3 Results

3.1 Dataset properties

TCGA projects are described here and here.

Figure 3.1: Available metadata for samples from selected projects.

Figure 3.2: Available metadata for samples from selected projects.

shortLetterCode

definition

Primary solid Tumor
Recurrent Solid Tumor
Metastatic
Solid Tissue Normal

sample_type_id

sample_type

Primary Tumor
Recurrent Tumor
Metastatic
Solid Tissue Normal

synchronous_malignancy

No
Not Reported
Yes

tumor_stage

not reported
stage ib
stage i
stage iia
stage iii
stage iib
stage iiia
stage iva
stage iiic
stage iiib
stage ia
stage iv
stage ii
stage x
stage ivb

tissue_or_organ_of_origin

Overlapping lesion of connective, subcutaneous and other soft tissues
Connective, subcutaneous and other soft tissues of pelvis
Connective, subcutaneous and other soft tissues of abdomen
Connective, subcutaneous and other soft tissues of lower limb and hip
Connective, subcutaneous and other soft tissues of thorax
Connective, subcutaneous and other soft tissues of trunk, NOS
Retroperitoneum
Uterus, NOS
Connective, subcutaneous and other soft tissues, NOS
Descending colon
Short bones of lower limb and associated joints
Myometrium
Connective, subcutaneous and other soft tissues of head, face, and neck
Connective, subcutaneous and other soft tissues of upper limb and shoulder
Ovary
Kidney, NOS
Spinal meninges
Long bones of lower limb and associated joints
Stomach, NOS
Spermatic cord
Isthmus uteri
Specified parts of peritoneum
Peripheral nerves and autonomic nervous system of upper limb and shoulder
Tongue, NOS
Corpus uteri
Lower third of esophagus
Middle third of esophagus
Esophagus, NOS
Cardia, NOS
Upper third of esophagus
Thoracic esophagus
Head of pancreas
Pancreas, NOS
Body of pancreas
Tail of pancreas
Overlapping lesion of pancreas
Pleura, NOS
Breast, NOS
Overlapping lesion of breast
Lower-inner quadrant of breast
Upper-outer quadrant of breast
Lower-outer quadrant of breast
Upper-inner quadrant of breast
Liver
Bladder, NOS
Lateral wall of bladder
Posterior wall of bladder
Trigone of bladder
Dome of bladder
Anterior wall of bladder
Bladder neck
Ureteric orifice
Fundus of stomach
Body of stomach
Gastric antrum
Lesser curvature of stomach, NOS
Pylorus
Middle lobe, lung
Lower lobe, lung
Upper lobe, lung
Lung, NOS
Main bronchus
Overlapping lesion of lung

primary_diagnosis

Leiomyosarcoma, NOS
Undifferentiated sarcoma
Fibromyxosarcoma
Dedifferentiated liposarcoma
Malignant peripheral nerve sheath tumor
Malignant fibrous histiocytoma
Synovial sarcoma, spindle cell
Abdominal fibromatosis
Synovial sarcoma, NOS
Synovial sarcoma, biphasic
Pleomorphic liposarcoma
Myxoid leiomyosarcoma
Aggressive fibromatosis
Giant cell sarcoma
Liposarcoma, well differentiated
Serous cystadenocarcinoma, NOS
Papillary serous cystadenocarcinoma
Squamous cell carcinoma, NOS
Adenocarcinoma, NOS
Squamous cell carcinoma, keratinizing, NOS
Mucinous adenocarcinoma
Tubular adenocarcinoma
Basaloid squamous cell carcinoma
Infiltrating duct carcinoma, NOS
Neuroendocrine carcinoma, NOS
Adenocarcinoma with mixed subtypes
Carcinoma, undifferentiated, NOS
Fibrous mesothelioma, malignant
Mesothelioma, malignant
Epithelioid mesothelioma, malignant
Mesothelioma, biphasic, malignant
Lobular carcinoma, NOS
Infiltrating duct and lobular carcinoma
Metaplastic carcinoma, NOS
Infiltrating duct mixed with other types of carcinoma
Papillary carcinoma, NOS
Infiltrating lobular mixed with other types of carcinoma
Intraductal papillary adenocarcinoma with invasion
Paget disease and infiltrating duct carcinoma of breast
Adenoid cystic carcinoma
Medullary carcinoma, NOS
Phyllodes tumor, malignant
Basal cell carcinoma, NOS
Large cell neuroendocrine carcinoma
Intraductal micropapillary carcinoma
Carcinoma, NOS
Pleomorphic carcinoma
Apocrine adenocarcinoma
Secretory carcinoma of breast
Cribriform carcinoma, NOS
Hepatocellular carcinoma, NOS
Combined hepatocellular carcinoma and cholangiocarcinoma
Hepatocellular carcinoma, clear cell type
Hepatocellular carcinoma, fibrolamellar
Hepatocellular carcinoma, spindle cell variant
Clear cell adenocarcinoma, NOS
Transitional cell carcinoma
Papillary transitional cell carcinoma
Papillary adenocarcinoma, NOS
Carcinoma, diffuse type
Adenocarcinoma, intestinal type
Signet ring cell carcinoma
Squamous cell carcinoma, large cell, nonkeratinizing, NOS
Papillary squamous cell carcinoma
Squamous cell carcinoma, small cell, nonkeratinizing
Bronchio-alveolar carcinoma, mucinous
Bronchiolo-alveolar carcinoma, non-mucinous
Acinar cell carcinoma
Solid carcinoma, NOS
Micropapillary carcinoma, NOS
Bronchiolo-alveolar adenocarcinoma, NOS

