Data Analysis
The GDC DAVE tools use the same API as the rest of the Data Portal and takes advantage of several new endpoints. Similar to the GDC Data Portal Exploration feature, the GDC data analysis endpoints allow API users to programmatically explore data in the GDC using advanced filters at a gene and mutation level. Survival analysis data is also available.
Endpoints
The following data analysis endpoints are available from the GDC API:
| Node | Endpoint | Description |
|---|---|---|
| Genes | /genes | Allows users to access summary information about each gene using its Ensembl ID. |
| SSMS | /ssms | Allows users to access information about each somatic mutation. For example, a ssm would represent the transition of C to T at position 52000 of chromosome 1. |
/ssms/<ssm_id> |
Get information about a specific ssm using a <ssm_id>, often supplemented with the expand option to show fields of interest. |
|
| /ssm_occurrences | A ssm entity as applied to a single instance (case). An example of a ssm occurrence would be that the transition of C to T at position 52000 of chromosome 1 occurred in patient TCGA-XX-XXXX. |
|
/ssm_occurrences/<ssm_occurrences_id> |
Get information about a specific ssm occurrence using a <ssm_occurrences_id>, often supplemented with the expand option to show fields of interest. |
|
| CNVS | /cnvs | Allows users to access data about copy number variations (cnvs). This data will be specifc to cnvs and not a specific case. |
/cnvs/<cnv_id> |
Get information about a specific copy number variation using a <cnv_id>, often supplemented with the expand option to show fields of interest. |
|
| /cnvs/ids | This endpoint will retrieve nodes that contain the queried cnv_id. This is accomplished by adding the query parameter: /cnvs/ids?query=<cnv_id>. |
|
| /cnv_occurrences | A cnv entity as applied to a single case. |
|
/cnv_occurrences/<cnv_occurrence_id> |
Get information about a specific copy number variation occurrence using a <cnv_occurrence_id>, often supplemented with the expand option to show fields of interest. |
|
| /cnv_occurrences/ids | This endpoint will retrieve nodes that contain the queried cnv_occurrence_id. This is accomplished by adding the query parameter: /cnv_occurrences/ids?query=<cnv_occurrences_id> |
|
| Analysis | /analysis/top_cases_counts_by_genes | Returns the number of cases with a mutation in each gene listed in the gene_ids parameter for each project. Note that this endpoint cannot be used with the format or fields parameters. |
| /analysis/top_mutated_genes_by_project | Returns a list of genes that have the most mutations within a given project. | |
| /analysis/top_mutated_cases_by_gene | Generates information about the cases that are most affected by mutations in a given number of genes | |
| /analysis/mutated_cases_count_by_project | Returns counts for the number of cases that have associated ssm data in each project. The number of affected cases can be found under "case_with_ssm": {"doc_count": $case_count}. |
|
| /analysis/survival | Survival plots can be generated in the Data Portal for different subsets of data, based upon many query factors such as variants, disease type and projects. This endpoint can be used to programmatically retrieve the raw data to generate these plots and apply different filters to the data. (see Survival Example) |
The methods for retrieving information from these endpoints are very similar to those used for the cases and files endpoints. These methods are explored in depth in the API Search and Retrieval documentation. The _mapping parameter can also be used with each of these endpoints to generate a list of potential fields. For example:
https://api.gdc.cancer.gov/ssms/_mapping
While it is not an endpoint, the observation entity is featured in the visualization section of the API. The observation entity provides information from the MAF file, such as read depth and normal genotype, that supports the validity of the associated ssm. An example is demonstrated below:
curl "https://api.gdc.cancer.gov/ssms/57bb3f2e-ec05-52c2-ab02-7065b7d24849?expand=occurrence.case.observation.read_depth&pretty=true"
{
"data": {
"ncbi_build": "GRCh38",
"occurrence": [
{
"case": {
"observation": [
{
"read_depth": {
"t_ref_count": 321,
"t_alt_count": 14,
"t_depth": 335,
"n_depth": 115
}
}
]
}
}
],
"tumor_allele": "G",
"mutation_type": "Simple Somatic Mutation",
"end_position": 14304578,
"reference_allele": "C",
"ssm_id": "57bb3f2e-ec05-52c2-ab02-7065b7d24849",
"start_position": 14304578,
"mutation_subtype": "Single base substitution",
"cosmic_id": null,
"genomic_dna_change": "chr5:g.14304578C>G",
"gene_aa_change": [
"TRIO L229V",
"TRIO L437V",
"TRIO L447V",
"TRIO L496V"
],
"chromosome": "chr5"
},
"warnings": {}
}
Genes Endpoint Examples
Example 1: A user would like to access information about the gene ZMPSTE24, which has an Ensembl gene ID of ENSG00000084073. This would be accomplished by appending ENSG00000084073 (gene_id) to the genes endpoint.
curl "https://api.gdc.cancer.gov/genes/ENSG00000084073?pretty=true"
{
"data": {
"canonical_transcript_length": 3108,
"description": "This gene encodes a member of the peptidase M48A family. The encoded protein is a zinc metalloproteinase involved in the two step post-translational proteolytic cleavage of carboxy terminal residues of farnesylated prelamin A to form mature lamin A. Mutations in this gene have been associated with mandibuloacral dysplasia and restrictive dermopathy. [provided by RefSeq, Jul 2008]",
"cytoband": [
"1p34.2"
],
"gene_start": 40258107,
"canonical_transcript_length_genomic": 36078,
"gene_id": "ENSG00000084073",
"gene_strand": 1,
"canonical_transcript_length_cds": 1425,
"gene_chromosome": "1",
"synonyms": [
"FACE-1",
"HGPS",
"PRO1",
"STE24",
"Ste24p"
],
"is_cancer_gene_census": null,
"biotype": "protein_coding",
"gene_end": 40294184,
"canonical_transcript_id": "ENST00000372759",
"symbol": "ZMPSTE24",
"name": "zinc metallopeptidase STE24"
},
"warnings": {}
}
curl "https://api.gdc.cancer.gov/genes?pretty=true&fields=gene_id,symbol,gene_start,gene_end&format=tsv&size=2000&filters=%7B%0D%0A%22op%22%3A%22in%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22gene_chromosome%22%2C%0D%0A%22value%22%3A%5B%0D%0A%227%22%0D%0A%5D%0D%0A%7D%0D%0A%7D"
gene_start gene_end symbol id
28995231 29195451 CPVL ENSG00000106066
33014114 33062797 NT5C3A ENSG00000122643
143052320 143053347 OR6V1 ENSG00000225781
100400826 100428992 ZCWPW1 ENSG00000078487
73861159 73865893 WBSCR28 ENSG00000175877
64862999 64864370 EEF1DP4 ENSG00000213640
159231435 159233377 PIP5K1P2 ENSG00000229435
141972631 141973773 TAS2R38 ENSG00000257138
16646131 16706523 BZW2 ENSG00000136261
149239651 149255609 ZNF212 ENSG00000170260
57405025 57405090 MIR3147 ENSG00000266168
130393771 130442433 CEP41 ENSG00000106477
150800403 150805120 TMEM176A ENSG00000002933
93591573 93911265 GNGT1 ENSG00000127928
117465784 117715971 CFTR ENSG00000001626
5879827 5886362 OCM ENSG00000122543
144118461 144119360 OR2A15P ENSG00000239981
30424527 30478784 NOD1 ENSG00000106100
137227341 137343865 PTN ENSG00000105894
84876554 84876956 HMGN2P11 ENSG00000232605
107470018 107475659 GPR22 ENSG00000172209
31330711 31330896 RP11-463M14.1 ENSG00000271027
78017057 79453574 MAGI2 ENSG00000187391
55736779 55739605 CICP11 ENSG00000237799
142111749 142222324 RP11-1220K2.2 ENSG00000257743
(truncated)
Simple Somatic Mutation Endpoint Examples
Example 1: Similar to the /genes endpoint, a user would like to retrieve information about the mutation based on its COSMIC ID. This would be accomplished by creating a JSON filter, which will then be encoded to URL for the curl command.
{
"op":"in",
"content":{
"field":"cosmic_id",
"value":[
"COSM1135366"
]
}
}
curl 'https://api.gdc.cancer.gov/ssms?pretty=true&filters=%7B%0A%22op%22%3A%22in%22%2C%0A%22content%22%3A%7B%0A%22field%22%3A%22cosmic_id%22%2C%0A%2value%22%3A%5B%0A%22COSM1135366%22%0A%5D%0A%7D%0A%7D%0A'
{
"data": {
"hits": [
{
"id": "edd1ae2c-3ca9-52bd-a124-b09ed304fcc2",
"start_position": 25245350,
"gene_aa_change": [
"KRAS G12D"
],
"reference_allele": "C",
"ncbi_build": "GRCh38",
"cosmic_id": [
"COSM1135366",
"COSM521"
],
"mutation_subtype": "Single base substitution",
"mutation_type": "Simple Somatic Mutation",
"chromosome": "chr12",
"ssm_id": "edd1ae2c-3ca9-52bd-a124-b09ed304fcc2",
"genomic_dna_change": "chr12:g.25245350C>T",
"tumor_allele": "T",
"end_position": 25245350
}
],
"pagination": {
"count": 1,
"total": 1,
"size": 10,
"from": 0,
"sort": "",
"page": 1,
"pages": 1
}
},
"warnings": {}
}
ssm_id (8b3c1a7a-e4e0-5200-9d46-5767c2982145), a user would like to look at the consequences and the VEP impact due to this ssm.
