Q (sonnet-5.5): What kind of cancer are there in the database?

▶ read_guide
{
 "uri": "cbioportal://faq-guide"
}

◀ result
# cBioPortal FAQ Guide

Curated answers to frequently asked general questions about cBioPortal. Source: [cBioPortal FAQ](https://docs.cbioportal.org/user-guide/faq/).

## What is cBioPortal?

cBioPortal for Cancer Genomics is an open-access, open-source resource for interactive exploration of multidimensional cancer genomics data sets. It was originally developed at Memorial Sloan Kettering Cancer Center (MSK) and is now maintained by a multi-institutional team.

## History

- **2008**: cBioPortal first became available online.
- **2012**: First major publication — Cerami et al., *Cancer Discovery*.
- **2013**: Second major publication — Gao et al., *Science Signaling*.
- **2023**: Third major publication — de Bruijn et al., *Cancer Research*.

## How to Cite cBioPortal

When using cBioPortal in publications, cite these three papers:

1. Cerami et al. "The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data." *Cancer Discovery* 2, 401–404 (2012). doi:10.1158/2159-8290.CD-12-0095
2. Gao et al. "Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal." *Science Signaling* 6, pl1 (2013). doi:10.1126/scisignal.2004088
3. de Bruijn et al. "Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal." *Cancer Research* 83, 3861–3867 (2023). doi:10.1158/0008-5472.CAN-23-0816

Also cite the specific study publication(s) whose data you used.

## What Data Types Does cBioPortal Contain?

- **Mutations** (non-synonymous somatic mutations)
- **DNA copy-number alterations** (CNA) from GISTIC or other methods
- **mRNA expression** data (RNA-seq, microarray)
- **Protein/phosphoprotein** levels (RPPA, mass spectrometry)
- **DNA methylation** data
- **Structural variants** (gene fusions, rearrangements)
- **Clinical data** (demographics, diagnosis, treatment, outcomes)

Note: Synonymous mutations are not included in cBioPortal.

## What Cancer Types Are in the Database?

Answer from the studies actually loaded, not from the OncoTree ontology (OncoTree lists hundreds of codes, most with no study here). One query:

```sql
SELECT tc.type_of_cancer_id, tc.name, tc.tissue, count() AS studies
FROM cancer_study cs
JOIN type_of_cancer tc ON cs.type_of_cancer_id = tc.type_of_cancer_id
GROUP BY tc.type_of_cancer_id, tc.name, tc.tissue
ORDER BY studies DESC;
```

Report how many distinct cancer types there are across how many studies, grouped by `tissue`. `mixed` ("Mixed Cancer Types") marks multi-cancer studies such as MSK-IMPACT and MSK-CHORD; their per-sample cancer types are in `clinical_data_derived` (`CANCER_TYPE`).

## Data Types Usually Not Stored Directly

cBioPortal generally does not store:

- raw CT, MRI, pathology-slide, or histology image files
- raw sequencing files such as BAM, CRAM, or FASTQ
- polygenic risk scores as a standard data type
- full external clinical-trial databases

However, this deployment … (7371 more chars)

▶ clickhouse_run_select_query
{
 "query": "SELECT tc.type_of_cancer_id, tc.name, tc.tissue, count() AS studies
FROM cancer_study cs
JOIN type_of_cancer tc ON cs.type_of_cancer_id = tc.type_of_cancer_id
GROUP BY tc.type_of_cancer_id, tc.name, tc.tissue
ORDER BY studies DESC",
 "max_rows": 1000
}