prior_malignancy

no
yes
not reported

year_of_diagnosis

2012
2013
2007
2011
2008
1998
2006
2003
2004
1997
2009
NA
2005
2002
2010
1995
1994
2000
1996
2001
1999
1992
1993
1988
1989
1990
1991

prior_treatment

No
Yes
Not Reported

morphology

8890/3
8805/3
8811/3
8858/3
9540/3
8830/3
9041/3
8822/1
9040/3
9043/3
8854/3
8896/3
8821/1
8802/3
8851/3
8441/3
8460/3
8070/3
8140/3
8071/3
8480/3
8211/3
8083/3
8500/3
8246/3
8255/3
8020/3
9051/3
9050/3
9052/3
9053/3
8520/3
8522/3
8575/3
8523/3
8050/3
8524/3
8503/3
8541/3
8200/3
8510/3
9020/3
8090/3
8013/3
8507/3
8010/3
8022/3
8401/3
8502/3
8201/3
8170/3
8180/3
8174/3
8171/3
8173/3
8310/3
8120/3
8130/3
8260/3
8145/3
8144/3
8490/3
8072/3
8052/3
8073/3
8253/3
8252/3
8550/3
8230/3
8265/3
8250/3

icd_10_code

C49.8
C49.5
C49.4
C49.2
C49.3
C49.6
C48.0
C55
C49.9
C18.6
C40.3
C54.2
C49.0
C49.10
C56.9
C49.1
C64.9
C70.1
C40.2
C16.9
C63.1
C54.0
C48.1
C71.0
C47.1
C02.9
C54.9
C48.2
C15.5
C15.4
C15.9
C16.0
C15.3
C25.0
C25.9
C25.1
C25.2
C25.8
C38.4
C45.0
C34.90
C50.9
C50.8
C50.3
C50.4
C50.5
C50.2
C50.919
C22.0
C67.9
C67.2
C67.4
C67.0
C67.1
C67.3
C67.5
C67.6
C16.1
C16.2
C16.3
C16.5
C34.2
C34.3
C34.1
C34.9
C34.8
C34.10
C34.0
C34.30

site_of_resection_or_biopsy

Overlapping lesion of connective, subcutaneous and other soft tissues
Connective, subcutaneous and other soft tissues of pelvis
Connective, subcutaneous and other soft tissues of abdomen
Connective, subcutaneous and other soft tissues of lower limb and hip
Connective, subcutaneous and other soft tissues of thorax
Connective, subcutaneous and other soft tissues of trunk, NOS
Retroperitoneum
Uterus, NOS
Connective, subcutaneous and other soft tissues, NOS
Descending colon
Short bones of lower limb and associated joints
Myometrium
Connective, subcutaneous and other soft tissues of head, face, and neck
Connective, subcutaneous and other soft tissues of upper limb and shoulder
Ovary
Kidney, NOS
Spinal meninges
Long bones of lower limb and associated joints
Stomach, NOS
Spermatic cord
Isthmus uteri
Specified parts of peritoneum
Peripheral nerves and autonomic nervous system of upper limb and shoulder
Tongue, NOS
Corpus uteri
Lower third of esophagus
Middle third of esophagus
Esophagus, NOS
Cardia, NOS
Upper third of esophagus
Thoracic esophagus
Head of pancreas
Pancreas, NOS
Body of pancreas
Tail of pancreas
Overlapping lesion of pancreas
Pleura, NOS
Lung, NOS
Breast, NOS
Overlapping lesion of breast
Lower-inner quadrant of breast
Upper-outer quadrant of breast
Lower-outer quadrant of breast
Upper-inner quadrant of breast
Liver
Bladder, NOS
Lateral wall of bladder
Posterior wall of bladder
Trigone of bladder
Dome of bladder
Anterior wall of bladder
Bladder neck
Ureteric orifice
Fundus of stomach
Body of stomach
Gastric antrum
Lesser curvature of stomach, NOS
Pylorus
Middle lobe, lung
Lower lobe, lung
Upper lobe, lung
Main bronchus
Overlapping lesion of lung

alcohol_history

Not Reported
Yes
No

ethnicity

not hispanic or latino
not reported
hispanic or latino

vital_status

Alive
Dead
Not Reported

race

black or african american
white
not reported
asian
american indian or alaska native
native hawaiian or other pacific islander

age_at_index

project_id

TCGA-SARC
TCGA-OV
TCGA-ESCA
TCGA-PAAD
TCGA-MESO
TCGA-BRCA
TCGA-LIHC
TCGA-BLCA
TCGA-STAD
TCGA-LUSC
TCGA-LUAD

name

Sarcoma
Ovarian Serous Cystadenocarcinoma
Esophageal Carcinoma
Pancreatic Adenocarcinoma
Mesothelioma
Breast Invasive Carcinoma
Liver Hepatocellular Carcinoma
Bladder Urothelial Carcinoma
Stomach Adenocarcinoma
Lung Squamous Cell Carcinoma
Lung Adenocarcinoma

ajcc_pathologic_t

ajcc_pathologic_n

NA
N0
N1
N3
N2
NX
N1b
N3a
N1mi
N1a
N0 (i-)
N2a
N0 (i+)
N0 (mol+)
N1c
N3b
N3c

ajcc_pathologic_m

NA
M0
M1a
MX
M1
cM0 (i+)
M1b

VNN1_tertiles_by_state

OMA1_tertiles_by_state

OPA1_tertiles_by_state

VNN1_tertiles_by_primary_diagnosis

OMA1_tertiles_by_primary_diagnosis

OPA1_tertiles_by_primary_diagnosis

VNN1_tertiles_by_project_id

OMA1_tertiles_by_project_id

OPA1_tertiles_by_project_id