curl 'https://api.gdc.cancer.gov/ssms/edd1ae2c-3ca9-52bd-a124-b09ed304fcc2?pretty=true&expand=consequence.transcript&fields=consequence.transcript.annotation.vep_impact'
{
"data": {
"consequence": [
{
"transcript": {
"annotation": {
"vep_impact": "MODERATE"
},
"transcript_id": "ENST00000557334",
"aa_end": 12,
"consequence_type": "missense_variant",
"aa_start": 12,
"is_canonical": false,
"aa_change": "G12D",
"ref_seq_accession": ""
}
},
{
"transcript": {
"annotation": {
"vep_impact": "MODERATE"
},
"transcript_id": "ENST00000256078",
"aa_end": 12,
"consequence_type": "missense_variant",
"aa_start": 12,
"is_canonical": true,
"aa_change": "G12D",
"ref_seq_accession": "NM_001369786.1&NM_033360.4"
}
},
{
"transcript": {
"annotation": {
"vep_impact": "MODERATE"
},
"transcript_id": "ENST00000311936",
"aa_end": 12,
"consequence_type": "missense_variant",
"aa_start": 12,
"is_canonical": false,
"aa_change": "G12D",
"ref_seq_accession": "NM_001369787.1&NM_004985.5"
}
},
{
"transcript": {
"annotation": {
"vep_impact": "MODERATE"
},
"transcript_id": "ENST00000556131",
"aa_end": 12,
"consequence_type": "missense_variant",
"aa_start": 12,
"is_canonical": false,
"aa_change": "G12D",
"ref_seq_accession": ""
}
}
]
},
"warnings": {}
}
Simple Somatic Mutation Occurrence Endpoint Examples
Example 1: A user wants to determine the chromosome in case TCGA-DU-6407 that contains the greatest number of ssms. As this relates to mutations that are observed in a case, the ssm_occurrences endpoint is used.
{
"op":"in",
"content":{
"field":"case.submitter_id",
"value":["TCGA-DU-6407"]
}
}
curl "https://api.gdc.cancer.gov/ssm_occurrences?format=tsv&fields=ssm.chromosome&size=5000&filters=%7B%0D%0A%22op%22%3A%22in%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22case.submitter_id%22%2C%0D%0A%22value%22%3A%5B%0D%0A%22TCGA-DU-6407%22%0D%0A%5D%0D%0A%7D%0D%0A%7D"
id ssm.chromosome
105e7811-4601-5ccb-ae93-e7107923599e chr16
faee73a9-4804-58ea-a91f-18c3d901774f chr2
99b3aad4-d368-506d-99d6-047cbe5dff0f chr2
2cb06277-993e-5502-b2c5-263037c45d18 chr10
f08dcc53-eadc-5ceb-bf31-f6b38629e4cb chr19
97c5b38b-fc96-57f5-8517-cc702b3aa70a chr6
19ca262d-b354-54a0-b582-c4719e37e91d chrX
b4822fc9-f0cc-56fd-9d97-f916234e309d chr2
22a07c7c-16ba-51df-a9a9-1e41e2a45225 chrX
0010a89d-9434-5d97-8672-36ee394767d0 chr17
3a023e72-da92-54f7-aa18-502c1076b2b0 chr5
391011ff-c1fd-5e2a-a128-652bc660f64c chr10
3548ecfe-5186-51e7-8f40-37f4654cd260 chr2
b67f31b5-0341-518e-8fcc-811cd2e36af1 chr3
4a93d7a5-988d-5055-80da-999dc3b45d80 chr1
9dc3f7cd-9efa-530a-8524-30d067e49d54 chr13
552c09d1-69b1-5c04-b543-524a6feae3eb chr3
dbc5eafa-ea26-5f1c-946c-b6974a345b69 chr12
d25129ad-3ad7-584f-bdeb-fba5c3881d32 chr17
1378cbc4-af88-55bb-b2e5-185bb4246d7a chr10
c44a93a1-5c73-5cff-b40e-98ce7e5fe57b chr19
1267330b-ae6d-5e25-b19e-34e98523679e chr21
1476a543-2951-5ec4-b165-67551b47d810 chr17
727c9d57-7b74-556f-aa5b-e1ca1f76d119 chr10
94abd5fd-d539-5a4a-8719-9615cf7cec5d chr1
a76469cb-973c-5d4d-bf82-7cf4e8f6c129 chr17
ssm_occurrence, and would like to determine if that case also has diagnostic information.
curl 'https://api.gdc.cancer.gov/ssm_occurrences/6fd8527d-5c40-5604-8fa9-0ce798eec231?pretty=true&expand=case.diagnoses'
{
"data": {
"ssm_occurrence_id": "6fd8527d-5c40-5604-8fa9-0ce798eec231",
"case": {
"diagnoses": [
{
"ajcc_pathologic_t": "T3b",
"synchronous_malignancy": "No",
"morphology": "8720/3",
"ajcc_pathologic_stage": "Stage IIB",
"ajcc_pathologic_n": "N0",
"ajcc_pathologic_m": "M0",
"submitter_id": "TCGA-Z2-A8RT_diagnosis",
"days_to_diagnosis": 0,
"last_known_disease_status": "not reported",
"tissue_or_organ_of_origin": "Skin, NOS",
"days_to_last_follow_up": 839.0,
"age_at_diagnosis": 15342,
"primary_diagnosis": "Malignant melanoma, NOS",
"classification_of_tumor": "not reported",
"prior_malignancy": "no",
"year_of_diagnosis": 2012,
"diagnosis_id": "1d06a202-c51a-52e2-805f-eeb5f7fac14e",
"icd_10_code": "C44.6",
"site_of_resection_or_biopsy": "Skin of upper limb and shoulder",
"prior_treatment": "No",
"state": "released",
"tumor_grade": "not reported",
"progression_or_recurrence": "not reported",
"ajcc_staging_system_edition": "7th"
}
]
}
},
"warnings": {}
}
Copy Number Variation Endpoint Examples
Example 1: A user is interested in finding the first 30 cnvs found on chromosome 4 that have a cnv loss.
{
"op": "and",
"content": [
{
"op": "in",
"content": {
"field": "chromosome",
"value": [
"4"
]
}
},
{
"op": "in",
"content": {
"field": "cnv_change",
"value": [
"Loss"
]
}
}
]
}
curl 'https://api.gdc.cancer.gov/cnvs?filters=%7B%0D%0A+++%22op%22%3A+%22and%22%2C%0D%0A++++%22content%22%3A+%5B%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22chromosome%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%224%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%2C%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22cnv_change%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%22Loss%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%0D%0A++++%5D%0D%0A%7D&size=30&sort=start_position&format=tsv'
chromosome cnv_change cnv_id end_position gene_level_cn id ncbi_build start_position
4 Loss 11381600-f064-5c42-90d2-a5c79c8b23e1 88208 True 11381600-f064-5c42-90d2-a5c79c8b23e1 GRCh38 53286
4 Loss edef0f2f-c1a7-507c-842f-e1f8a568df9d 202303 True edef0f2f-c1a7-507c-842f-e1f8a568df9d GRCh38 124501
4 Loss eba92f9a-b045-54a8-948a-451e439ed418 305474 True eba92f9a-b045-54a8-948a-451e439ed418 GRCh38 270675
4 Loss 89319453-2a3f-5ebe-be30-8af0426e0343 384868 True 89319453-2a3f-5ebe-be30-8af0426e0343 GRCh38 337814
4 Loss 6567929c-4b6f-582b-aedf-acde2c0ec736 499156 True 6567929c-4b6f-582b-aedf-acde2c0ec736 GRCh38 425815
4 Loss 2daff58b-5065-50cd-8239-253180eaee81 540200 True 2daff58b-5065-50cd-8239-253180eaee81 GRCh38 499210
4 Loss 2b42c8d4-6d85-5352-96e1-9e52e722c248 576295 True 2b42c8d4-6d85-5352-96e1-9e52e722c248 GRCh38 573880
4 Loss 2646cdc7-7602-59a4-ae4f-d171352bae88 670782 True 2646cdc7-7602-59a4-ae4f-d171352bae88 GRCh38 625573
4 Loss c11ad392-949f-593f-a3ab-d834b2f82809 674330 True c11ad392-949f-593f-a3ab-d834b2f82809 GRCh38 672436
4 Loss f31be658-4de0-549e-81be-e79759879acf 682033 True f31be658-4de0-549e-81be-e79759879acf GRCh38 673580
4 Loss d72c62f2-fc29-5b83-9839-7f6b03970aff 689271 True d72c62f2-fc29-5b83-9839-7f6b03970aff GRCh38 681829
4 Loss 45448d47-6e13-5d30-824d-96150a7f55c6 770640 True 45448d47-6e13-5d30-824d-96150a7f55c6 GRCh38 705748
4 Loss 517e65ea-9084-54c2-abe0-b1b47e9f872c 826129 True 517e65ea-9084-54c2-abe0-b1b47e9f872c GRCh38 784957
4 Loss b5a09c9b-d842-5b76-a500-56f18252c29d 932373 True b5a09c9b-d842-5b76-a500-56f18252c29d GRCh38 849276
4 Loss e3a3b61d-2881-5ad4-90bf-58ef29ae9ecb 958656 True e3a3b61d-2881-5ad4-90bf-58ef29ae9ecb GRCh38 932387
4 Loss 8630a1b6-3215-5b71-903a-ad9845505afc 986895 True 8630a1b6-3215-5b71-903a-ad9845505afc GRCh38 958887
4 Loss f748b06f-1fb7-53a9-a7d6-2c22a3ae6de5 993440 True f748b06f-1fb7-53a9-a7d6-2c22a3ae6de5 GRCh38 979073
4 Loss a5e4a63f-c5f6-5f0f-a6b6-f51bfb643533 1004564 True a5e4a63f-c5f6-5f0f-a6b6-f51bfb643533 GRCh38 986997
4 Loss 73f6fbbe-6fd9-524c-a7c8-a7cf3f08ada4 1026898 True 73f6fbbe-6fd9-524c-a7c8-a7cf3f08ada4 GRCh38 1009936
4 Loss adad579a-b002-5022-823a-570c59549065 1113564 True adad579a-b002-5022-823a-570c59549065 GRCh38 1056250
4 Loss d5a5c45e-594b-5cbc-97d5-75fc5155d021 1208962 True d5a5c45e-594b-5cbc-97d5-75fc5155d021 GRCh38 1166932
4 Loss 6c910993-faa8-5abc-b433-b3afcc5e9e11 1249953 True 6c910993-faa8-5abc-b433-b3afcc5e9e11 GRCh38 1211445
4 Loss 4453b4cb-7d8a-5e26-a856-eac62eec287a 1340147 True 4453b4cb-7d8a-5e26-a856-eac62eec287a GRCh38 1289887
4 Loss 6db1001a-a41b-518d-9491-2bf41544d90f 1395989 True 6db1001a-a41b-518d-9491-2bf41544d90f GRCh38 1345691
4 Loss 6bef981a-ead1-5aa7-8a69-8d38e576e5c0 1406442 True 6bef981a-ead1-5aa7-8a69-8d38e576e5c0 GRCh38 1402932
4 Loss af6e0b49-922a-587e-b353-4b9414605cf1 1684261 True af6e0b49-922a-587e-b353-4b9414605cf1 GRCh38 1617915
4 Loss 400352ad-8526-562a-bbf4-29b90a48f46f 1712344 True 400352ad-8526-562a-bbf4-29b90a48f46f GRCh38 1692731
4 Loss 8811414d-2434-56c6-afe5-a998c9b18d47 1745171 True 8811414d-2434-56c6-afe5-a998c9b18d47 GRCh38 1712891
4 Loss 169c4409-0256-5841-9314-f1a4dd2bcc38 1721358 True 169c4409-0256-5841-9314-f1a4dd2bcc38 GRCh38 1715952
4 Loss 1712ccac-6e70-5fb3-b71e-1a029eaf047c 1808872 True 1712ccac-6e70-5fb3-b71e-1a029eaf047c GRCh38 1793293
544c4896-0152-5787-8d77-894a16f0ded0, and determine whether the gene is found within the Cancer Gene Census.
