--- 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 patient data from The Cancer Genome Atlas (TCGA), pulled from the National Cancer Institute (NCI) Genomic Data Commons (GDC). One HuggingFace (HF) subset per TCGA project; one row per patient. - **Projects included:** `TCGA-CHOL`, `TCGA-DLBC`, `TCGA-LUAD` - **Generated:** 2026-05-04 23:16:21 UTC - **Source:** GDC `/cases` endpoint, open-access tier only. - **Schema:** derived from the [GDC Data Dictionary][gdc-dict]; the live dictionary the GDC was serving when the data was fetched is hashed into each project's `gdc_status.json` for provenance. - **GDC data release:** Data Release 45.0 - December 04, 2025 ## Data model Closely follows the GDC data model — see the [GDC Data Dictionary][gdc-dict] for the canonical entity-by-entity definitions. Each row is one `case` (one patient) with the full biospecimen subtree: ``` 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 ``` Every `days_to_*` field anchors to the case's `index_date` (TCGA: almost always `"Diagnosis"`), per the dictionary, so clinical and biospecimen events share a single timeline. ### Where this dataset deviates from the GDC The few places this row layout differs from a direct mapping of the GDC `case` tree: - **Top-level convenience columns.** Each row carries `gdc_portal_url` (templated link to the patient's GDC Data Portal page) and `samples_` molecular vectors (e.g. `samples_masked_somatic_mutation`, `samples_gene_expression_quantification`). These let consumers column-project just the modalities they need; each entry carries foreign keys (FKs) back to `samples[].portions[].analytes[].aliquots[]`. - **Resolved sample FKs on Mutation Annotation Format (MAF) rows.** The GDC ships MAF variants with aliquot UUIDs in `Tumor_Sample_UUID` / `Matched_Norm_Sample_UUID`; we additionally resolve those to `tumor_sample_id` / `matched_normal_sample_id` so consumers can join straight to `samples[]`. - **Lifted expression QC counts.** Each Gene Expression Quantification record has the STAR per-feature quality-control counts `N_unmapped`, `N_multimapping`, `N_noFeature`, `N_ambiguous` lifted from the source Tab-Separated Values (TSV) file onto the row as scalar fields. The `stranded_first` / `stranded_second` columns are dropped — TCGA used unstranded library prep, so they're zero or unused. ## Loading The [`tcga2hf` package][repo] ships a typed `TcgaHfPatient` pydantic model that mirrors this schema and adds convenience joins (tumor/normal pairs, mutations-by-gene, expression-by-gene, longitudinal timeline). ```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()] ``` ## 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/) ## 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 Policy references: [GDC Policies](https://gdc.cancer.gov/about-gdc/gdc-policies), [GDC Encyclopedia — Controlled Access][controlled] (defines what is *not* in this dataset), [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. [gdc-dict]: https://docs.gdc.cancer.gov/Data_Dictionary/ [repo]: https://github.com/galtay/tcga2hf