◀ result
{"rows":[{"tc.type_of_cancer_id":"mixed","tc.name":"Mixed Cancer Types","tissue":"Other","studies":48},{"tc.type_of_cancer_id":"brca","tc.name":"Invasive Breast Carcinoma","tissue":"Breast","studies":27},{"tc.type_of_cancer_id":"prad","tc.name":"Prostate Adenocarcinoma","tissue":"Prostate","studies":25},{"tc.type_of_cancer_id":"difg","tc.name":"Diffuse Glioma","tissue":"CNS/Brain","studies":20},{"tc.type_of_cancer_id":"blca","tc.name":"Bladder Urothelial Carcinoma","tissue":"Bladder/Urinary Tract","studies":18},{"tc.type_of_cancer_id":"luad","tc.name":"Lung Adenocarcinoma","tissue":"Lung","studies":17},{"tc.type_of_cancer_id":"coadread","tc.name":"Colorectal Adenocarcinoma","tissue":"Bowel","studies":16},{"tc.type_of_cancer_id":"soft_tissue","tc.name":"Soft Tissue","tissue":"Soft Tissue","studies":13},{"tc.type_of_cancer_id":"hcc","tc.name":"Hepatocellular Carcinoma","tissue":"Liver","studies":12},{"tc.type_of_cancer_id":"ucec","tc.name":"Endometrial Carcinoma","tissue":"Uterus","studies":12},{"tc.type_of_cancer_id":"skcm","tc.name":"Cutaneous Melanoma","tissue":"Skin","studies":12},{"tc.type_of_cancer_id":"ccrcc","tc.name":"Renal Clear Cell Carcinoma","tissue":"Kidney","studies":10},{"tc.type_of_cancer_id":"paad","tc.name":"Pancreatic Adenocarcinoma","tissue":"Pancreas","studies":10},{"tc.type_of_cancer_id":"aml","tc.name":"Acute Myeloid Leukemia","tissue":"Myeloid","studies":9},{"tc.type_of_cancer_id":"nsclc","tc.name":"Non-Small Cell Lung Cancer","tissue":"Lung","studies":9},{"tc.type_of_cancer_id":"breast","tc.name":"Breast","tissue":"Breast","studies":8},{"tc.type_of_cancer_id":"hnsc","tc.name":"Head and Neck Squamous Cell Carcinoma","tissue":"Head and Neck","studies":8},{"tc.type_of_cancer_id":"stad","tc.name":"Stomach Adenocarcinoma","tissue":"Esophagus/Stomach","studies":8},{"tc.type_of_cancer_id":"chol","tc.name":"Cholangiocarcinoma","tissue":"Biliary Tract","studies":8},{"tc.type_of_cancer_id":"mel","tc.name":"Melanoma","tissue":"Skin","studies":7},{"tc.type_of_cancer_id":"acyc","tc.name":"Adenoid Cystic Carcinoma","tissue":"Head and Neck","studies":7},{"tc.type_of_cancer_id":"lusc","tc.name":"Lung Squamous Cell Carcinoma","tissue":"Lung","studies":6},{"tc.type_of_cancer_id":"egc","tc.name":"Esophagogastric Adenocarcinoma","tissue":"Esophagus/Stomach","studies":6},{"tc.type_of_cancer_id":"cllsll","tc.name":"Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma","tissue":"Lymphoid","studies":6},{"tc.type_of_cancer_id":"prostate","tc.name":"Prostate","tissue":"Prostate","studies":6},{"tc.type_of_cancer_id":"nbl","tc.name":"Neuroblastoma","tissue":"Peripheral Nervous System","studies":6},{"tc.type_of_cancer_id":"dlbclnos","tc.name":"Diffuse Large B-Cell Lymphoma, NOS","tissue":"Lymphoid","studies":6},{"tc.type_of_cancer_id":"utuc","tc.name":"Upper Tract Urothelial Carcinoma","tissue":"Bladder/Urinary Tract","studies":5},{"tc.type_of_cancer_id":"mbl","tc.name":"Medulloblastoma","tissue":"CNS/Brain","studies":5},{"tc.type_of_cancer_id":"co … (9117 more chars)

═ answer (success)
The database has **119 cancer type categories**. One of them is "Mixed Cancer Types", which holds 48 multi-cancer studies such as MSK-IMPACT and MSK-CHORD. The counts below are the number of studies loaded for each type.

**Breast:** invasive breast carcinoma (27 studies), plus generic breast (8), metaplastic breast cancer, adenoid cystic breast cancer and breast fibroepithelial neoplasms (1 each)

**Lung and thoracic**
- Lung adenocarcinoma (17)
- Non-small cell lung cancer (9)
- Lung squamous cell carcinoma (6)
- Small cell lung cancer (4)
- Generic lung (5)
- Pleural mesothelioma (5)
- Thymoma (3)
- Thymic epithelial tumor (1)

**Prostate, bladder and kidney**
- Prostate adenocarcinoma (25) and generic prostate (6)
- Bladder urothelial carcinoma (18)
- Upper tract urothelial carcinoma (5)
- Generic bladder (4)
- Renal clear cell carcinoma (10)
- Chromophobe renal cell carcinoma (4)
- Papillary renal cell carcinoma (3)
- Rhabdoid cancer (2)
- Wilms' tumor (2)
- Renal cell carcinoma, non-clear cell and unclassified renal cell carcinoma