curl 'https://api.gdc.cancer.gov/cnvs/544c4896-0152-5787-8d77-894a16f0ded0?pretty=true&expand=consequence.gene'
{
"data": {
"start_position": 27100354,
"consequence": [
{
"gene": {
"biotype": "protein_coding",
"symbol": "HOXA2",
"gene_id": "ENSG00000105996"
}
}
],
"gene_level_cn": true,
"cnv_change": "Gain",
"ncbi_build": "GRCh38",
"chromosome": "7",
"cnv_id": "544c4896-0152-5787-8d77-894a16f0ded0",
"end_position": 27102686
},
"warnings": {}
}
Copy Number Variation Occurrence Enpoint Examples
Example 1: A user is interested in finding cases that have both cnv and ssm data for females diagnosed with Squamous Cell Neoplasms and have a cnv gain change on chromosome 9. It is important to note that for a case like this, where multiple arguments are need for one filtered field, it is easier for the API to have multiple filters for the same field, case.available_variation_data in this example, than having one filter with multiple arguments.
{
"op": "and",
"content": [
{
"op": "in",
"content": {
"field": "cnv.cnv_change",
"value": [
"Gain"
]
}
},
{
"op": "in",
"content": {
"field": "case.demographic.gender",
"value": [
"female"
]
}
},
{
"op": "in",
"content": {
"field": "case.available_variation_data",
"value": [
"cnv"
]
}
},
{
"op": "in",
"content": {
"field": "case.available_variation_data",
"value": [
"ssm"
]
}
},
{
"op": "in",
"content": {
"field": "cnv.chromosome",
"value": [
"9"
]
}
},
{
"op": "in",
"content": {
"field": "case.disease_type",
"value": [
"Squamous Cell Neoplasms"
]
}
}
]
}
curl 'https://api.gdc.cancer.gov/cnv_occurrences?filters=%7B%0D%0A++++%22op%22%3A+%22and%22%2C%0D%0A++++%22content%22%3A+%5B%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22cnv.cnv_change%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%22Gain%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%2C%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22case.demographic.gender%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%22female%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%2C%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22case.available_variation_data%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%22cnv%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%2C%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22case.available_variation_data%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%22ssm%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%2C%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22cnv.chromosome%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%229%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%2C%0D%0A++++++++%7B%0D%0A++++++++++++%22op%22%3A+%22in%22%2C%0D%0A++++++++++++%22content%22%3A+%7B%0D%0A++++++++++++++++%22field%22%3A+%22case.disease_type%22%2C%0D%0A++++++++++++++++%22value%22%3A+%5B%0D%0A++++++++++++++++++++%22Squamous+Cell+Neoplasms%22%0D%0A++++++++++++++++%5D%0D%0A++++++++++++%7D%0D%0A++++++++%7D%0D%0A++++%5D%0D%0A%7D&fields=case.available_variation_data,case.case_id&format=tsv'
case.available_variation_data.0 case.available_variation_data.1 case.case_id id
cnv ssm da30a845-c4d3-4c78-b8b0-210239224f8f 3caf6e3b-024f-57b6-bdd9-3b67e423cc11
cnv ssm 0809ba8b-4ab6-4f43-934c-c1ccbc014a7e e6afe58e-c99c-5c8d-920e-8ba4daad4d89
cnv ssm 8e0e456e-85ee-4de5-8f0b-72393d6acde0 9d983d9c-8320-53f1-9054-e46926c5b834
cnv ssm 64a195f6-2212-4e81-bccc-e39c77a10908 8caeaecc-ad68-539d-8b3c-8320b3684763
cnv ssm 2f6a0e87-1e6c-41f3-93e0-3e505fa654b0 4862c166-0f37-5e3c-ae4e-a2964de01cea
cnv ssm f0daf315-8909-4cda-886d-a2770b08db94 099ff6cd-bd28-56f4-a181-6b02f3ba7503
cnv ssm ff3808e4-eece-4046-819b-fe1019317f8e 0c936aa2-393e-5463-a431-3613b4510021
cnv ssm 9205dc07-93f5-4b5e-924e-8e097616160f 133d27a7-fdc6-5082-a1f3-022b89f4e851
cnv ssm 79ae5209-f476-4d65-a6c0-ebc18d7c8942 7a5e6bb1-8af3-5964-a3cc-c53602c8b099
cnv ssm ff7099e1-8ff9-48e4-842d-46e98076e7e6 fb27fa8f-aa31-5e20-84da-8f45bb675405
3b9f7ecc-2280-5b89-80f9-ec8d6c5e604e) from the previous example, and would like to know more about the case exposures and demographics.
curl 'https://api.gdc.cancer.gov/cnv_occurrences/3b9f7ecc-2280-5b89-80f9-ec8d6c5e604e?pretty=true&expand=cnv,case,case.exposures,case.demographic'
{
"data": {
"cnv": {
"start_position": 68815994,
"gene_level_cn": true,
"cnv_change": "Gain",
"ncbi_build": "GRCh38",
"chromosome": "4",
"variant_status": "Tumor Only",
"cnv_id": "1a889109-30d5-51e3-848f-9f615c69f407",
"end_position": 68832023
},
"cnv_occurrence_id": "3b9f7ecc-2280-5b89-80f9-ec8d6c5e604e",
"case": {
"exposures": [
{
"cigarettes_per_day": 5.47945205479452,
"alcohol_history": "Not Reported",
"exposure_id": "f7b08a8e-d22b-5cb0-be9f-b922c9ca87d2",
"submitter_id": "TCGA-38-4629_exposure",
"state": "released",
"pack_years_smoked": 100.0
}
],
"primary_site": "Bronchus and lung",
"disease_type": "Adenomas and Adenocarcinomas",
"available_variation_data": [
"cnv",
"ssm"
],
"case_id": "127bf818-f7e5-46b5-a9de-39f6d96b8b83",
"submitter_id": "TCGA-38-4629",
"state": "released",
"demographic": {
"demographic_id": "9ea1f795-9510-5acc-a9a5-bf1379e6635a",
"ethnicity": "not hispanic or latino",
"gender": "male",
"race": "white",
"vital_status": "Dead",
"age_at_index": 68,
"submitter_id": "TCGA-38-4629_demographic",
"days_to_death": 864,
"days_to_birth": -25104,
"state": "released",
"year_of_death": 2005,
"year_of_birth": 1935
}
}
},
"warnings": {}
}
Analysis Endpoints
In addition to the ssms, ssm_occurrences, and genes endpoints mentioned previously, several /analysis endpoints were designed to quickly retrieve specific datasets used for visualization display.
