{"id":"gdc-rebc-thyr","title":"Comprehensive genomic characterization of radiation-related papillary thyroid cancer in the Ukraine","short_title":"REBC-THYR","aliases":["REBC-THYR"],"summary":"This cohort characterises papillary thyroid carcinoma arising in people who were children or in utero in Ukraine at the time of the 1986 Chernobyl accident, and it exists because no comparable exposure can ethically be reconstructed. Whole genome sequencing is available on 395 cases, RNA sequencing on 438 and microRNA on 437. The scientific question it was built for - what radiation does to a genome, and whether the resulting tumors differ mechanistically from sporadic ones - is answerable here and almost nowhere else.\nIt is also an object lesson in why a catalog entry is not enough. The harmonized clinical records report a median follow-up of 115 months - but that median rests on just 12 of the 449 cases. They also record vital status for 440 of 449 cases as \"not reported\". A researcher who selected this dataset on the strength of its follow-up figure would discover only after obtaining access that no survival analysis is possible, and that the follow-up figure itself rests on under 3% of the cohort.","one_liner":"449 papillary thyroid carcinomas from Ukrainians exposed to Chernobyl fallout as children - an irreplaceable radiation-exposure cohort with essentially no clinical annotation and no usable outcome data at all.","identifiers":[{"scheme":"gdc_project_id","value":"REBC-THYR","url":"https://portal.gdc.cancer.gov/projects/REBC-THYR","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.gdc.cancer.gov/projects/REBC-THYR?expand=summary,summary.data_categories,summary.experimental_strategies,program","source_label":"GDC API 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Not machine-generated."}]},{"question":"Do radiation-associated papillary thyroid carcinomas differ transcriptionally from sporadic ones, and can a classifier separate them?","rationale":"RNA sequencing on 438 cases and microRNA on 437 gives a well-powered expression cohort. TCGA-THCA provides a 507-case sporadic comparison group in the same repository with the same harmonization, which makes a cross-cohort contrast unusually tractable.","required_fields":[],"required_modalities":["rna_seq","mirna"],"feasibility":"needs_linkage","approx_n":437,"statistical_note":"Batch and platform differences between this cohort and TCGA-THCA are confounded with the exposure of interest. Any classifier must be evaluated with that confound stated, ideally with a batch-aware design rather than naive merging.","exemplar_pmid":null,"topics":["expression","radiation-carcinogenesis","classifier-validation"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"question":"Does age at exposure shape the resulting tumor genome, given that participants were children or in utero at the time?","rationale":"The cohort's defining feature is exposure during a developmental window. Age variables together with the genomic data allow the question to be posed, and it is one of the few human settings where exposure timing is externally fixed by a single dated event rather than self-reported.","required_fields":[],"required_modalities":["wgs","rna_seq"],"feasibility":"needs_access","approx_n":395,"statistical_note":"Age at diagnosis is not summarized in the harmonized records for this project, so age variables must be obtained through controlled access before this can be designed.","exemplar_pmid":null,"topics":["radiation-carcinogenesis","developmental-exposure"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"question":"Can microRNA profiles discriminate radiation-associated thyroid tumors, as a cheaper assay than whole genome sequencing for future screening cohorts?","rationale":"microRNA data exist on 437 of 449 cases, an unusually complete layer, and microRNA assays are far more tractable in resource-limited screening settings than sequencing.","required_fields":[],"required_modalities":["mirna"],"feasibility":"needs_access","approx_n":437,"statistical_note":null,"exemplar_pmid":null,"topics":["biomarkers","screening"],"evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. 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Contact the submitting investigators through the dbGaP study page if outcome data are essential to your question, and do not plan the analysis on the assumption that they will be released.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"missing_data","statement":"Individual reconstructed radiation dose is not present in the harmonized clinical records, although it is the variable that distinguishes this cohort from any other thyroid cancer resource and is analyzed in the marker paper.","severity":"blocking","affected_analyses":["Dose-response modeling","Any claim about radiation dose thresholds"],"mitigation":"Request the full phenotype file through dbGaP. Until you hold it, treat the cohort as an exposed group without a dose gradient.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"missing_data","statement":"Tumor stage is recorded for 2.7% of cases and treatment for 2.7%. The cohort supports genomic description but carries essentially no clinical annotation.","severity":"major","affected_analyses":["Stage-stratified analyses","Treatment-context interpretation"],"mitigation":"Restrict claims to tumor biology. Do not interpret molecular differences as prognostic or predictive without the clinical variables to support it.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"population_coverage","statement":"Race and ethnicity are recorded as \"not reported\" for all 440 cases with a value, and the cohort is drawn from one country and one exposure event. It describes Ukrainian patients exposed to a specific accident.","severity":"minor","affected_analyses":["Ancestry-stratified analyses"],"mitigation":"Ancestry can be estimated from the germline sequence data if required, subject to the consent terms in the data use agreement.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"kind":"access_constraint","statement":"14,315 of 18,583 files are controlled access. The whole genome sequencing that makes this cohort valuable is entirely in the controlled tier.","severity":"major","affected_analyses":["Signature analysis","Structural variant analysis"],"mitigation":"Begin the dbGaP request early; plan several weeks of lead time.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]}],"inappropriate_uses":[{"statement":"Survival or prognostic analysis of any kind.","reason":"Vital status is uninformative for every case. The long recorded follow-up in the metadata is not accompanied by outcome status, and using it would produce a survival curve with no events.