Genome-wide discovery of circulating cell-free DNA methylation signatures for the differential diagnosis of triple-negative breast cancer.

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of source sha256 6b8fb88b231ceed0635d5555230d223ba9e0e813aba2c77fccb9f91bcf69971e"}, "recorded_at": "2026-10-31T15:32:39.594150+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "bc07db5a4b01b04940307de7e1e7b4087f06d625f122c27e90b0a8f268cacd81", "source_hash": "6b8fb88b231ceed0635d5555230d223ba9e0e813aba2c77fccb9f91bcf69971e", "raw_response": "<think>We need answer JSON only. Need identify single numerical result replication registered target main finding. Likely headline AUC 0.728 for combination both markers in cfDNA, main finding perhaps paper title and abstract. Need exact contiguous quotation containing number, whole clause attribution. We need infer \"registered target: headline numerical result paper states for its main finding\". Main finding is cfDNA methylation signatures differential diagnosis TNBC. In abstract conclusion: combination of both markers yielded AUC 0.728. Likely headline number = 0.728, unit AUC. Need evidence exact contiguous quote perhaps \"In the cfDNA cohort, cg06268921 significantly differentiated TNBC from non-TNBC (P &lt; 0.001), and the combination of both markers yielded an AUC of 0.728.\" This contains another number P&lt;.001 but target value. They ask single numerical result headline. Could quote whole clause. Unit must unit paper prints. \"AUC\" is dimensionless. parent_value 0.728, unit \"AUC\". target_result perhaps \"The combination of both markers yielded an AUC of 0.728 in the cfDNA cohort.\" Evidence exact quote clause. Ensure JSON valid. number_stated true.\n\nCould alternatively headline is eight-marker panel AUC 0.922 in TCGA and 0.875 in GSE69914, but that's two numbers, while target asks single numerical result replication of registered target. \"main finding\" perhaps \"headline numerical result\" is AUC 0.728 from abstract. We should identify likely benchmark extraction target. Let's parse prompt: \"find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed.\" Registered target generic \"the headline numerical result the paper states for its main finding\". They expect one number. Source abstract has several. Main finding perhaps cfDNA combination AUC 0.728, because study developed assay and this is final applied result. Evidence exact contiguous quote. Use target_result plain.\n\nNeed perhaps unit printed \"AUC\" not \"%\". Let's answer.</think>\n\n{\"parent_value\":0.728,\"unit\":\"AUC\",\"evidence\":\"In the cfDNA cohort, cg06268921 significantly differentiated TNBC from non-TNBC (P < 0.001), and the combination of both markers yielded an AUC of 0.728.\",\"target_result\":\"The combination of both cfDNA markers yielded an AUC of 0.728.\",\"number_stated\":true}", "reading": {"parent_value": 0.728, "unit": "AUC", "evidence": "In the cfDNA cohort, cg06268921 significantly differentiated TNBC from non-TNBC (P < 0.001), and the combination of both markers yielded an AUC of 0.728.", "target_result": "The combination of both cfDNA markers yielded an AUC of 0.728.", "number_stated": true, "source_locator": "chars 1854-2007 of source sha256 6b8fb88b231ceed0635d5555230d223ba9e0e813aba2c77fccb9f91bcf69971e"}, "recorded_at": "2026-10-31T15:32:40.224876+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "In the cfDNA cohort, the combination of cg06268921 and cg23247845 yielded an AUC of 0.728 for differentiating TNBC from non-TNBC.", "minimax_alt": "Then an eight-marker diagnostic panel was developed with an AUC of 0.922 in TCGA and 0.875 in GSE69914.", "decisive": false}, "analysis_methods": {"minimax": ["Differential methylation analysis using ChAMP or Limma", "Least absolute shrinkage and selection operator (LASSO) regression", "area under the receiver operating characteristic curve (AUC)", "Cox regression analysis"], "minimax_alt": ["Differential methylation analysis using ChAMP (2.32.0) or Limma", "t-test, Wilcoxon test, or Mann-Whitney U test", "Least absolute shrinkage and selection operator (LASSO) regression", "receiver operating characteristic curve analysis using area under the curve (AUC)"], "decisive": false}, "parent_value": {"minimax": 0.922, "minimax_alt": 0.728, "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:efb271ada7fd207bc854c6341e66a30216a34e3d3f1b30382d754d8d4abbda9b", "type": "sep_package", "label": "SEP v1 package for pmid:40860669"}], "activities": [{"id": "activity:conversion:pmid:40860669", "type": "conversion", "used": ["package:efb271ada7fd207bc854c6341e66a30216a34e3d3f1b30382d754d8d4abbda9b"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40860669", "parent_hash": "sha256:f2aea4e39452c0abc15790367a91d3a8022786ea71e3f5fdc63ab7a574e42470", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40860669 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40860669' does not resolve to a declared asset", "targets"]}