Example 1: The /analysis/top_cases_counts_by_genes endpoint gives the number of cases with a mutation in each gene listed in the gene_ids parameter for each project. Note that this endpoint cannot be used with the format or fields parameters. In this instance, the query will produce the number of cases in each projects with mutations in the gene ENSG00000155657.
curl "https://api.gdc.cancer.gov/analysis/top_cases_counts_by_genes?gene_ids=ENSG00000155657&pretty=true"
$ curl "https://api.gdc.cancer.gov/analysis/top_cases_counts_by_genes?gene_ids=ENSG00000155657&pretty=true"
{
"took": 6,
"timed_out": false,
"_shards": {
"total": 12,
"successful": 12,
"skipped": 0,
"failed": 0
},
"hits": {
"total": {
"value": 5967,
"relation": "eq"
},
"max_score": null,
"hits": []
},
"aggregations": {
"projects": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "TCGA-BRCA",
"doc_count": 425,
"genes": {
"doc_count": 4031450,
"my_genes": {
"doc_count": 425,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 425
}
]
}
}
}
},
{
"key": "TCGA-LUSC",
"doc_count": 423,
"genes": {
"doc_count": 4123089,
"my_genes": {
"doc_count": 423,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 423
}
]
}
}
}
},
{
"key": "CPTAC-3",
"doc_count": 421,
"genes": {
"doc_count": 251552,
"my_genes": {
"doc_count": 421,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 421
}
]
}
}
}
},
{
"key": "TCGA-SKCM",
"doc_count": 391,
"genes": {
"doc_count": 3040929,
"my_genes": {
"doc_count": 391,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 391
}
]
}
}
}
},
{
"key": "TCGA-LUAD",
"doc_count": 345,
"genes": {
"doc_count": 3188761,
"my_genes": {
"doc_count": 345,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 345
}
]
}
}
}
},
{
"key": "TCGA-OV",
"doc_count": 341,
"genes": {
"doc_count": 3728561,
"my_genes": {
"doc_count": 341,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 341
}
]
}
}
}
},
{
"key": "TCGA-STAD",
"doc_count": 300,
"genes": {
"doc_count": 2145783,
"my_genes": {
"doc_count": 300,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 300
}
]
}
}
}
},
{
"key": "TCGA-UCEC",
"doc_count": 297,
"genes": {
"doc_count": 1637055,
"my_genes": {
"doc_count": 297,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 297
}
]
}
}
}
},
{
"key": "TCGA-HNSC",
"doc_count": 293,
"genes": {
"doc_count": 2325617,
"my_genes": {
"doc_count": 293,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 293
}
]
}
}
}
},
{
"key": "TCGA-COAD",
"doc_count": 288,
"genes": {
"doc_count": 1695280,
"my_genes": {
"doc_count": 288,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 288
}
]
}
}
}
},
{
"key": "TCGA-BLCA",
"doc_count": 280,
"genes": {
"doc_count": 2466835,
"my_genes": {
"doc_count": 280,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 280
}
]
}
}
}
},
{
"key": "MMRF-COMMPASS",
"doc_count": 181,
"genes": {
"doc_count": 45977,
"my_genes": {
"doc_count": 181,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 181
}
]
}
}
}
},
{
"key": "TCGA-LIHC",
"doc_count": 167,
"genes": {
"doc_count": 1216775,
"my_genes": {
"doc_count": 167,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 167
}
]
}
}
}
},
{
"key": "TCGA-CESC",
"doc_count": 161,
"genes": {
"doc_count": 1103281,
"my_genes": {
"doc_count": 161,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 161
}
]
}
}
}
},
{
"key": "TCGA-KIRC",
"doc_count": 161,
"genes": {
"doc_count": 842546,
"my_genes": {
"doc_count": 161,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 161
}
]
}
}
}
},
{
"key": "CPTAC-2",
"doc_count": 131,
"genes": {
"doc_count": 72575,
"my_genes": {
"doc_count": 131,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 131
}
]
}
}
}
},
{
"key": "TCGA-GBM",
"doc_count": 131,
"genes": {
"doc_count": 756809,
"my_genes": {
"doc_count": 131,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 131
}
]
}
}
}
},
{
"key": "TCGA-ESCA",
"doc_count": 129,
"genes": {
"doc_count": 1210888,
"my_genes": {
"doc_count": 129,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 129
}
]
}
}
}
},
{
"key": "TCGA-PRAD",
"doc_count": 101,
"genes": {
"doc_count": 379949,
"my_genes": {
"doc_count": 101,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 101
}
]
}
}
}
},
{
"key": "HCMI-CMDC",
"doc_count": 99,
"genes": {
"doc_count": 54829,
"my_genes": {
"doc_count": 99,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 99
}
]
}
}
}
},
{
"key": "TCGA-READ",
"doc_count": 98,
"genes": {
"doc_count": 726313,
"my_genes": {
"doc_count": 98,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 98
}
]
}
}
}
},
{
"key": "TCGA-LGG",
"doc_count": 95,
"genes": {
"doc_count": 424689,
"my_genes": {
"doc_count": 95,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 95
}
]
}
}
}
},
{
"key": "TCGA-KIRP",
"doc_count": 93,
"genes": {
"doc_count": 521936,
"my_genes": {
"doc_count": 93,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 93
}
]
}
}
}
},
{
"key": "TCGA-SARC",
"doc_count": 93,
"genes": {
"doc_count": 903111,
"my_genes": {
"doc_count": 93,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 93
}
]
}
}
}
},
{
"key": "TCGA-TGCT",
"doc_count": 51,
"genes": {
"doc_count": 524456,
"my_genes": {
"doc_count": 51,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 51
}
]
}
}
}
},
{
"key": "TARGET-ALL-P2",
"doc_count": 50,
"genes": {
"doc_count": 1882,
"my_genes": {
"doc_count": 50,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 50
}
]
}
}
}
},
{
"key": "TCGA-KICH",
"doc_count": 43,
"genes": {
"doc_count": 353674,
"my_genes": {
"doc_count": 43,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 43
}
]
}
}
}
},
{
"key": "TCGA-PAAD",
"doc_count": 43,
"genes": {
"doc_count": 300427,
"my_genes": {
"doc_count": 43,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 43
}
]
}
}
}
},
{
"key": "CGCI-HTMCP-CC",
"doc_count": 37,
"genes": {
"doc_count": 3606,
"my_genes": {
"doc_count": 37,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 37
}
]
}
}
}
},
{
"key": "CDDP_EAGLE-1",
"doc_count": 32,
"genes": {
"doc_count": 16980,
"my_genes": {
"doc_count": 32,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 32
}
]
}
}
}
},
{
"key": "TCGA-ACC",
"doc_count": 29,
"genes": {
"doc_count": 283969,
"my_genes": {
"doc_count": 29,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 29
}
]
}
}
}
},
{
"key": "CMI-MBC",
"doc_count": 28,
"genes": {
"doc_count": 3581,
"my_genes": {
"doc_count": 28,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 28
}
]
}
}
}
},
{
"key": "TCGA-THCA",
"doc_count": 28,
"genes": {
"doc_count": 89120,
"my_genes": {
"doc_count": 28,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 28
}
]
}
}
}
},
{
"key": "TCGA-UCS",
"doc_count": 28,
"genes": {
"doc_count": 283673,
"my_genes": {
"doc_count": 28,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 28
}
]
}
}
}
},
{
"key": "TCGA-MESO",
"doc_count": 21,
"genes": {
"doc_count": 137002,
"my_genes": {
"doc_count": 21,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 21
}
]
}
}
}
},
{
"key": "TCGA-PCPG",
"doc_count": 19,
"genes": {
"doc_count": 99444,
"my_genes": {
"doc_count": 19,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 19
}
]
}
}
}
},
{
"key": "TARGET-NBL",
"doc_count": 15,
"genes": {
"doc_count": 829,
"my_genes": {
"doc_count": 15,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 15
}
]
}
}
}
},
{
"key": "TCGA-UVM",
"doc_count": 12,
"genes": {
"doc_count": 68201,
"my_genes": {
"doc_count": 12,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 12
}
]
}
}
}
},
{
"key": "EXCEPTIONAL_RESPONDERS-ER",
"doc_count": 11,
"genes": {
"doc_count": 10617,
"my_genes": {
"doc_count": 11,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 11
}
]
}
}
}
},
{
"key": "TCGA-THYM",
"doc_count": 11,
"genes": {
"doc_count": 59647,
"my_genes": {
"doc_count": 11,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 11
}
]
}
}
}
},
{
"key": "BEATAML1.0-COHORT",
"doc_count": 10,
"genes": {
"doc_count": 279,
"my_genes": {
"doc_count": 10,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 10
}
]
}
}
}
},
{
"key": "TARGET-OS",
"doc_count": 10,
"genes": {
"doc_count": 414,
"my_genes": {
"doc_count": 10,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 10
}
]
}
}
}
},
{
"key": "TCGA-LAML",
"doc_count": 10,
"genes": {
"doc_count": 10175,
"my_genes": {
"doc_count": 10,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 10
}
]
}
}
}
},
{
"key": "TCGA-DLBC",
"doc_count": 9,
"genes": {
"doc_count": 63497,
"my_genes": {
"doc_count": 9,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 9
}
]
}
}
}
},
{
"key": "TCGA-CHOL",
"doc_count": 8,
"genes": {
"doc_count": 52960,
"my_genes": {
"doc_count": 8,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 8
}
]
}
}
}
},
{
"key": "CMI-MPC",
"doc_count": 7,
"genes": {
"doc_count": 365,
"my_genes": {
"doc_count": 7,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 7
}
]
}
}
}
},
{
"key": "CMI-ASC",
"doc_count": 6,
"genes": {
"doc_count": 5745,
"my_genes": {
"doc_count": 6,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 6
}
]
}
}
}
},
{
"key": "TARGET-WT",
"doc_count": 3,
"genes": {
"doc_count": 51,
"my_genes": {
"doc_count": 3,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 3
}
]
}
}
}
},
{
"key": "TARGET-ALL-P3",
"doc_count": 2,
"genes": {
"doc_count": 66,
"my_genes": {
"doc_count": 2,
"gene_id": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "ENSG00000155657",
"doc_count": 2
}
]
}
}
}
}
]
}
}
ssms in the gene ENSG00000155657.
Example 2: The following demonstrates a use of the /analysis/top_mutated_genes_by_project endpoint. This will output the genes that are mutated in the most cases in "TCGA-DLBC" and will count the mutations that have a HIGH or MODERATE impact on gene function. Note that the score field does not represent the number of mutations in a given gene, but a calculation that is used to determine which genes have the greatest number of unique mutations.