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"statement":"Quantifying cancer risk attributable to Chernobyl exposure.","reason":"This is a case series of tumors, with no unexposed comparison group and no population denominator. Risk estimation requires an epidemiological cohort design that these data do not constitute.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. Not machine-generated."}]},{"statement":"Treatment-effect or response analysis.","reason":"Treatment fields are populated for 2.7% of cases and contain no outcome.","evidence":[{"method":"curated","source_url":null,"source_label":"Expert review","retrieved_at":"2026-09-21T12:30:56.908389Z","snippet":null,"locator":null,"confidence":"high","reviewer":"CD2S project curation","reviewed_at":"2026-09-18","note":"Written by a named reviewer after reading the source documentation and the measured field coverage. 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Not machine-generated."}]},{"order":4,"action":"Query the project from code, with no credentials","detail":"The file index is public even where files are not, so an agent can size the cohort before anyone requests access.","url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","requires":[],"est_time":null,"cli_snippet":"curl -s 'https://api.gdc.cancer.gov/files' --get \\\n  --data-urlencode 'filters={\"op\":\"in\",\"content\":{\"field\":\"cases.project.project_id\",\"value\":[\"REBC-THYR\"]}}' \\\n  --data-urlencode 'fields=file_id,file_name,data_type' \\\n  --data-urlencode 'size=10000' --data-urlencode 'format=TSV'","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.430019Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":5,"action":"Pass the token when the agent needs controlled files","detail":"Without a token, an API query may return only the open subset. Compare returned counts with the record before treating them as the whole cohort.","url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","requires":["GDC authentication token"],"est_time":null,"cli_snippet":"curl -H \"X-Auth-Token: $GDC_TOKEN\" https://api.gdc.cancer.gov/data/<file_id>","audience":"agent","evidence":[{"method":"derived","source_url":"https://docs.gdc.cancer.gov/API/Users_Guide/Getting_Started/","source_label":"GDC access documentation","retrieved_at":"2026-09-21T12:30:59.430021Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[{"level":"beginner","title":"Audit whether this dataset can answer your question","question":"Which classes of analysis do this cohort's clinical records actually support, and which are ruled out before I request access?","problem":"A portal can list a field even when every value is an unusable non-answer.","lesson":"Decide whether the analysis is possible before requesting data or writing a protocol.","figure":"Horizontal bars for each probed clinical field, showing the share of cases the field is populated for against the smaller share that carries an informative value, with one-to-many fields marked as not derivable per case.","featured":true,"inputs":["A GDC project identifier","Network access to api.gdc.cancer.gov"],"outputs":["Per-field coverage table separating populated from informative values","Assay coverage as a percentage of the cohort","A yes/no verdict for six common analysis classes","A chart contrasting populated with informative coverage, field by field"],"steps":["Fetch project summary and per-assay case counts","Request facet counts for the clinical fields that gate common analyses","Separate absent fields from fields populated with non-answers","Flag one-to-many fields where per-case percentages cannot be inferred","Retrieve case-level fields and test whether a survival endpoint is derivable","Print a verdict for each analysis class"],"findings":["Four of the six analysis classes pass for CGCI-HTMCP-CC; stage-adjusted modelling and progression-free endpoints are blocked.","Vital status is informative for all 212 cases with 116 deaths, so an overall-survival endpoint is derivable.","Both stage fields and the progression field are informative for 0% of cases, which no case count can fix.","Four fields hold several records per case, so their per-case share cannot be inferred from a facet count at all."],"contributor":null,"contributor_url":null,"language":"python","est_runtime":"about a minute","est_compute":null,"workbook_path":"workbooks/python/01_can_i_answer_this.py","workbook_url":null,"notebook_download_url":"/data/notebooks/01_can_i_answer_this.ipynb","notebook_preview_url":"/data/notebooks/01_can_i_answer_this.png","notebook_preview_width":1021,"notebook_preview_height":813,"colab_url":null,"binder_url":null,"receipt":{"executed":true,"executed_at":"2026-09-21T00:40:59.561676Z","runtime_seconds":6.57,"executor":"nbclient / python 3.12.13 / Darwin 25.5.0 arm64","package_versions":{"python":"3.12.13","pandas":"3.0.6","numpy":"2.5.3","matplotlib":"3.11.2","lifelines":"0.30.0","scipy":"1.18.1","requests":"2.34.2","httpx":"0.28.1"},"n_cells":7,"n_cells_executed":7,"output_hash":"dc14b4c93e7e9d6aff322ff2d0de47b8","data_retrieved_at":null,"error":null},"template_source":"01_can_i_answer_this","evidence":[{"method":"curated","source_url":null,"source_label":"CD2S workbook","retrieved_at":"2026-09-21T12:30:59.450262Z","snippet":null,"locator":"workbooks/python/01_can_i_answer_this.py","confidence":"high","reviewer":null,"reviewed_at":null,"note":"Executed end to end against the live public APIs; the receipt records when, with which package versions and how long it took."}]}],"agent_package":{"json_url":"/data/datasets/gdc-rebc-thyr.json","jsonld_url":"/data/jsonld/gdc-rebc-thyr.jsonld","croissant_url":"/data/croissant/gdc-rebc-thyr.json","instructions_url":"/data/agent/gdc-rebc-thyr.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"project_curated","reviewer":"CD2S project curation","reviewer_affiliation":null,"reviewed_at":"2026-09-18","sections_reviewed":["useful_for","limitations","inappropriate_uses","access_steps","primary_publications"],"open_questions":["Individual radiation dose reconstruction is the defining variable of this cohort and is reported in the marker paper, but it is not present in the GDC harmonized clinical records. Confirm through dbGaP whether per-case absorbed thyroid dose is releasable.","Vital status is populated for 98% of cases and informative for none. Confirm with the submitters whether outcome data were collected at all or simply not submitted."],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":true,"completeness_score":100.0,"tags":["cautionary","distinctive-population","gdc","longitudinal-recorded","radiation-exposure","rebc","released"],"search_text":null}