{"id":"idc-htan-hms","title":"HTAN-HMS","short_title":"htan_hms","aliases":["htan_hms"],"summary":"We are constructing a multi-dimensional atlas of pre-melanoma focused on understanding genetic and epigenetic events that transform melanocytes into invasive tumors. Melanoma is a cancer of increasing prevalence that is curable with minor surgery if detected early but life-threatening when it metastasizes. Melanomas metastasize when still small, making early detection essential but challenging. Our atlas will delineate the precise sequence of events leading up to pre-melanoma through detailed spatial analysis of cell-autonomous events such as oncogene mutation and non-autonomous events such as escape from immune surveillance. The atlas is based on highly-multiplexed tissue imaging and single cell sequencing and focused on samples in which the full sequence of events from atypia to invasive melanoma can be visualized in a single specimen. The atlas will serve as a publicly accessible resource for research scientists, physicians, and patients and improve our ability to (i) highlight lesions likely to progress to cancer, (ii) identify high-risk patients to inform decisions on surgery, (iii) identify low-risk patients to reduce unnecessary procedures, (iv) design improved procedures for routine screening of all individuals, and (v) inform treatment options when surgery is insufficient. Complementary studies with similar goals (but not supported by HTAN) are studying later stage melanomas. Please see the DICOM converted Slide Microscopy images for the HTAN-HMS collection information page to learn more about the images and to obtain any supporting metadata for this collection.","one_liner":null,"identifiers":[{"scheme":"idc_collection_id","value":"htan_hms","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=htan_hms","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/htan_hms","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"tcia_collection","value":"HTAN-HMS","url":"https://www.cancerimagingarchive.net/collections/","is_primary":false,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/htan_hms","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"zenodo","value":"10.5281/zenodo.12666872","url":null,"is_primary":false,"evidence":[{"method":"fulltext","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/htan_hms","source_label":"IDC collection description","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":"er stage melanomas. Please see the DICOM converted Slide Microscopy images for the HTAN-HMS collection information page to learn more about the images and to obtain any supporting metadata for this","locator":"accession extracted from description prose","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Cross-repository link recovered from prose; verify before relying on it."}]}],"repository":{"name":"NCI Imaging Data Commons","short_name":"IDC","url":"https://portal.imaging.datacommons.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"NCI Imaging Data Commons / The Cancer Imaging Archive","program_url":"https://imaging.datacommons.cancer.gov/","nci_program":"IDC","generating_institutions":[],"data_generation_funding_role":"unknown","version":null,"release_date":null,"last_upstream_update":null,"retrieved_at":"2026-09-18T02:44:36.389375Z","landing_page_url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=htan_hms","cancer_types":[{"label":"Adenocarcinoma","ontology":null,"code":null,"url":null}],"primary_sites":["Colon"],"subject":{"scope":"single","tissues":["BOWEL"],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Adenocarcinoma; primary_sites: Colon","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Repository disease labels or primary sites mapped to pinned tissues."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":16,"n_samples":null,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[]},"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/htan_hms","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"radiology","label":"DICOM medical imaging","platform":null,"n_cases":16,"n_samples":null,"n_files":null,"data_levels":["DICOM series"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/htan_hms","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[],"longitudinal":{"has_followup":null,"has_survival_endpoint":null,"survival_endpoints":[],"median_followup_months":null,"max_followup_months":null,"n_cases_with_followup":null,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":null,"response_criteria":[],"evidence":[]},"access":{"tier":"open","open_components":[],"controlled_components":[],"mechanism":"Public DICOM download from the IDC portal, its API, or the idc-index Python package; no account required for public collections.","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the collection DOI and the IDC/TCIA data-citation guidance.","license":"Per-collection license, typically CC BY 3.0/4.0 or CC BY-NC","publication_policy_url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/htan_hms","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[{"kind":"missing_data","statement":"IDC serves no clinical table for this collection, so nothing about outcome, stage, treatment or demographics can be read from the repository. Any such variable would have to come from the originating trial or publication.","severity":"blocking","affected_analyses":["survival","treatment response","stage-adjusted modelling","analysis by race or ethnicity"],"mitigation":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/clinical/tables","source_label":"IDC v3 API /clinical/tables","retrieved_at":"2026-09-19T03:20:46.830869Z","snippet":null,"locator":"collection_id=htan_hms: no clinical table is served","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"inappropriate_uses":[],"primary_publications":[],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{},"n_by_tier_raw":{},"accession_precision":null,"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":false,"n_verified_reuse":null,"n_reuse_examined":0,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":null,"latest_reuse_year":null,"years_since_release":null,"expected_reuse":null,"reuse_gap_index":null,"reuse_gap_percentile":null,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:49.710022Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:49.710022Z","snippet":null,"locator":null,"confidence":"low","reviewer":null,"reviewed_at":null,"note":"This dataset has no accession specific enough to search for in the literature, so citation-based reuse cannot be measured. Absence of a count here is not evidence of absence of reuse."}]},"underexplored":{"is_underexplored":false,"basis":["Not assessed: this dataset has no accession specific enough for citation-based reuse tracing, so a shortfall cannot be measured."],"index_value":null,"percentile":null,"comparator_set":"rgi-huber-v2","evidence":[]},"grants":[],"access_steps":[{"order":1,"action":"Open the collection in the IDC portal","detail":"Browse the series before downloading; imaging collections can be very large.","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=htan_hms","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=htan_hms","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.440121Z","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":2,"action":"Read the collection's own licence","detail":"Per-collection license, typically CC BY 3.0/4.0 or CC BY-NC. IDC licences differ by collection.","url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.440123Z","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":3,"action":"Download with idc-index","detail":"The package resolves the collection to its buckets and pulls selected data.","url":"https://github.com/ImagingDataCommons/idc-index","requires":[],"est_time":"hours for a full collection","cli_snippet":"pip install idc-index\npython - <<'PY'\nfrom idc_index import IDCClient\nIDCClient().download_from_selection(collection_id=\"htan_hms\", downloadDir=\".\")\nPY","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/ImagingDataCommons/idc-index","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.440125Z","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":4,"action":"List the series before pulling pixels","detail":"List modality and size first so an agent can choose what to fetch.","url":"https://learn.canceridc.dev/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nfrom idc_index import IDCClient\ni = IDCClient().index\ns = i[i[\"collection_id\"] == \"htan_hms\"]\nprint(len(s), \"series\", s[\"PatientID\"].nunique(), \"patients\",\n      round(s[\"series_size_MB\"].sum() / 1024, 1), \"GB\")\nprint(s[\"Modality\"].value_counts().to_dict())\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://learn.canceridc.dev/","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.440126Z","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":[],"agent_package":{"json_url":"/data/datasets/idc-htan-hms.json","jsonld_url":"/data/jsonld/idc-htan-hms.jsonld","croissant_url":"/data/croissant/idc-htan-hms.json","instructions_url":"/data/agent/idc-htan-hms.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"open_questions":[],"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":false,"completeness_score":16.1,"tags":["idc","imaging"],"search_text":null}