{
"op":"AND",
"content":[
{
"op":"in",
"content":{
"field":"case.project.project_id",
"value":[
"TCGA-DLBC"
]
}
},
{
"op":"in",
"content":{
"field":"case.ssm.consequence.transcript.annotation.vep_impact",
"value":[
"HIGH",
"MODERATE"
]
}
}
]
}
curl "https://api.gdc.cancer.gov/analysis/top_mutated_genes_by_project?fields=gene_id,symbol&filters=%7B%20%20%0A%20%20%20%22op%22%3A%22AND%20%20%20%22content%22%3A%5B%20%20%0A%20%20%20%20%20%20%7B%20%20%0A%20%20%20%20%20%20%20%20%20%22op%22%3A%22in%22%2C%0A%20%20%20%20%20%20%20%20%20%22content%22%3A%7B%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%22field%22%3A%22case.project.project_id%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22value%22%3A%5B%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%22TCGA-DLBC%22%0A%20%20%20%20%20%20%20%20%20%20%20%20%5D%0A%20%20%20%20%20%20%20%20%20%7D%0A%20%20%20%20%20%20%7D%2C%0A%20%20%20%20%20%20%7B%20%20%0A%20%20%20%20%20%20%20%20%20%22op%22%3A%22in%22%2C%0A%20%20%20%20%20%20%20%20%20%22content%22%3A%7B%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%22field%22%3A%22case.ssm.consequence.transcript.annotation.vep_impact%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%22value%22%3A%5B%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%22HIGH%22%2C%0A%20%20%20%20%20%20%20%20%20%20%20%20%20%20%20%22MODERATE%22%0A%20%20%20%20%20%20%20%20%20%20%20%20%5D%0A%20%20%20%20%20%20%20%20%20%7D%0A%20%20%20%20%20%20%7D%0A%20%20%20%5D%0A%7D%0A&pretty=true"
{
"data": {
"hits": [
{
"symbol": "KMT2D",
"gene_id": "ENSG00000167548",
"_score": 13.0
},
{
"symbol": "BTG2",
"gene_id": "ENSG00000159388",
"_score": 13.0
},
{
"symbol": "B2M",
"gene_id": "ENSG00000166710",
"_score": 11.0
},
{
"symbol": "PIM1",
"gene_id": "ENSG00000137193",
"_score": 10.0
},
{
"symbol": "IGHG1",
"gene_id": "ENSG00000211896",
"_score": 10.0
},
{
"symbol": "CARD11",
"gene_id": "ENSG00000198286",
"_score": 10.0
},
{
"symbol": "H1-4",
"gene_id": "ENSG00000168298",
"_score": 9.0
},
{
"symbol": "PCLO",
"gene_id": "ENSG00000186472",
"_score": 9.0
},
{
"symbol": "IGHG2",
"gene_id": "ENSG00000211893",
"_score": 9.0
},
{
"symbol": "FAT4",
"gene_id": "ENSG00000196159",
"_score": 8.0
}
],
"pagination": {
"count": 10,
"total": 3500,
"size": 10,
"from": 0,
"sort": "None",
"page": 1,
"pages": 350
}
},
"warnings": {}
}
/analysis/top_mutated_cases_by_gene endpoint will generate information about the cases that are most affected by mutations in a given number of genes. Below, the file count for each category is given for the cases most affected by mutations in these 50 genes. The size of the output is limited to two cases with the size=2 parameter, but a higher value can be set by the user.
curl "https://api.gdc.cancer.gov/analysis/top_mutated_cases_by_gene?fields=diagnoses.age_at_diagnosis,diagnoses.primary_diagnosis,demographic.gender,demographic.race,demographic.ethnicity,case_id,summary.data_categories.file_count,summary.data_categories.data_category&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-DLBC%22%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22genes.gene_id%22%2C%22value%22%3A%5B%22ENSG00000166710%22%2C%22ENSG00000005339%22%2C%22ENSG00000083857%22%2C%22ENSG00000168769%22%2C%22ENSG00000100906%22%2C%22ENSG00000184677%22%2C%22ENSG00000101680%22%2C%22ENSG00000101266%22%2C%22ENSG00000028277%22%2C%22ENSG00000140968%22%2C%22ENSG00000181827%22%2C%22ENSG00000116815%22%2C%22ENSG00000275221%22%2C%22ENSG00000139083%22%2C%22ENSG00000112851%22%2C%22ENSG00000112697%22%2C%22ENSG00000164134%22%2C%22ENSG00000009413%22%2C%22ENSG00000071626%22%2C%22ENSG00000135407%22%2C%22ENSG00000101825%22%2C%22ENSG00000104814%22%2C%22ENSG00000166415%22%2C%22ENSG00000142867%22%2C%22ENSG00000254585%22%2C%22ENSG00000139718%22%2C%22ENSG00000077721%22%2C%22ENSG00000130294%22%2C%22ENSG00000117245%22%2C%22ENSG00000117318%22%2C%22ENSG00000270550%22%2C%22ENSG00000163637%22%2C%22ENSG00000166575%22%2C%22ENSG00000065526%22%2C%22ENSG00000156453%22%2C%22ENSG00000128191%22%2C%22ENSG00000055609%22%2C%22ENSG00000204469%22%2C%22ENSG00000187605%22%2C%22ENSG00000185875%22%2C%22ENSG00000110888%22%2C%22ENSG00000007341%22%2C%22ENSG00000173198%22%2C%22ENSG00000115568%22%2C%22ENSG00000163714%22%2C%22ENSG00000125772%22%2C%22ENSG00000080815%22%2C%22ENSG00000189079%22%2C%22ENSG00000120837%22%2C%22ENSG00000143951%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22ssms.consequence.transcript.annotation.vep_impact%22%2C%22value%22%3A%5B%22HIGH%22%5D%7D%7D%5D%7D&pretty=true&size=2"
{
"data": {
"hits": [
{
"summary": {
"data_categories": [
{
"file_count": 6,
"data_category": "Sequencing Reads"
},
{
"file_count": 14,
"data_category": "Biospecimen"
},
{
"file_count": 8,
"data_category": "Copy Number Variation"
},
{
"file_count": 16,
"data_category": "Simple Nucleotide Variation"
},
{
"file_count": 4,
"data_category": "Transcriptome Profiling"
},
{
"file_count": 3,
"data_category": "DNA Methylation"
},
{
"file_count": 8,
"data_category": "Clinical"
},
{
"file_count": 4,
"data_category": "Structural Variation"
},
{
"file_count": 1,
"data_category": "Proteome Profiling"
}
]
},
"case_id": "eda9496e-be80-4a13-bf06-89f0cc9e937f",
"diagnoses": [
{
"age_at_diagnosis": 18691,
"primary_diagnosis": "Malignant lymphoma, large B-cell, diffuse, NOS"
}
],
"demographic": {
"ethnicity": "hispanic or latino",
"gender": "male",
"race": "white"
},
"_score": 7.0
},
{
"summary": {
"data_categories": [
{
"file_count": 4,
"data_category": "Sequencing Reads"
},
{
"file_count": 13,
"data_category": "Biospecimen"
},
{
"file_count": 8,
"data_category": "Copy Number Variation"
},
{
"file_count": 16,
"data_category": "Simple Nucleotide Variation"
},
{
"file_count": 2,
"data_category": "Transcriptome Profiling"
},
{
"file_count": 3,
"data_category": "DNA Methylation"
},
{
"file_count": 8,
"data_category": "Clinical"
},
{
"file_count": 4,
"data_category": "Structural Variation"
}
]
},
"case_id": "7a589441-11ef-4158-87e7-3951d86bc2aa",
"diagnoses": [
{
"age_at_diagnosis": 20812,
"primary_diagnosis": "Malignant lymphoma, large B-cell, diffuse, NOS"
}
],
"demographic": {
"ethnicity": "not hispanic or latino",
"gender": "female",
"race": "white"
},
"_score": 4.0
}
],
"pagination": {
"count": 2,
"total": 32,
"size": 2,
"from": 0,
"sort": "None",
"page": 1,
"pages": 16
}
},
"warnings": {}
}
/analysis/mutated_cases_count_by_project endpoint produces counts for the number of cases that have associated ssm data in each project. The number of affected cases can be found under "case_with_ssm": {"doc_count": $case_count}.
