Data acquisition
All inputs are open access. None is redistributed in this repository; the instructions below are sufficient to obtain byte-identical copies.
Retrieved 26 October 2026.
1. Somatic mutations — TCGA MC3 public callset
| File | mc3.v0.2.8.PUBLIC.maf.gz |
| Source | GDC PanCanAtlas publication page |
| URL | https://api.gdc.cancer.gov/data/1c8cfe5f-e52d-41ba-94da-f15ea1337efc |
| Size | 718.4 MB |
| SHA-256 | cb0caa0e3a80a24cc4ccaaacc95c690a4032cc87c8ac78519a5b33f3aa3f6b81 |
| Rows | 3,600,963 |
| Genome build | GRCh37 (verified: NCBI_Build is GRCh37 on all rows) |
| Reference | Ellrott K, Bailey MH, Saksena G, et al. Cell Systems 2018;6(3):271–281.e7. doi:10.1016/j.cels.2018.03.002 |
Access tier. This is the public MC3 release and requires no dbGaP application or data use agreement. It should not be cited to accession phs000178, which is the controlled-access accession and implies a different access tier.
2. Reference pMHC burden — PanImmune
| File | TCGA_pMHC_SNV_sampleSummary_MC3_v0.2.8.CONTROLLED_170404.tsv |
| Source | GDC "The Immune Landscape of Cancer" publication page |
| URL | https://api.gdc.cancer.gov/data/0d3ee0a7-0557-447b-9ada-bc7838d1effb |
| Rows | 8,546 samples |
| Columns used | barcode, numberOfNonSynonymousSNP, numberOfPeptideTested, numberOfBindingPMHC, numberOfBindingExpressedPMHC |
| Reference | Thorsson V, Gibbs DL, Brown SD, et al. Immunity 2018 |
Note the filename. CONTROLLED refers to the source MAF used to generate
it, not to the file's own access tier. It downloads over plain HTTP with no
credentials.
3. Tumour type and indel neoantigens — PanImmune
| File | TCGA_PCA.mc3.v0.2.8.CONTROLLED.filtered.sample_neoantigens_10062017.tsv |
| URL | https://api.gdc.cancer.gov/data/5ecff039-a050-4ad3-bff0-c112cbd8d2ff |
| Rows | 6,610 samples; GBM 123, LGG 408 |
| Columns used | sample, cancer_type |
Used to assign tumour type. The indel-derived neoantigen counts are not used in the present analysis, which is restricted to missense variants.
4. Protein sequences — Ensembl GRCh37
Retrieved per transcript from the Ensembl REST API rather than a local
annotation install, because the originating machine could not execute the
pyensembl package under its Application Control policy.
| Endpoint | https://grch37.rest.ensembl.org/sequence/id (POST, type=protein) |
| Batch size | 50 transcript IDs |
| Transcripts requested | 13,539 |
| Transcripts returned | 13,539 (100%) |
| Failed batches | 0 |
Caveat. The GRCh37 REST endpoint serves Ensembl's frozen GRCh37
annotation. It is a close match to release 75 but is not pinned to a release
number, and it receives occasional patches. A replication using a local
pyensembl release 75 install would be preferable and is expected to agree;
any discrepancy should be reported rather than reconciled silently.
Responses are keyed by the query field, which carries the submitted
transcript ID. The id field carries the protein ID (ENSP…), not the
transcript ID — keying on id silently matches nothing.
5. Outstanding
Per-sample HLA class I genotypes for TCGA GBM/LGG have been requested from the ICBI group at the Medical University of Innsbruck (26 October 2026). The TCIA portal, which normally serves this data, is offline for redesign.
If obtained, the study runs as a paired comparison — the same pipeline twice, supertypes against true genotype — which isolates the HLA effect. If not, the comparison is against the PanImmune reference above, which confounds HLA handling with other pipeline differences and supports a correspondingly narrower claim.
Checked and found not to hold these genotypes: Synapse syn10337516
(CRI iAtlas, full tree listed), and the GDC PanImmune page itself.