncation, CTNNB1 p.T41A p.S45F
Lung	Lung Adenocarcinoma	KRAS p.G12X, STK11 truncation, TP53 truncation	KEAP1 loss-of-function missense mutation truncation, SETD2 truncation, ARID1A truncation
Lung	Lung Adenocarcinoma	EGFR p.L858R exon 19 deletion exon 20 insertion, STK11 truncation, TP53 truncation	KEAP1 loss-of-function missense mutation truncation, SETD2 truncation, ARID1A truncation
Lung	Lung Adenocarcinoma	EML4-ALK fusion, STK11 truncation, TP53 truncation	KEAP1 loss-of-function missense mutation truncation, SETD2 truncation, ARID1A truncation
Lung	Lung Adenocarcinoma	MET exon 14 skipping, STK11 truncation, TP53 truncation	KEAP1 loss-of-function missense mutation truncation, SETD2 truncation, ARID1A truncation
Lung	Lung Adenocarcinoma	GOPC-ROS1 fusion, STK11 truncation, TP53 truncation	KEAP1 loss-of-function missense mutation truncation, SETD2 truncation, ARID1A truncation
Lung	Lung Adenocarcinoma	KIF5B-RET fusion, STK11 truncation, TP53 truncation	KEAP1 loss-of-function missense mutation truncation, SETD2 truncation, ARID1A truncation
Lung	Small Cell Lung Cancer	RB1 truncation, TP53 truncation
Lung	Squamous Cell Carcinoma	NFE2L2 p.R34G p.R34L p.E79K p.E79Q, TP53 truncation	CDKN2A loss, PIK3CA p.E545K p.H1047R amplification, KEAP1 loss-of-function missense mutation truncation
Ovary	Clear Cell Ovarian Cancer	ARID1A truncation, PIK3CA p.E545K p.H1047R	TP53 truncation
Ovary	High-Grade Serous Ovarian Cancer	TP53 truncation, HRD-High	BRCA1 truncation
Ovary	High-Grade Serous Ovarian Cancer	TP53 truncation, HRD-High	BRCA2 truncation
Ovary	Low-Grade Serous Ovarian Cancer	BRAF p.V600E/K
Ovary	Low-Grade Serous Ovarian Cancer	KRAS p.G12X
Ovary	Low-Grade Serous Ovarian Cancer	NRAS p.Q61X
Pancreas	Intraductal Papillary Mucinous Neoplasm	KRAS p.G12X, TP53 truncation, GNAS p.R201C/H
Pancreas	Pancreatic Adenocarcinoma	KRAS p.G12X, TP53 truncation	CDKN2A loss, CDKN2B loss, MTAP loss
Pancreas	Pancreatic Adenocarcinoma	KRAS p.G12X, TP53 truncation, BRCA2 truncation	CDKN2A loss, CDKN2B loss, MTAP loss
Pancreas	Pancreatic Adenocarcinoma	KRAS p.G12X, TP53 truncation, ATM truncation	CDKN2A loss, CDKN2B loss, MTAP loss
Pancreas	Pancreatic Adenocarcinoma	KRAS p.G12X, TP53 truncation, BRCA1 truncation	CDKN2A loss, CDKN2B loss, MTAP loss
Peritoneum	Mesothelioma	BAP1 loss, TP53 truncation	NF2 truncation loss
Pleura	Mesothelioma	BAP1 loss, TP53 truncation	NF2 truncation loss
Prostate	Adenocarcinoma	ATM truncation	HRD-High, AR amplification, TP53 truncation, PIK3CA p.E545K p.H1047R, PTEN truncation, MYC amplification, SPOP p.F133C/L/V, RB1 loss
Prostate	Adenocarcinoma	AR amplification, TP53 truncation, PTEN truncation	PIK3CA p.E545K p.H1047R, MYC amplification, SPOP p.F133C/L/V, RB1 loss
Prostate	Adenocarcinoma	BRCA2 truncation	HRD-High, AR amplification, TP53 truncation, PIK3CA p.E545K p.H1047R, PTEN truncation, MYC amplification, SPOP p.F133C/L/V, RB1 loss
Prostate	Adenocarcinoma	BRCA1 truncation	HRD-High, AR amplification, TP53 truncation, PIK3CA p.E545K p.H1047R, PTEN truncation, MYC amplification, SPOP p.F133C/L/V, RB1 loss
Prostate	Adenocarcinoma	CDK12 truncation	HRD-High, AR amplification, TP53 truncation, PIK3CA p.E545K p.H1047R, PTEN truncation, MYC amplification, SPOP p.F133C/L/V, RB1 loss
Prostate	Adenocarcinoma	TMPRSS2-ERG fusion, TP53 truncation, PTEN truncation	AR amplification, PIK3CA p.E545K p.H1047R, MYC amplification, RB1 loss, SPOP p.F133C/L/V
Salivary Gland	Adenoid Cystic Carcinoma	MYB-NFIB fusion	TP53 truncation, NOTCH1 truncation
Salivary Gland	Mucoepidermoid Carcinoma	HRAS p.G12V, PIK3CA p.E542K p.E545K p.H1047R	TP53 truncation, CDKN2A loss, CDKN2B loss
Salivary Gland	Salivary Duct Carcinoma	NF1 truncation, TP53 truncation	CDKN2A loss
Salivary Gland	Salivary Duct Carcinoma	ERBB2 amplification, CDK12 amplification, TP53 truncation	CDKN2A loss