curl "https://api.gdc.cancer.gov/analysis/mutated_cases_count_by_project?size=0&pretty=true"
{
"took": 8,
"timed_out": false,
"_shards": {
"total": 12,
"successful": 12,
"skipped": 0,
"failed": 0
},
"hits": {
"total": {
"value": 86962,
"relation": "eq"
},
"max_score": null,
"hits": []
},
"aggregations": {
"projects": {
"doc_count_error_upper_bound": 0,
"sum_other_doc_count": 0,
"buckets": [
{
"key": "FM-AD",
"doc_count": 18004,
"case_summary": {
"doc_count": 54012,
"case_with_ssm": {
"doc_count": 18004
}
}
},
{
"key": "GENIE-MSK",
"doc_count": 16824,
"case_summary": {
"doc_count": 36470,
"case_with_ssm": {
"doc_count": 16823
}
}
},
{
"key": "GENIE-DFCI",
"doc_count": 14232,
"case_summary": {
"doc_count": 28464,
"case_with_ssm": {
"doc_count": 14232
}
}
},
{
"key": "GENIE-MDA",
"doc_count": 3857,
"case_summary": {
"doc_count": 3857,
"case_with_ssm": {
"doc_count": 3857
}
}
},
{
"key": "GENIE-JHU",
"doc_count": 3320,
"case_summary": {
"doc_count": 3320,
"case_with_ssm": {
"doc_count": 3320
}
}
},
{
"key": "GENIE-UHN",
"doc_count": 2632,
"case_summary": {
"doc_count": 2632,
"case_with_ssm": {
"doc_count": 2632
}
}
},
{
"key": "TARGET-AML",
"doc_count": 2492,
"case_summary": {
"doc_count": 10671,
"case_with_ssm": {
"doc_count": 22
}
}
},
{
"key": "GENIE-VICC",
"doc_count": 2052,
"case_summary": {
"doc_count": 3833,
"case_with_ssm": {
"doc_count": 2052
}
}
},
{
"key": "TARGET-ALL-P2",
"doc_count": 1587,
"case_summary": {
"doc_count": 6114,
"case_with_ssm": {
"doc_count": 717
}
}
},
{
"key": "CPTAC-3",
"doc_count": 1185,
"case_summary": {
"doc_count": 8162,
"case_with_ssm": {
"doc_count": 1169
}
}
},
{
"key": "TARGET-NBL",
"doc_count": 1132,
"case_summary": {
"doc_count": 3284,
"case_with_ssm": {
"doc_count": 220
}
}
},
{
"key": "TCGA-BRCA",
"doc_count": 1098,
"case_summary": {
"doc_count": 9660,
"case_with_ssm": {
"doc_count": 1098
}
}
},
{
"key": "GENIE-GRCC",
"doc_count": 1038,
"case_summary": {
"doc_count": 1038,
"case_with_ssm": {
"doc_count": 1038
}
}
},
{
"key": "MMRF-COMMPASS",
"doc_count": 995,
"case_summary": {
"doc_count": 3528,
"case_with_ssm": {
"doc_count": 959
}
}
},
{
"key": "BEATAML1.0-COHORT",
"doc_count": 826,
"case_summary": {
"doc_count": 2576,
"case_with_ssm": {
"doc_count": 444
}
}
},
{
"key": "GENIE-NKI",
"doc_count": 801,
"case_summary": {
"doc_count": 801,
"case_with_ssm": {
"doc_count": 801
}
}
},
{
"key": "TARGET-WT",
"doc_count": 652,
"case_summary": {
"doc_count": 1931,
"case_with_ssm": {
"doc_count": 39
}
}
},
{
"key": "TCGA-GBM",
"doc_count": 617,
"case_summary": {
"doc_count": 3840,
"case_with_ssm": {
"doc_count": 600
}
}
},
{
"key": "TCGA-OV",
"doc_count": 608,
"case_summary": {
"doc_count": 4927,
"case_with_ssm": {
"doc_count": 599
}
}
},
{
"key": "TCGA-LUAD",
"doc_count": 585,
"case_summary": {
"doc_count": 4821,
"case_with_ssm": {
"doc_count": 571
}
}
},
{
"key": "TCGA-UCEC",
"doc_count": 560,
"case_summary": {
"doc_count": 4551,
"case_with_ssm": {
"doc_count": 558
}
}
},
{
"key": "TCGA-KIRC",
"doc_count": 537,
"case_summary": {
"doc_count": 4757,
"case_with_ssm": {
"doc_count": 534
}
}
},
{
"key": "TCGA-HNSC",
"doc_count": 528,
"case_summary": {
"doc_count": 4569,
"case_with_ssm": {
"doc_count": 528
}
}
},
{
"key": "TCGA-LGG",
"doc_count": 516,
"case_summary": {
"doc_count": 4557,
"case_with_ssm": {
"doc_count": 516
}
}
},
{
"key": "TCGA-THCA",
"doc_count": 507,
"case_summary": {
"doc_count": 4429,
"case_with_ssm": {
"doc_count": 507
}
}
},
{
"key": "TCGA-LUSC",
"doc_count": 504,
"case_summary": {
"doc_count": 4356,
"case_with_ssm": {
"doc_count": 504
}
}
},
{
"key": "TCGA-PRAD",
"doc_count": 500,
"case_summary": {
"doc_count": 4341,
"case_with_ssm": {
"doc_count": 500
}
}
},
{
"key": "NCICCR-DLBCL",
"doc_count": 489,
"case_summary": {
"doc_count": 1451,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "TCGA-SKCM",
"doc_count": 470,
"case_summary": {
"doc_count": 4108,
"case_with_ssm": {
"doc_count": 470
}
}
},
{
"key": "TCGA-COAD",
"doc_count": 461,
"case_summary": {
"doc_count": 3868,
"case_with_ssm": {
"doc_count": 461
}
}
},
{
"key": "TCGA-STAD",
"doc_count": 443,
"case_summary": {
"doc_count": 3869,
"case_with_ssm": {
"doc_count": 443
}
}
},
{
"key": "REBC-THYR",
"doc_count": 440,
"case_summary": {
"doc_count": 2456,
"case_with_ssm": {
"doc_count": 380
}
}
},
{
"key": "TCGA-BLCA",
"doc_count": 412,
"case_summary": {
"doc_count": 3633,
"case_with_ssm": {
"doc_count": 412
}
}
},
{
"key": "TARGET-OS",
"doc_count": 383,
"case_summary": {
"doc_count": 1362,
"case_with_ssm": {
"doc_count": 97
}
}
},
{
"key": "TCGA-LIHC",
"doc_count": 377,
"case_summary": {
"doc_count": 3193,
"case_with_ssm": {
"doc_count": 377
}
}
},
{
"key": "CPTAC-2",
"doc_count": 342,
"case_summary": {
"doc_count": 1349,
"case_with_ssm": {
"doc_count": 328
}
}
},
{
"key": "TRIO-CRU",
"doc_count": 339,
"case_summary": {
"doc_count": 339,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "TCGA-CESC",
"doc_count": 307,
"case_summary": {
"doc_count": 2621,
"case_with_ssm": {
"doc_count": 306
}
}
},
{
"key": "TCGA-KIRP",
"doc_count": 291,
"case_summary": {
"doc_count": 2541,
"case_with_ssm": {
"doc_count": 291
}
}
},
{
"key": "TCGA-SARC",
"doc_count": 261,
"case_summary": {
"doc_count": 2309,
"case_with_ssm": {
"doc_count": 261
}
}
},
{
"key": "HCMI-CMDC",
"doc_count": 228,
"case_summary": {
"doc_count": 1973,
"case_with_ssm": {
"doc_count": 227
}
}
},
{
"key": "CGCI-HTMCP-CC",
"doc_count": 212,
"case_summary": {
"doc_count": 1447,
"case_with_ssm": {
"doc_count": 205
}
}
},
{
"key": "CMI-MBC",
"doc_count": 200,
"case_summary": {
"doc_count": 653,
"case_with_ssm": {
"doc_count": 174
}
}
},
{
"key": "TCGA-LAML",
"doc_count": 200,
"case_summary": {
"doc_count": 1533,
"case_with_ssm": {
"doc_count": 200
}
}
},
{
"key": "TARGET-ALL-P3",
"doc_count": 191,
"case_summary": {
"doc_count": 783,
"case_with_ssm": {
"doc_count": 87
}
}
},
{
"key": "TCGA-ESCA",
"doc_count": 185,
"case_summary": {
"doc_count": 1605,
"case_with_ssm": {
"doc_count": 185
}
}
},
{
"key": "TCGA-PAAD",
"doc_count": 185,
"case_summary": {
"doc_count": 1585,
"case_with_ssm": {
"doc_count": 185
}
}
},
{
"key": "TCGA-PCPG",
"doc_count": 179,
"case_summary": {
"doc_count": 1512,
"case_with_ssm": {
"doc_count": 179
}
}
},
{
"key": "OHSU-CNL",
"doc_count": 176,
"case_summary": {
"doc_count": 336,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "TCGA-READ",
"doc_count": 172,
"case_summary": {
"doc_count": 1414,
"case_with_ssm": {
"doc_count": 171
}
}
},
{
"key": "TCGA-TGCT",
"doc_count": 150,
"case_summary": {
"doc_count": 1318,
"case_with_ssm": {
"doc_count": 150
}
}
},
{
"key": "TCGA-THYM",
"doc_count": 124,
"case_summary": {
"doc_count": 1078,
"case_with_ssm": {
"doc_count": 124
}
}
},
{
"key": "CGCI-BLGSP",
"doc_count": 120,
"case_summary": {
"doc_count": 804,
"case_with_ssm": {
"doc_count": 74
}
}
},
{
"key": "TCGA-KICH",
"doc_count": 113,
"case_summary": {
"doc_count": 685,
"case_with_ssm": {
"doc_count": 66
}
}
},
{
"key": "WCDT-MCRPC",
"doc_count": 101,
"case_summary": {
"doc_count": 299,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "TCGA-ACC",
"doc_count": 92,
"case_summary": {
"doc_count": 745,
"case_with_ssm": {
"doc_count": 92
}
}
},
{
"key": "APOLLO-LUAD",
"doc_count": 87,
"case_summary": {
"doc_count": 510,
"case_with_ssm": {
"doc_count": 83
}
}
},
{
"key": "TCGA-MESO",
"doc_count": 87,
"case_summary": {
"doc_count": 758,
"case_with_ssm": {
"doc_count": 87
}
}
},
{
"key": "EXCEPTIONAL_RESPONDERS-ER",
"doc_count": 84,
"case_summary": {
"doc_count": 412,
"case_with_ssm": {
"doc_count": 20
}
}
},
{
"key": "TCGA-UVM",
"doc_count": 80,
"case_summary": {
"doc_count": 652,
"case_with_ssm": {
"doc_count": 80
}
}
},
{
"key": "ORGANOID-PANCREATIC",
"doc_count": 70,
"case_summary": {
"doc_count": 226,
"case_with_ssm": {
"doc_count": 58
}
}
},
{
"key": "TARGET-RT",
"doc_count": 69,
"case_summary": {
"doc_count": 404,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "CMI-MPC",
"doc_count": 63,
"case_summary": {
"doc_count": 199,
"case_with_ssm": {
"doc_count": 60
}
}
},
{
"key": "TCGA-DLBC",
"doc_count": 58,
"case_summary": {
"doc_count": 441,
"case_with_ssm": {
"doc_count": 50
}
}
},
{
"key": "TCGA-UCS",
"doc_count": 57,
"case_summary": {
"doc_count": 504,
"case_with_ssm": {
"doc_count": 57
}
}
},
{
"key": "BEATAML1.0-CRENOLANIB",
"doc_count": 56,
"case_summary": {
"doc_count": 108,
"case_with_ssm": {
"doc_count": 52
}
}
},
{
"key": "MP2PRT-WT",
"doc_count": 52,
"case_summary": {
"doc_count": 361,
"case_with_ssm": {
"doc_count": 51
}
}
},
{
"key": "TCGA-CHOL",
"doc_count": 51,
"case_summary": {
"doc_count": 378,
"case_with_ssm": {
"doc_count": 51
}
}
},
{
"key": "CDDP_EAGLE-1",
"doc_count": 50,
"case_summary": {
"doc_count": 384,
"case_with_ssm": {
"doc_count": 50
}
}
},
{
"key": "CTSP-DLBCL1",
"doc_count": 45,
"case_summary": {
"doc_count": 201,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "CGCI-HTMCP-LC",
"doc_count": 39,
"case_summary": {
"doc_count": 292,
"case_with_ssm": {
"doc_count": 34
}
}
},
{
"key": "CMI-ASC",
"doc_count": 36,
"case_summary": {
"doc_count": 124,
"case_with_ssm": {
"doc_count": 36
}
}
},
{
"key": "MATCH-Z1D",
"doc_count": 36,
"case_summary": {
"doc_count": 212,
"case_with_ssm": {
"doc_count": 34
}
}
},
{
"key": "MATCH-Q",
"doc_count": 35,
"case_summary": {
"doc_count": 203,
"case_with_ssm": {
"doc_count": 34
}
}
},
{
"key": "MATCH-Y",
"doc_count": 31,
"case_summary": {
"doc_count": 181,
"case_with_ssm": {
"doc_count": 30
}
}
},
{
"key": "TARGET-ALL-P1",
"doc_count": 24,
"case_summary": {
"doc_count": 62,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "TARGET-CCSK",
"doc_count": 13,
"case_summary": {
"doc_count": 100,
"case_with_ssm": {
"doc_count": 0
}
}
},
{
"key": "VAREPOP-APOLLO",
"doc_count": 7,
"case_summary": {
"doc_count": 14,
"case_with_ssm": {
"doc_count": 7
}
}
}
]
}
}
}
Survival Analysis Endpoint
Survival plots are generated for different subsets of data, based on variants or projects, in the GDC Data Portal. The /analysis/survival endpoint can be used to programmatically retrieve the raw data used to generate these plots and apply different filters. Note that the fields and format parameters cannot be modified.
