--- license: other license_name: nih-genomic-data-sharing license_link: https://gdc.cancer.gov/analyze-data/data-analysis-policies pretty_name: TCGA Patients (Open Access) tags: - cancer - tcga - clinical - genomics configs: - config_name: TCGA-CHOL data_files: - split: train path: TCGA-CHOL/*.parquet - config_name: TCGA-DLBC data_files: - split: train path: TCGA-DLBC/*.parquet - config_name: TCGA-LUAD data_files: - split: train path: TCGA-LUAD/*.parquet --- # TCGA Patients (Open Access) **Open-access** TCGA patient data from the NCI Genomic Data Commons (GDC). One HuggingFace subset per TCGA project; one row per patient. - **Projects included:** `TCGA-CHOL`, `TCGA-DLBC`, `TCGA-LUAD` - **Generated:** 2026-05-04 05:19:32 UTC - **Source:** NCI GDC `/cases` endpoint, open-access tier only. - **Schema:** derived from the [GDC Data Dictionary][gdc-dict]; the live dictionary snapshot the GDC was serving when the data was fetched is hashed into each project's `gdc_status.json` (and stored alongside the raw data on the producer side, not shipped with the parquet). - **GDC data release:** Data Release 45.0 - December 04, 2025 ## GDC data model primer A short orientation for downstream users. The GDC organizes everything around a **case** (a single patient) with a hierarchy of physical biospecimens beneath it, plus assay-derived data files attached to those biospecimens. **Biospecimen hierarchy** (per GDC's [data dictionary][gdc-dict]): ``` case one patient (TCGA-XX-1234) └── sample physical specimen taken from the patient at one timepoint (Primary Tumor, Solid Tissue Normal, Blood Derived Normal, ...) └── portion a piece of that sample for a specific lab process └── analyte extracted material of one type (DNA or RNA) └── aliquot a vial of that analyte handed off for sequencing ``` We preserve this hierarchy verbatim — each `samples[i]` carries `portions[j].analytes[k].aliquots[m]` exactly as the GDC returns it. No flattening, no field hoisting; portion- and analyte-level fields like `is_ffpe`, `a260_a280_ratio`, and `normal_tumor_genotype_snp_match` are preserved. The `TcgaHfPatient` reference implementation (below) provides flat-aliquot convenience views over this tree. **Top-level molecular columns** are named `samples_` (e.g. `samples_masked_somatic_mutation`, `samples_gene_expression_quantification`). Each entry carries FK fields back to the patient's `samples[].portions[].analytes[].aliquots[]` so cross-modality joins are local to the row. **Timeline anchor is uniform per the GDC dictionary.** Every `days_to_*` field is documented as days from the case's `index_date` (a top-level field on each row; for TCGA usually `"Diagnosis"`). `TcgaHfPatient.timeline()` returns every dated event for the patient on this single anchor — clinical (consent → diagnosis → treatments → follow-ups → lost-to-follow-up → death) plus biospecimen (`sample_procurement` from `days_to_sample_procurement`, `bcr_receipt` from `days_to_collection`). For some TCGA cases `days_to_collection` exceeds `days_to_death`. We don't attempt to reinterpret these — we surface the count via `TcgaHfPatient.consistency_check()` as `bcr_receipts_after_death` and leave interpretation to the consumer. **Reference Python implementation:** the `tcga2hf` package on GitHub ships a fully-typed pydantic `TcgaHfPatient` model that mirrors this schema and adds convenience joins (tumor/normal pairs, mutations-by-gene, expression-by-gene, longitudinal timeline). Useful both as a loader and as documentation for what the data means. ```python import pyarrow.parquet as pq from tcga2hf.models import TcgaHfPatient t = pq.read_table("TCGA-CHOL/train.parquet") patients = [TcgaHfPatient.model_validate(r) for r in t.to_pylist()] ``` **Authoritative GDC references:** - [Data dictionary][gdc-dict] (every entity + field definition) - [Biospecimen Encyclopedia](https://docs.gdc.cancer.gov/Encyclopedia/pages/Biospecimen/) - [MAF format spec](https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/) - [Gene Expression Quantification spec](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/) - [Sample Type codes](https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes) - [TCGA Barcode reference](https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/) [gdc-dict]: https://docs.gdc.cancer.gov/Data_Dictionary/ ## License & redistribution Per the [NCI GDC Data Analysis Policy](https://gdc.cancer.gov/analyze-data/data-analysis-policies): > The GDC itself places no restrictions (other than attempts at reidentification) > on analysis or publication of open access data provided through the GDC Data Portal. Per the [NCI TCGA citation page](https://www.cancer.gov/ccg/research/genome-sequencing/tcga/using-tcga-data/citing): > Moratoria on all cancer types are now lifted and all TCGA data are available > without restrictions on their use in publications or presentations. Per the [GDC Data Access Processes and Tools page](https://gdc.cancer.gov/access-data/data-access-processes-and-tools): > Open access data generally includes high level genomic data that is not > individually identifiable, as well as most clinical and all biospecimen data > elements. ## Restrictions on use > Users of any data provided by GDC, whether open or controlled access, agree > not to attempt to reidentify any individual participant in any study > represented by GDC data, for any purpose whatever. > ([source](https://gdc.cancer.gov/analyze-data/data-analysis-policies)) ## Required acknowledgement If you publish or present results derived from this dataset, include the [NCI-required TCGA acknowledgement](https://www.cancer.gov/ccg/research/genome-sequencing/tcga/using-tcga-data/citing): > The results here are in whole or part based upon data > generated by the TCGA Research Network: https://www.cancer.gov/tcga. Suggested citations: - Grossman, R. L., et al. (2016). Toward a Shared Vision for Cancer Genomic Data. *NEJM*, 375(12), 1109-1112. - The Cancer Genome Atlas Research Network. https://www.cancer.gov/tcga - NCI Genomic Data Commons. https://gdc.cancer.gov References: [GDC Policies](https://gdc.cancer.gov/about-gdc/gdc-policies), [GDC Encyclopedia — Controlled Access][controlled] (defines what is *not* here), [NIH Genomic Data Sharing Policy](https://sharing.nih.gov/genomic-data-sharing). [controlled]: https://docs.gdc.cancer.gov/Encyclopedia/pages/Controlled_Access/ ## Disclaimer Prototype dataset. Schema, included projects, and column coverage are still evolving. Re-derive from the GDC for any analysis where freshness matters.