**CNS and brain**
- Diffuse glioma (20)
- Medulloblastoma (5)
- Miscellaneous neuroepithelial tumor (2)
- Pituitary adenoma (2)
- Generic CNS/brain (2)
- Adult-type diffuse glioma, pilocytic astrocytoma and meningioma (1 each)

**Peripheral nervous system:** neuroblastoma (6), plus schwannoma, neurofibroma, nerve sheath tumor and malignant peripheral nerve sheath tumor (1 each)

**GI, liver, biliary and pancreas**
- Colorectal adenocarcinoma (16)
- Colon adenocarcinoma (5)
- Rectal adenocarcinoma (3)
- Generic bowel (4)
- Appendiceal adenocarcinoma (1)
- Stomach adenocarcinoma (8)
- Esophagogastric adenocarcinoma (6)
- Esophageal adenocarcinoma (4)
- Esophageal squamous cell carcinoma (2)
- Generic esophagus/stomach (2)
- Hepatocellular carcinoma (12)
- Hepatocellular adenoma (1)
- Combined hepatocellular carcinoma and intrahepatic cholangiocarcinoma (1)
- Cholangiocarcinoma (8)
- Intrahepatic cholangiocarcinoma (5)
- Gallbladder cancer (3)
- Generic biliary tract (2)
- Ampullary carcinoma (1)
- Pancreatic adenocarcinoma (10)
- Pancreatic neuroendocrine tumor (4)
- Generic pancreas (4)
- Acinar cell carcinoma of the pancreas (2)
- Cystic tumor of the pancreas (1)

**Gynecologic**
- Endometrial carcinoma (12)
- Uterine carcinosarcoma (4)
- Uterine clear cell carcinoma, uterine endometrioid carcinoma and uterine sarcoma (1 each)
- High-grade serous ovarian cancer (5)
- Generic ovary/fallopian tube (4)
- Low-grade serous ovarian cancer and small cell carcinoma of the ovary (1 each)
- Cervical squamous cell carcinoma (3)
- Generic cervix (1)
- Vulvar/vaginal squamous cell carcinoma (1)

**Skin and eye**
- Cutaneous melanoma (12)
- Melanoma (7)
- Cutaneous squamous cell carcinoma (4)
- Generic skin (3)
- Basal cell carcinoma (1)
- Desmoplastic melanoma (1)
- Uveal melanoma (4)
- Retinoblastoma (2)

**Head and neck:** head and neck squamous cell carcinoma (8), adenoid cystic carcinoma (7), plus generic head and neck, other head and neck carcinoma and nasopharyngeal carcinoma (1 each)

**Sarcoma, soft tissue and bone**
- Soft tissue (13)
- Rhabdomyosarcoma (5)
- Gastrointestinal stromal tumor (3)
- Angiosarcoma (3)
- Liposarcoma (2)
- Soft tissue myoepithelial carcinoma (1)
- Ewing sarcoma (3)
- Osteosarcoma (1)

**Heme (myeloid and lymphoid)**
- Acute myeloid leukemia (9)
- Myelodysplastic syndromes (3)
- Histiocytic and dendritic cell neoplasms (2)
- Myeloproliferative neoplasms, myeloid neoplasm, generic myeloid, and acute leukemias of ambiguous lineage (1 each)
- Chronic lymphocytic leukemia/small lymphocytic lymphoma (6)
- Diffuse large B-cell lymphoma, NOS (6)
- B-lymphoblastic leukemia/lymphoma (4)
- Non-Hodgkin lymphoma (3)
- Mature B-cell neoplasms (3)
- Primary CNS DLBCL (2)
- Plasma cell myeloma (2)
- Classical Hodgkin lymphoma, mantle cell lymphoma, mature T and NK neoplasms, and generic lymphoid (1 each)

**Other**
- Thyroid: papillary thyroid cancer (4) and generic thyroid (2)
- Testis: generic testis (3) and non-seminomatous germ cell tumor (2)
- Adrenal: adrenocortical carcinoma (3)

Some entries are broad organ-level categories (for example "Lung", "Bowel" and "Breast"). These sit alongside more specific subtypes, so the same disease can appear under more than one label. For the multi-cancer studies, each sample's own cancer type is recorded separately. I can break those down if you want.

You can browse all studies at [cBioPortal](https://www.cbioportal.org). I can also pull the studies or sample counts for any cancer type above.