Example 1: A user wants to download data to generate a survival plot for cases from the project TCGA-DLBC.
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-DLBC%22%7D%7D%5D&pretty=true"
{
"results": [
{
"meta": {
"id": 139834474037000
},
"donors": [
{
"time": 1.0,
"censored": true,
"survivalEstimate": 1,
"id": "dc87a809-95de-4eb7-a1c2-2650475f2d7e",
"submitter_id": "TCGA-RQ-A6JB",
"project_id": "TCGA-DLBC"
},
{
"time": 17.0,
"censored": true,
"survivalEstimate": 1,
"id": "4dd86ebd-ef16-4b2b-9ea0-5d1d7afef257",
"submitter_id": "TCGA-RQ-AAAT",
"project_id": "TCGA-DLBC"
},
{
"time": 58,
"censored": false,
"survivalEstimate": 1,
"id": "0bf573ac-cd1e-42d8-90cf-b30d7b08679c",
"submitter_id": "TCGA-FA-A6HN",
"project_id": "TCGA-DLBC"
},
{
"time": 126.0,
"censored": true,
"survivalEstimate": 0.9777777777777777,
"id": "f978cb0f-d319-4c01-b4c5-23ae1403a106",
"submitter_id": "TCGA-FF-8047",
"project_id": "TCGA-DLBC"
},
{
"time": 132.0,
"censored": true,
"survivalEstimate": 0.9777777777777777,
"id": "1843c82e-7a35-474f-9f79-c0a9af9aa09c",
"submitter_id": "TCGA-FA-A4BB",
"project_id": "TCGA-DLBC"
},
{
"time": 132.0,
"censored": true,
"survivalEstimate": 0.9777777777777777,
"id": "a43e5f0e-a21f-48d8-97e0-084d413680b7",
"submitter_id": "TCGA-FA-8693",
"project_id": "TCGA-DLBC"
},
{
"time": 248,
"censored": false,
"survivalEstimate": 0.9777777777777777,
"id": "0030a28c-81aa-44b0-8be0-b35e1dcbf98c",
"submitter_id": "TCGA-FA-A7Q1",
"project_id": "TCGA-DLBC"
},
{
"time": 298.0,
"censored": true,
"survivalEstimate": 0.9539295392953929,
"id": "f553f1a9-ecf2-4783-a609-6adca7c4c597",
"submitter_id": "TCGA-FF-A7CQ",
"project_id": "TCGA-DLBC"
},
{
"time": 313,
"censored": false,
"survivalEstimate": 0.9539295392953929,
"id": "f784bc3a-751b-4025-aab2-0af2f6f24266",
"submitter_id": "TCGA-FF-A7CR",
"project_id": "TCGA-DLBC"
},
{
"time": 385.0,
"censored": true,
"survivalEstimate": 0.929469807518588,
"id": "29e3d122-15a1-4235-a356-b1a9f94ceb39",
"submitter_id": "TCGA-FF-A7CX",
"project_id": "TCGA-DLBC"
},
{
"time": 391,
"censored": false,
"survivalEstimate": 0.929469807518588,
"id": "0e251c03-bf86-4ed8-b45d-3cbc97160502",
"submitter_id": "TCGA-GS-A9U4",
"project_id": "TCGA-DLBC"
},
{
"time": 427.0,
"censored": true,
"survivalEstimate": 0.9043490019099776,
"id": "e6365b38-bc44-400c-b4aa-18ce8ff5bfce",
"submitter_id": "TCGA-FA-A82F",
"project_id": "TCGA-DLBC"
},
{
"time": 553.0,
"censored": true,
"survivalEstimate": 0.9043490019099776,
"id": "b56bdbdb-43af-4a03-a072-54dd22d7550c",
"submitter_id": "TCGA-FA-A86F",
"project_id": "TCGA-DLBC"
},
{
"time": 595,
"censored": false,
"survivalEstimate": 0.9043490019099776,
"id": "31bbad4e-3789-42ec-9faa-1cb86970f723",
"submitter_id": "TCGA-G8-6907",
"project_id": "TCGA-DLBC"
},
{
"time": 679.0,
"censored": true,
"survivalEstimate": 0.8777505018538018,
"id": "0e9fcccc-0630-408d-a121-2c6413824cb7",
"submitter_id": "TCGA-FF-8062",
"project_id": "TCGA-DLBC"
},
{
"time": 708,
"censored": false,
"survivalEstimate": 0.8777505018538018,
"id": "a5b188f0-a6d3-4d4a-b04f-36d47ec05338",
"submitter_id": "TCGA-FA-A4XK",
"project_id": "TCGA-DLBC"
},
{
"time": 719.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "ed746cb9-0f2f-48ce-923a-3a9f9f00b331",
"submitter_id": "TCGA-FA-A7DS",
"project_id": "TCGA-DLBC"
},
{
"time": 730.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "c85f340e-584b-4f3b-b6a5-540491fc8ad2",
"submitter_id": "TCGA-GS-A9TV",
"project_id": "TCGA-DLBC"
},
{
"time": 749.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "69f23725-adca-48ac-9b33-80a7aae24cfe",
"submitter_id": "TCGA-FA-A6HO",
"project_id": "TCGA-DLBC"
},
{
"time": 751.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "67325322-483f-443f-9ffa-2a20d108a2fb",
"submitter_id": "TCGA-FF-8046",
"project_id": "TCGA-DLBC"
},
{
"time": 765.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "eda9496e-be80-4a13-bf06-89f0cc9e937f",
"submitter_id": "TCGA-GS-A9TZ",
"project_id": "TCGA-DLBC"
},
{
"time": 788.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "25ff86af-beb4-480c-b706-f3fe0306f7cf",
"submitter_id": "TCGA-RQ-A68N",
"project_id": "TCGA-DLBC"
},
{
"time": 791.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "1d0db5d7-39ca-466d-96b3-0d278c5ea768",
"submitter_id": "TCGA-FF-A7CW",
"project_id": "TCGA-DLBC"
},
{
"time": 832.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "c8cde9ea-89e9-4ee8-8a46-417a48f6d3ab",
"submitter_id": "TCGA-FF-8061",
"project_id": "TCGA-DLBC"
},
{
"time": 946.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "f0a326d2-1f3e-4a5d-bca8-32aaccc52338",
"submitter_id": "TCGA-FF-8042",
"project_id": "TCGA-DLBC"
},
{
"time": 965.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "a8e2df1e-4042-42af-9231-3a00e83489f0",
"submitter_id": "TCGA-FF-8043",
"project_id": "TCGA-DLBC"
},
{
"time": 972.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "e56e4d9c-052e-4ec6-a81b-dbd53e9c8ffe",
"submitter_id": "TCGA-FM-8000",
"project_id": "TCGA-DLBC"
},
{
"time": 982.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "45b0cf9f-a879-417f-8f39-7770552252c0",
"submitter_id": "TCGA-GS-A9TQ",
"project_id": "TCGA-DLBC"
},
{
"time": 1081.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "1f971af1-6772-4fe6-8d35-bbe527a037fe",
"submitter_id": "TCGA-FF-8041",
"project_id": "TCGA-DLBC"
},
{
"time": 1163.0,
"censored": true,
"survivalEstimate": 0.8503207986708705,
"id": "33365d22-cb83-4d8e-a2d1-06b675f75f6e",
"submitter_id": "TCGA-GS-A9TT",
"project_id": "TCGA-DLBC"
},
{
"time": 1252,
"censored": false,
"survivalEstimate": 0.8503207986708705,
"id": "6a21c948-cd85-4150-8c01-83017d7dc1ed",
"submitter_id": "TCGA-G8-6324",
"project_id": "TCGA-DLBC"
},
{
"time": 1299.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "f855dad1-6ffc-493e-ba6c-970874bc9210",
"submitter_id": "TCGA-GR-A4D5",
"project_id": "TCGA-DLBC"
},
{
"time": 1334.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "c1c06604-5ae2-4a53-b9c0-eb210d38e3f0",
"submitter_id": "TCGA-GR-A4D6",
"project_id": "TCGA-DLBC"
},
{
"time": 1373.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "58e66976-4507-4552-ac53-83a49a142dde",
"submitter_id": "TCGA-GS-A9TX",
"project_id": "TCGA-DLBC"
},
{
"time": 1581.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "ea54dbad-1b23-41cc-9378-d4002a8fca51",
"submitter_id": "TCGA-G8-6325",
"project_id": "TCGA-DLBC"
},
{
"time": 1581.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "d7df78b5-24f1-4ff4-bd9b-f0e6bec8289a",
