Q (sonnet-5.5): list the portal studies for pediatric cancers that were published in the last 5 years

▶ clickhouse_list_table_columns
{
 "table": "cancer_study"
}

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

◀ result
{"columns":[{"name":"cancer_study_id","type":"Int64","comment":"Internal numeric ID. Prefer cancer_study_identifier for queries as it is more readable and stable."},{"name":"cancer_study_identifier","type":"Nullable(String)","comment":"Stable string identifier for the study (e.g., \"msk_chord_2024\", \"brca_tcga\"). Use this for filtering, not cancer_study_id."},{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String","comment":"Full descriptive name of the study (e.g., \"MSK-CHORD (MSK, Nature 2024)\")."},{"name":"description","type":"String"},{"name":"public","type":"Int32"},{"name":"pmid","type":"Nullable(String)"},{"name":"citation","type":"Nullable(String)"},{"name":"groups","type":"Nullable(String)"},{"name":"status","type":"Nullable(Int64)"},{"name":"import_date","type":"Nullable(DateTime64(6))"},{"name":"reference_genome_id","type":"Nullable(Int64)"},{"name":"sample_count","type":"UInt32","comment":"Samples in the study (members of <study>_all), as shown in the portal study list. Precomputed daily at LLM-prep time."},{"name":"mutation_sample_count","type":"UInt32","comment":"Samples profiled for mutations (<study>_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (<study>_cna) — \"CNA\". 0 = no CNA data."},{"name":"structural_variant_sample_count","type":"UInt32","comment":"Distinct samples with at least one structural variant (fusions etc.). 0 = none."},{"name":"rna_seq_sample_count","type":"UInt32","comment":"Samples with RNA-Seq expression (<study>_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (<study>_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (<study>_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (<study>_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (<study>_protein_quantification) — \"Protein Mass-Spectrometry\"."},{"name":"treatment_patient_count","type":"UInt32","comment":"PATIENTS (not samples) with treatment clinical events — \"Treatment\". 0 = no treatment data."},{"name":"resource_sample_counts","type":"Map(String, UInt32)","comment":"Samples with each linked resource, keyed by display name: imaging and pathology such as 'Slide Microscopy', 'Computed Tomography', 'Magnetic Resonance', 'H&E Slide', 'MxIF Image'. Query with mapKeys(resource_sample_counts) or resource_sample_counts['Slide Microscopy'] > 0."},{"name":"mrna_expression_sample_count","type":"UInt32","comment":"Samples in any mRNA expression profile (RNA-Seq, microarray, TPM, z-scores; from sample_profile). Use this for \"does the study have expression data\" — rna_seq_sample_count and mrna_m … (136 more chars)

◀ 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 cancer_study_identifier, name, citation, pmid, sample_count, type_of_cancer_id, import_date FROM cancer_study WHERE (positionCaseInsensitive(name,'pediatric')>0 OR positionCaseInsensitive(description,'pediatric')>0 OR positionCaseInsensitive(description,'childhood')>0 OR positionCaseInsensitive(description,'children')>0 OR positionCaseInsensitive(name,'target')>0 OR positionCaseInsensitive(name,'ped')>0 OR positionCaseInsensitive(cancer_study_identifier,'ped')>0 OR positionCaseInsensitive(cancer_study_identifier,'pbta')>0 OR type_of_cancer_id IN ('nbl','wt','mrt','rt','es','os')) ORDER BY name",
 "max_rows": 200
}

◀ result
{"rows":[{"cancer_study_identifier":"alal_target_gdc","name":"Acute Leukemias of Ambiguous Lineage (TARGET GDC, 2025)","sample_count":251,"type_of_cancer_id":"alal","import_date":"2026-01-14 12:25:49"},{"cancer_study_identifier":"aml_target_gdc","name":"Acute Myeloid Leukemia (TARGET GDC, 2025)","sample_count":2766,"type_of_cancer_id":"aml","import_date":"2026-01-14 12:27:30"},{"cancer_study_identifier":"bll_target_gdc","name":"B-Lymphoblastic Leukemia/Lymphoma (TARGET GDC, 2025)","sample_count":989,"type_of_cancer_id":"bll","import_date":"2026-01-14 12:36:15"},{"cancer_study_identifier":"ccle_broad_2019","name":"Cancer Cell Line Encyclopedia (Broad, 2019)","citation":"Stransky et al. Nature. 2015, Nusinow et al. Cell. 2020","pmid":"31068700,31978347","sample_count":1739,"type_of_cancer_id":"mixed","import_date":"2026-01-05 21:05:38"},{"cancer_study_identifier":"ccle_broad_2025","name":"Cancer Cell Line Encyclopedia (Broad, Nat Rev Cancer 2025)","citation":"Arafeh, Rand et al. Nature Reviews 2025","pmid":"39468210","sample_count":1981,"type_of_cancer_id":"mixed","import_date":"2026-03-09 16:47:48"},{"cancer_study_identifier":"ccle_genentech_2014","name":"Cancer Cell Line Encyclopedia (Genentech, Nat biotech 2014)","citation":"Klijn, Christiaan et al. Nature biotechnology 2014","pmid":"25485619","sample_count":675,"type_of_cancer_id":"mixed","import_date":"2026-01-05 21:43:40"},{"cancer_study_identifier":"cellline_ccle_broad","name":"Cancer Cell Line Encyclopedia (Novartis/Broad, Nature 2012)","citation":"Barretina et al. Nature 2012","pmid":"22460905","sample_count":1020,"type_of_cancer_id":"mixed","import_date":"2026-01-05 20:30:46"},{"cancer_study_identifier":"msk_ch_ped_2021","name":"Cancer Therapy and Clonal Hematopoiesis (MSK, Clin Cancer Res 2022)","citation":"Barbara et al. Clin Cancer Res 2022","pmid":"35078859","sample_count":657,"type_of_cancer_id":"mixed","import_date":"2026-01-08 16:49:33"},{"cancer_study_identifier":"nfib_ctf_biobank_2025","name":"Cutaneous Neurofibroma Data Resource (CTF, Scientific Data 2021)","citation":"Gosline, S et al. Scientific Data 2021","pmid":"33585982","sample_count":38,"type_of_cancer_id":"nfib","import_date":"2026-03-05 19:34:46"},{"cancer_study_identifier":"es_iocurie_2014","name":"Ewing Sarcoma (Institut Curie, Cancer Discov 2014)","citation":"Tirode et al. Cancer Discov 2014","pmid":"25223734","sample_count":115,"type_of_cancer_id":"es","import_date":"2026-01-07 12:41:57"},{"cancer_study_identifier":"es_dsrct_msk_2023","name":"Ewing Sarcoma (MSK, Cancer Research 2024)","citation":"Josephine K et al. Cancer Research 2024","pmid":"38335254","sample_count":290,"type_of_cancer_id":"es","import_date":"2026-02-14 19:54:37"},{"cancer_study_identifier":"mbl_pcgp","name":"Medulloblastoma (PCGP, Nature 2012)","citation":"Robinson et al. Nature 2012","pmid":"22722829","sample_count":37,"type_of_cancer_id":"mbl","import_date":"2026-01-07 19:46:22"},{"cancer_study_identifier":"nbl_amc_2012","name":"Neuroblastoma  … (6306 more chars)

