{ "artifact_type": "post_publication_public_processed_data_reanalysis", "clinical_claim": false, "dataset": { "name": "FORESEE / Walker 2022 colorectal cancer cfDNA input-WGS fragmentomics", "bioproject": "PRJNA755688", "sra_study": "SRP332946", "zenodo_record": "5170265", "license": "CC BY 4.0 for the Zenodo processed-data record", "paper_doi": "10.1038/s41598-022-20975-1", "input_level_used_here": "authors' released 512 regional within-sample normalized values; channel identity is not explicit", "raw_reads_used_here": false, "training_matrix_sha256": "c966445a2ba92db561b6beab563f9bb24e8c55ea7644003bd143ba77669869b0", "validation_matrix_sha256": "3eaaf2add7be7e9a7921c52864d54d9df0d8e6d93665deab71c44028f08853ac", "metadata_sha256": "cd5c1c32ece6748352f2b3bbb043ad97efa4af9cc146a251b2d0958afcba0e9d", "published_partition_respected_in_code": true, "split_rule": "matrix membership; metadata description is incorrectly 'Training sample' for all rows", "evaluation_label": "held-out published split; fitting and thresholds do not use validation labels, but this reanalysis is post hoc, not blinded or preregistered" }, "sample_counts": { "training_total": 701, "training_crc": 405, "training_noncancer": 296, "validation_total": 384, "validation_crc": 220, "validation_noncancer": 164, "training_by_indication": { "COLORECTAL CANCER": 405, "CONTROL": 273, "COPD": 6, "PEPTIC ULCER": 6, "RHEUMATOID ARTHRITIS": 11 }, "validation_by_indication": { "COLORECTAL CANCER": 220, "CONTROL": 149, "COPD": 2, "PEPTIC ULCER": 6, "RHEUMATOID ARTHRITIS": 7 }, "training_crc_by_stage": { "I": 82, "II": 161, "III": 116, "IV": 46 }, "validation_crc_by_stage": { "I": 45, "II": 87, "III": 61, "IV": 27 } }, "feature_matrix": { "features": 512, "training_delimiter_detected": "tab", "validation_delimiter_detected": "comma", "sample_overlap_count": 0, "exact_row_overlap_count": 0, "max_cross_split_cosine_similarity": 0.9964304821718002, "max_similarity_training_sample": "CEG99_801_79PC", "max_similarity_validation_sample": "CEG99_814_63PC", "median_absolute_training_feature_mean": 0.5187861691122089, "median_absolute_validation_feature_mean": 0.515244109637877, "median_training_feature_sd": 0.40552246859124463, "median_validation_feature_sd": 0.4154696305943114, "max_absolute_training_sample_mean": 2.7538735181131813e-16, "max_absolute_validation_sample_mean": 3.3046482217358175e-16, "training_sample_sd_range": [ 0.9990229601966103, 0.9990229601966121 ], "validation_sample_sd_range": [ 0.9990229601966103, 0.9990229601966121 ], "interpretation": "These checks detect sample copying and describe the supplied matrices. 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0.0, "conservative_ppv_corner_warning": "Sensitivity and specificity marginal interval bounds are combined as a descriptive corner, not a joint 95% confidence bound.", "screening_prevalence": 0.005 }, "at_99pct_target_specificity": { "threshold": 0.5295504294342016, "true_positive": 0, "false_negative": 220, "true_negative": 164, "false_positive": 0, "sensitivity": 0.0, "specificity": 1.0, "binomial_sensitivity_95ci": [ 0.0, 0.01662783953999374 ], "binomial_specificity_95ci": [ 0.9777579177961985, 1.0 ], "ppv_at_prevalence": null, "ppv_status": "undefined:no predicted-positive tests", "conservative_ppv_corner_from_separate_95pct_marginal_bounds": 0.0, "conservative_ppv_corner_warning": "Sensitivity and specificity marginal interval bounds are combined as a descriptive corner, not a joint 95% confidence bound.", "screening_prevalence": 0.005 } }, "subgroups": { "stages": { "I": { "n_cases": 45, "n_controls": 164, "roc_auc": 0.6441056910569105, "roc_auc_95ci": [ 0.5430877371273714, 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Zero cross-split overlap means study/batch effects cannot be excluded.", "fixed_c_prefix_grouped_training_oof_auc": 0.7990407073740408, "prefix_grouped_threshold_validation_operating_points": { "target_0.95": { "threshold": 0.6958919319339525, "true_positive": 113, "false_negative": 107, "true_negative": 155, "false_positive": 9, "sensitivity": 0.5136363636363637, "specificity": 0.9451219512195121, "binomial_sensitivity_95ci": [ 0.44552326884136456, 0.5813770825617532 ], "binomial_specificity_95ci": [ 0.8983827032799991, 0.9746022782667878 ], "ppv_at_prevalence": 0.044920397913475116, "ppv_status": "defined", "conservative_ppv_corner_from_separate_95pct_marginal_bounds": 0.021556848781970048, "conservative_ppv_corner_warning": "Sensitivity and specificity marginal interval bounds are combined as a descriptive corner, not a joint 95% confidence bound.", "screening_prevalence": 0.005 }, "target_0.99": { "threshold": 0.8761771580988397, "true_positive": 66, "false_negative": 154, "true_negative": 162, "false_positive": 2, "sensitivity": 0.3, "specificity": 0.9878048780487805, "binomial_sensitivity_95ci": [ 0.2402418216509552, 0.36524024579256825 ], "binomial_specificity_95ci": [ 0.9566431914607609, 0.9985196869442463 ], "ppv_at_prevalence": 0.11001788908765645, "ppv_status": "defined", "conservative_ppv_corner_from_separate_95pct_marginal_bounds": 0.027090114789337014, "conservative_ppv_corner_warning": "Sensitivity and specificity marginal interval bounds are combined as a descriptive corner, not a joint 95% confidence bound.", "screening_prevalence": 0.005 } }, "within_validation_prefix_case_control_pair_concordance_auc": 0.8318138950015719, "within_validation_prefix_rank_pooled_auc": 0.7986419068736141, "within_prefix_case_control_pairs": 3181, "score_prefix_number_spearman": { "noncancer": { "spearman_rho": -0.22566067490092828, "two_sided_p": 0.0036686184985473868 }, "crc": { "spearman_rho": -0.1907670846509147, "two_sided_p": 0.004517893190566102 } }, "fold_audit": [ { "fold": 0, "fit_prefixes": 16, "valid_prefixes": 4, "overlap_prefixes": 0 }, { "fold": 1, "fit_prefixes": 16, "valid_prefixes": 4, "overlap_prefixes": 0 }, { "fold": 2, "fit_prefixes": 16, "valid_prefixes": 4, "overlap_prefixes": 0 }, { "fold": 3, "fit_prefixes": 16, "valid_prefixes": 4, "overlap_prefixes": 0 }, { "fold": 4, "fit_prefixes": 16, "valid_prefixes": 4, "overlap_prefixes": 0 } ] }, "limitations": [ "This is colorectal-cancer detection, not multi-cancer early detection.", "The analysis starts from authors' processed within-sample normalized matrices, not raw FASTQ/BAM.", "The release does not identify which documented fragment channel is represented by the single 512-vector.", "The validation split is internal to the same study and is not an independent site or prospective screening cohort.", "Filename-prefix groups do not overlap between train and validation; residual technical/batch structure is measurable and cannot be excluded.", "Threshold resolution is limited by 296 training and 164 validation noncancer samples; 99.5% specificity is not estimated.", "An apparent published-partition result can still reflect collection, vendor, batch, or demographic structure rather than cancer biology." ] }