Salivary Gland	Salivary Duct Carcinoma	HRAS p.Q61X, TP53 truncation	PIK3CA p.E542K p.E545K p.H1047R, CDKN2A loss
Skin	Melanoma	NRAS p.Q61X	CDKN2A loss, CDKN2B loss, MTAP loss
Skin	Melanoma	BRAF p.V600E/K	CDKN2A loss, CDKN2B loss, MTAP loss
Skin	Melanoma	KIT p.L576P p.K642E	CDKN2A loss, CDKN2B loss, MTAP loss
Soft Tissue	Dedifferentiated Liposarcoma	MDM2 amplification, CDK4 amplification
Soft Tissue	Ewing Sarcoma	EWSR1-FLI1 fusion	TP53 truncation, CDKN2A loss, STAG2 truncation
Soft Tissue	Gastrointestinal Stromal Tumor	KIT p.W557_K558del p.V559G p.L576P
Soft Tissue	Leiomyosarcoma	TP53 loss, RB1 loss	ATRX truncation, PTEN loss truncation, MAP2K4 amplification
Soft Tissue	Paraganglioma	SDHB loss	TP53 truncation, ATRX truncation
Soft Tissue	Rhabdomyosarcoma	PAX3-FOXO1 fusion	MYCN amplification, CDK4 amplification, 11p15 loss
Soft Tissue	Rhabdomyosarcoma	PAX7-FOXO1 fusion	MYCN amplification, CDK4 amplification, 11p15 loss
Soft Tissue	Rhabdomyosarcoma	NRAS p.Q61X, 11p15 loss	TP53 loss
Soft Tissue	Rhabdomyosarcoma	FGFR4 p.V550E/L/M, 11p15 loss	TP53 loss
Soft Tissue	Synovial Sarcoma	SS18-SSX2 fusion	CTNNB1 p.S33A/Y/C p.S37A/F/Y p.T41A p.S45F, ATM truncation
Stomach	Diffuse Type Stomach Adenocarcinoma	CDH1 truncation, RHOA p.Y42C/S	CLDN18-ARHGAP26 fusion
Stomach	Intestinal Type Stomach Adenocarcinoma	PIK3CA p.E545K p.H1047R, ARID1A truncation, CD274 amplification, ERBB2 amplification	PTEN truncation
Stomach	Intestinal Type Stomach Adenocarcinoma	ERBB2 amplification, TP53 truncation	CCNE1 amplification, CCND1 amplification
Stomach	Intestinal Type Stomach Adenocarcinoma	KRAS amplification, TP53 truncation	CCNE1 amplification, CCND1 amplification
Stomach	Intestinal Type Stomach Adenocarcinoma	MLH1 truncation, TMB-High, MSI-High	ARID1A truncation, PIK3CA p.E545K p.H1047R, PTEN truncation, KRAS p.G12X, RNF43 truncation, TP53 truncation
Stomach	Intestinal Type Stomach Adenocarcinoma	PIK3CA amplification, TP53 truncation	CCNE1 amplification, CCND1 amplification
Stomach	Intestinal Type Stomach Adenocarcinoma	PIK3CA p.E545K p.H1047R, ARID1A truncation, CD274 amplification, EGFR amplification	PTEN truncation
Stomach	Intestinal Type Stomach Adenocarcinoma	EGFR amplification, TP53 truncation	CCNE1 amplification, CCND1 amplification
Thymus	Thymic carcinoma	TP53 truncation, CDKN2A loss, CDKN2B loss
Thyroid	Anaplastic Carcinoma	BRAF p.V600E, TP53 truncation	CDKN2A loss, CDKN2B loss, PTEN truncation
Thyroid	Follicular Carcinoma	NRAS p.Q61X	TP53 truncation
Thyroid	Follicular Carcinoma	PAX8-PPARG fusion	TP53 truncation
Thyroid	Papillary Carcinoma	CCDC6-RET fusion	TP53 truncation
Thyroid	Papillary Carcinoma	BRAF p.V600E	TP53 truncation
Uterus	Endometrial Stromal Sarcoma	YWHAE-NUTM2A fusion	16q loss, CDKN2A loss, TP53 loss, RB1 loss
Uterus	Endometrial Stromal Sarcoma	JAZF1-SUZ12 fusion	CDKN2A loss
Uterus	Endometrial Stromal Sarcoma	ZC3H7B-BCOR fusion	16q loss, CDKN2A loss, TP53 loss, RB1 loss
Uterus	Uterine Endometrioid Carcinoma	PTEN truncation, PIK3CA p.E542K p.E545K p.H1047R, ARID1A truncation, KRAS p.G12X	TP53 truncation
Uterus	Uterine Endometrioid Carcinoma	PTEN truncation, PIK3CA p.E542K p.E545K p.H1047R, ARID1A truncation, CTNNB1 p.S33A/C/F/Y p.S37A/F/Y p.T41A p.S45F	TP53 truncation
Uterus	Uterine Endometrioid Carcinoma	PTEN truncation, PIK3R1 truncation, ARID1A truncation	CTNNB1 p.S33A/C/F/Y p.S37A/F/Y p.T41A p.S45F, KRAS p.G12X, PPP2R1A p.P179L/R p.R183G/P/Q/W, TP53 truncation

Count of Profiles by Tissue Type

• Adrenal Gland: 2
• Biliary Tract: 8
• Bladder: 3
• Bone: 1
• Bowel: 9
• Brain: 13
• Breast: 8
• Esophagus: 3
• Kidney: 2
• Lung: 8
• Ovary: 6
• Pancreas: 5
• Peritoneum: 1
• Pleura: 1
• Prostate: 6
• Salivary Gland: 5
• Skin: 3
• Soft Tissue: 10
• Stomach: 8
• Thymus: 1
• Thyroid: 5
• Uterus: 6

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Copyright 2024 Xcoo, Inc.

Licensed under the GPLv3.