Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30857229", "kind": "science-record", "revision": 4, "content_hash": "sha256:0db2ae9accdca4b5f955223970e967fa54d35c4db9a815d8b6e62f6078d6aa5e", "created_at": "2026-11-01T15:40:43Z", "updated_at": "2026-11-01T21:22:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Population Substructure Has Implications in Validating Next-Generation Cancer Genomics Studies with TCGA.", "doi": "10.3390/ijms20051192", "pmid": "30857229", "authors": ["Marina D Miller", "Eric J Devor", "Erin A Salinas", "Andreea M Newtson", "Michael J Goodheart", "Kimberly K Leslie", "Jesus Gonzalez-Bosquet"], "journal": "International journal of molecular sciences", "year": 2019, "abstract": "In the era of large genetic and genomic datasets, it has become crucially important to validate results of individual studies using data from publicly available sources, such as The Cancer Genome Atlas (TCGA). However, how generalizable are results from either an independent or a large public dataset to the remainder of the population? The study presented here aims to answer that question. Utilizing next generation sequencing data from endometrial and ovarian cancer patients from both the University of Iowa and TCGA, genomic admixture of each population was analyzed using STRUCTURE and ADMIXTURE software. In our independent data set, one subpopulation was identified, whereas in TCGA 4⁻6 subpopulations were identified. Data presented here demonstrate how different the genetic substructures of the TCGA and University of Iowa populations are. Validation of genomic studies between two different population samples must be aware of, account for and be corrected for background genetic substructure.", "claims": [{"id": "claim-method", "statement": "For the subpopulation analysis we used ADMIXTURE and STRUCTURE software packages.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30857229", "locator": "sections[9] \"4.5. Data Analysis\" paragraph 2", "quote": "For the subpopulation analysis we used ADMIXTURE and STRUCTURE software packages."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Endometrial and ovarian cancer data were downloaded from The Cancer Genome Atlas (TCGA) from the National Cancer Institute, following TCGA Human Subject Protection and Data Access Policies. 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Molecular data from RNAseq were obtained for 395 samples of endometrioid endometrial cancer and 351 samples of high grade serous ovarian cancer (Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:30857229"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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