"submitter_id": "TCGA-GR-A4D4",
"project_id": "TCGA-DLBC"
},
{
"time": 1617.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "29aff186-c321-4ff9-b81b-105e27e620ff",
"submitter_id": "TCGA-GS-A9TW",
"project_id": "TCGA-DLBC"
},
{
"time": 1739.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "5eff68ff-f6c3-40c9-9fc8-00e684a7b712",
"submitter_id": "TCGA-GR-A4D9",
"project_id": "TCGA-DLBC"
},
{
"time": 2131.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "f8cf647b-1447-4ac3-8c43-bef07765cabf",
"submitter_id": "TCGA-G8-6326",
"project_id": "TCGA-DLBC"
},
{
"time": 2616.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "6e9437f0-a4ed-475c-ab0e-bf1431c70a90",
"submitter_id": "TCGA-GS-A9TY",
"project_id": "TCGA-DLBC"
},
{
"time": 2983.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "c3d662ee-48d0-454a-bb0c-77d3338d3747",
"submitter_id": "TCGA-GR-7353",
"project_id": "TCGA-DLBC"
},
{
"time": 3394.0,
"censored": true,
"survivalEstimate": 0.8003019281608192,
"id": "fdecb74f-ac4e-46b1-b23a-5f7fde96ef9f",
"submitter_id": "TCGA-GS-A9U3",
"project_id": "TCGA-DLBC"
},
{
"time": 3553,
"censored": false,
"survivalEstimate": 0.8003019281608192,
"id": "a468e725-ad4b-411d-ac5c-2eacc68ec580",
"submitter_id": "TCGA-G8-6909",
"project_id": "TCGA-DLBC"
},
{
"time": 3897.0,
"censored": true,
"survivalEstimate": 0.6402415425286554,
"id": "1ea575f1-f731-408b-a629-f5f4abab569e",
"submitter_id": "TCGA-GS-A9TU",
"project_id": "TCGA-DLBC"
},
{
"time": 4578.0,
"censored": true,
"survivalEstimate": 0.6402415425286554,
"id": "7a589441-11ef-4158-87e7-3951d86bc2aa",
"submitter_id": "TCGA-GR-7351",
"project_id": "TCGA-DLBC"
},
{
"time": 5980.0,
"censored": true,
"survivalEstimate": 0.6402415425286554,
"id": "3622cf29-600f-4410-84d4-a9afeb41c475",
"submitter_id": "TCGA-G8-6914",
"project_id": "TCGA-DLBC"
},
{
"time": 6425,
"censored": false,
"survivalEstimate": 0.6402415425286554,
"id": "3f5a897d-1eaa-4d4c-8324-27ac07c90927",
"submitter_id": "TCGA-G8-6906",
"project_id": "TCGA-DLBC"
}
]
}
],
"overallStats": {}
}
chr3:g.179234297A>G) and the other plot will display information about cases without that mutation. This type of query will also print the results of a chi-squared analysis between the two subsets of cases.
[
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"=",
"content":{
"field":"gene.ssm.ssm_id",
"value":"edd1ae2c-3ca9-52bd-a124-b09ed304fcc2"
}
}
]
},
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"excludeifany",
"content":{
"field":"gene.ssm.ssm_id",
"value":"edd1ae2c-3ca9-52bd-a124-b09ed304fcc2"
}
}
]
}
]
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-BRCA%22%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22gene.ssm.ssm_id%22%2C%22value%22%3A%22edd1ae2c-3ca9-52bd-a124-b09ed304fcc2%22%7D%7D%5D%7D%2C%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%22TCGA-BRCA%22%7D%7D%2C%7B%22op%22%3A%22excludeifany%22%2C%22content%22%3A%7B%22field%22%3A%22gene.ssm.ssm_id%22%2C%22value%22%3A%22edd1ae2c-3ca9-52bd-a124-b09ed304fcc2%22%7D%7D%5D%7D%5D&pretty=true"
{
"overallStats": {
"degreesFreedom": 1,
"chiSquared": 0.8577589072612264,
"pValue": 0.35436660628146011
},
"results": [
{
"donors": [
{
"survivalEstimate": 1,
"id": "a991644b-3ee6-4cda-acf0-e37de48a49fc",
"censored": true,
"time": 10
},
{
"survivalEstimate": 1,
"id": "2e1e3bf0-1708-4b65-936c-48b89eb8966a",
"censored": true,
"time": 19
},
(truncated)
],
"meta": {
"id": 140055251282040
}
},
{
"donors": [
{
"survivalEstimate": 1,
"id": "5e4187c9-98f8-4bdb-a8da-6a914e96f47a",
"censored": true,
"time": -31
},
(truncated)
donors tag. One set of coordinates will generate a survival plot representing TCGA-BRCA cases that have the mutation of interest and the other will generate a survival plot for the remaining cases in TCGA-BRCA.
Example 3: Custom survival plots can be generated using the GDC API. For example, a user could generate survival plot data comparing patients with a mutation in genes associated with a biological pathway with patients without mutations in that pathway. The following example compares a patient with at least one mutation in either gene ENSG00000141510 or ENSG00000155657 with patients that do not have mutations in these genes.
[
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"=",
"content":{
"field":"gene.gene_id",
"value":["ENSG00000141510","ENSG00000155657"]
}
}
]
},
{
"op":"and",
"content":[
{
"op":"=",
"content":{
"field":"cases.project.project_id",
"value":"TCGA-BRCA"
}
},
{
"op":"excludeifany",
"content":{
"field":"gene.gene_id",
"value":["ENSG00000141510","ENSG00000155657"]
}
}
]
}
]
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%0D%0A%7B%0D%0A%22op%22%3A%22and%22%2C%0D%0A%22content%22%3A%5B%0D%0A%7B%0D%0A%22op%22%3A%22%3D%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22cases.project.project_id%22%2C%0D%0A%22value%22%3A%22TCGA-BRCA%22%0D%0A%7D%0D%0A%7D%2C%0D%0A%7B%0D%0A%22op%22%3A%22%3D%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22gene.gene_id%22%2C%0D%0A%22value%22%3A%5B%22ENSG00000141510%22%2C%22ENSG00000155657%22%5D%0D%0A%7D%0D%0A%7D%0D%0A%5D%0D%0A%7D%2C%0D%0A%7B%0D%0A%22op%22%3A%22and%22%2C%0D%0A%22content%22%3A%5B%0D%0A%7B%0D%0A%22op%22%3A%22%3D%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22cases.project.project_id%22%2C%0D%0A%22value%22%3A%22TCGA-BRCA%22%0D%0A%7D%0D%0A%7D%2C%0D%0A%7B%0D%0A%22op%22%3A%22excludeifany%22%2C%0D%0A%22content%22%3A%7B%0D%0A%22field%22%3A%22gene.gene_id%22%2C%0D%0A%22value%22%3A%5B%22ENSG00000141510%22%2C%22ENSG00000155657%22%5D%0D%0A%7D%0D%0A%7D%0D%0A%5D%0D%0A%7D%0D%0A%5D&pretty=true"
[{
"op":"=",
"content":{
"field":"cases.submitter_id",
"value":["TCGA-HT-A74J","TCGA-43-A56U","TCGA-GM-A3XL","TCGA-A1-A0SQ","TCGA-K1-A6RV","TCGA-J2-A4AD","TCGA-XR-A8TE"]
}
},
{
"op":"=",
"content":{
"field":"cases.submitter_id",
"value":["TCGA-55-5899","TCGA-55-6642","TCGA-55-7907","TCGA-67-6216","TCGA-75-5146","TCGA-49-4510","TCGA-78-7159"]
}
}]
curl "https://api.gdc.cancer.gov/analysis/survival?filters=%5B%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-HT-A74J%22%2C%22TCGA-43-A56U%22%2C%22TCGA-GM-A3XL%22%2C%22TCGA-A1-A0SQ%22%2C%22TCGA-K1-A6RV%22%2C%22TCGA-J2-A4AD%22%2C%22TCGA-XR-A8TE%22%5D%7D%7D%2C%7B%22op%22%3A%22%3D%22%2C%22content%22%3A%7B%22field%22%3A%22cases.submitter_id%22%2C%22value%22%3A%5B%22TCGA-55-5899%22%2C%22TCGA-55-6642%22%2C%22TCGA-55-7907%22%2C%22TCGA-67-6216%22%2C%22TCGA-75-5146%22%2C%22TCGA-49-4510%22%2C%22TCGA-78-7159%22%5D%7D%7D%5D"