Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30212242", "kind": "science-record", "revision": 3, "content_hash": "sha256:5bdd2560b537c1124b7bfd9bafb17ef22d911fc0b5ff37040ccb97609c9a6332", "created_at": "2026-11-01T17:32:22Z", "updated_at": "2026-11-01T21:21:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Positional integration of lung adenocarcinoma susceptibility loci with primary human alveolar epithelial cell epigenomes.", "doi": "10.2217/epi-2018-0003", "pmid": "30212242", "authors": ["Chenchen Yang", "Theresa Ryan Stueve", "Chunli Yan", "Suhn K Rhie", "Daniel J Mullen", "Jiao Luo", "Beiyun Zhou", "Zea Borok", "Crystal N Marconett", "Ite A Offringa"], "journal": "Epigenomics", "year": 2018, "abstract": "AIM: To identify functional lung adenocarcinoma (LUAD) risk SNPs.\nMATERIALS & METHODS: Eighteen validated LUAD risk SNPs (p ≤ 5 × 10-8) and 930 SNPs in high linkage disequilibrium (r2 > 0.5) were integrated with epigenomic information from primary human alveolar epithelial cells. Enhancer-associated SNPs likely affecting transcription factor-binding sites were predicted. Three SNPs were functionally investigated using luciferase assays, expression quantitative trait loci and cancer-specific expression.\nRESULTS: Forty-seven SNPs mapped to putative enhancers; 11 located to open chromatin. Of these, seven altered predicted transcription factor-binding motifs. Rs6942067 showed allele-specific luciferase expression and expression quantitative trait loci analysis indicates that it influences expression of DCBLD1, a gene that encodes an unknown membrane protein and is overexpressed in LUAD.\nCONCLUSION: Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression. Data deposition: Data are provided in GEO record GSE84273.", "claims": [{"id": "claim-method", "statement": "expression quantitative trait loci analysis indicates that it influences expression of DCBLD1", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30212242", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "expression quantitative trait loci analysis indicates that it influences expression of DCBLD1"}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data deposition: Data are provided in GEO record GSE84273.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30212242", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "Data deposition: Data are provided in GEO record GSE84273."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:30212242", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integration of candidate LUAD risk SNPS with epigenomic marks from normal alveolar epithelium identified numerous candidate functional LUAD risk SNPs including rs6942067, which appears to affect DCBLD1 expression.", "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:30212242"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE84273"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE84273"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30212242", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2217/epi-2018-0003", "sha256": "sha256:80394e0c32d8bfbd6f5923ee4a329459878e024fcafaae62d33c76759759db43", "bytes": 1147, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2217/epi-2018-0003", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6391636", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84273", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84273", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84273", "version": null, "note": "Data deposition: Data are provided in GEO record GSE84273.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data deposition: Data are provided in GEO record GSE84273.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2230648", "GSM2230649", "GSM2230650", "GSM2230651", "GSM2230652", "GSM2230653", "GSM2230654", "GSM2230655", "GSM2230656", "GSM2230657", "GSM2230658", "GSM2230659", "GSM2434059", "GSM2434060", "GSM2434061", "GSM2434062"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Identification of Functional Lung Adenocarcinoma Susceptibility Loci through Positional Integration with Human Alveolar Cell Epigenomes", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE84273 not downloaded", "asset:data:geo:GSE84273 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "expression quantitative trait loci analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "expression quantitative trait loci analysis indicates that it influences expression of DCBLD1"}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (expression quantitative trait loci analysis), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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