{
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    "name": "CRAG matched liver cfDNA fragment-coordinate subset",
    "zenodo_record": "6914806",
    "paper_doi": "10.1186/s13073-022-01141-8",
    "samples": 16,
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    "cancers": 8,
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    "coverage_logratio_mad": {
      "roc_auc": 0.96875
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    "negative_median_fragment_length": {
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  "paired_effects": {
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      "definition": "cancer minus matched control",
      "expected_direction": "higher_in_cancer",
      "pair_differences": {
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        "CRAG-LIVER-03": 0.0,
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        "CRAG-LIVER-05": -1.0,
        "CRAG-LIVER-06": 0.0,
        "CRAG-LIVER-07": -1.0,
        "CRAG-LIVER-08": -1.0
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      "median_difference": -1.0,
      "favorable_pairs": 5,
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  },
  "negative_controls": {
    "usable_fragment_count_only_lopo_auc": 0.140625,
    "declared_batch_only_lopo_auc": 0.5,
    "coverage_dispersion_vs_log_usable_fragments": {
      "spearman_rho": -0.008823529411764706,
      "two_sided_p": 0.9741279946623942
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  },
  "limitations": [
    "Only eight matched pairs are available; AUROC is extremely discrete and unstable.",
    "This is internal leave-pair-out cross-validation, not an independent cohort.",
    "The cases are liver cancer only, so this is not MCED validation.",
    "The coordinates are author-processed; raw-read alignment and duplicate removal were not reproduced.",
    "The 5 Mb bins use neutral GC/mappability placeholders and are not a production CNA implementation.",
    "No endpoint motif was computed because the coordinate files contain no reference sequence.",
    "The cohort helped derive the published CRAG method; this reanalysis is an engineering check, not external replication."
  ]
}