═ answer (success)
Here are the pediatric studies in cBioPortal with a publication year of 2021 or later. cBioPortal doesn't store an exact publication date, so I used the year in each study's citation. "Last 5 years" is therefore taken as 2021–2026. I picked "pediatric" studies from the study names and descriptions.

**Published pediatric studies (2021–2026)**

| Study | Publication | Samples |
|---|---|---|
| [Pediatric Acute Myeloid Leukemia (St. Jude)](https://www.cbioportal.org/study/summary?id=aml_stjude_2024) | Nat Genet 2024 | 887 |
| [Pediatric Neuroblastoma (MSK)](https://www.cbioportal.org/study/summary?id=nbl_msk_2023) | Nat Genet 2023 | 223 |
| [Pediatric Rhabdomyosarcomas (MSK)](https://www.cbioportal.org/study/summary?id=rms_msk_2023) | JCO Precis Oncol 2023 | 24 |
| [Pediatric solid tumor PDXs (UTHSA)](https://www.cbioportal.org/study/summary?id=pancan_pdx_uthsa_2023) | Nat Commun 2023 | 136 |
| [Pediatric European MAPPYACTS Trial (Gustave Roussy)](https://www.cbioportal.org/study/summary?id=pancan_mappyacts_2022) | Cancer Discov 2022 | 786 |
| [Pediatric Pancan Tumors (MSK)](https://www.cbioportal.org/study/summary?id=mixed_kunga_msk_2022) | Nat Commun 2022 | 135 |
| [Cancer Therapy and Clonal Hematopoiesis (MSK, pediatric cohort)](https://www.cbioportal.org/study/summary?id=msk_ch_ped_2021) | Clin Cancer Res 2022 | 657 |
| [Pediatric Low-Grade Glioma (CTF)](https://www.cbioportal.org/study/summary?id=lgg_ctf_synodos_2025) | Acta Neuropathol 2021 | 31 |
| [Pediatric Tumors (MSK, 2025)](https://www.cbioportal.org/study/summary?id=pancan_ped_mai_msk_2025) | 2025, no citation listed | 60 |

**TARGET GDC pediatric datasets (2025 release, no journal citation)**
- [Acute Leukemias of Ambiguous Lineage](https://www.cbioportal.org/study/summary?id=alal_target_gdc): 251 samples
- [Acute Myeloid Leukemia](https://www.cbioportal.org/study/summary?id=aml_target_gdc): 2,766 samples
- [B-Lymphoblastic Leukemia/Lymphoma](https://www.cbioportal.org/study/summary?id=bll_target_gdc): 989 samples
- [Neuroblastoma](https://www.cbioportal.org/study/summary?id=nbl_target_gdc): 533 samples
- [Osteosarcoma](https://www.cbioportal.org/study/summary?id=os_target_gdc): 159 samples
- [Wilms' Tumor](https://www.cbioportal.org/study/summary?id=wt_target_gdc): 132 samples

**Notes**
- Sample counts are per study, and some cohorts overlap (for example, TARGET GDC and the older TARGET 2018 studies), so don't add them up.
- Some studies just outside the window are the CPTAC/CHOP Pediatric Brain Cancer study (Cell 2020) and the TARGET 2018 studies.
- [Ewing Sarcoma (MSK, Cancer Research 2024)](https://www.cbioportal.org/study/summary?id=es_dsrct_msk_2023) and some Children's Tumor Foundation studies, such as the cutaneous neurofibroma and schwannoma resources, are not labeled pediatric. They may include pediatric patients, so I left them out.
- I searched study names and descriptions for pediatric terms. A pediatric cohort that doesn't use those terms could be missing. You can also browse the full list at [cbioportal.org](https://www.cbioportal.org).