{
  "accessed": "2026-08-01",
  "policy": "Human cfDNA data are staged only after verifying consent, data-use terms, donor identifiers, reference build, and redistribution restrictions.",
  "recommended_sequence": [
    "FORESEE published CRC training/validation matrices for an immediate locked-by-code processed-data baseline",
    "CRAG and FinaleMe open fragment coordinates for coordinate-level feature and domain-shift work",
    "Six small Snyder SRA runs for raw FASTQ/BAM plumbing only",
    "DELFI development after EGA authorization",
    "LUCAS and prospective gastric cohorts as locked external challenges",
    "A new prospective, multisite intended-use cohort for any clinical claim"
  ],
  "datasets": [
    {
      "name": "FORESEE CRC input-WGS fragmentomics",
      "accession": "PRJNA755688 / SRP332946 / Zenodo 5170265",
      "url": "https://zenodo.org/records/5170265",
      "composition": "Released DELFI-style matrices: training 405 CRC plus 296 noncancers; validation 220 CRC plus 164 noncancers, including small rheumatoid arthritis, peptic-ulcer and COPD subsets",
      "assay": "Ordinary paired-end plasma cfDNA input-control WGS; this reanalysis uses the released 512 regional within-sample normalized values",
      "burden": "Processed matrices about 10.7 MB; 1,392 raw input-WGS SRA runs are roughly 5.76 TB",
      "access": "Open processed data, CC BY 4.0; raw SRA public",
      "best_use": "Immediate post-publication training/published-holdout CRC benchmark with stage and benign-control audits",
      "not_for": "Independent-site, prospective, raw-pipeline or multi-cancer validation"
    },
    {
      "name": "CRAG open fragment-coordinate cohort",
      "accession": "Zenodo 6914806; raw study phs003062.v1.p1",
      "url": "https://zenodo.org/records/6914806",
      "composition": "8 stage I-II HCC plus 8 matched controls; 25 stage I-III breast cancers plus 25 matched controls",
      "assay": "hg19 fragment-coordinate files derived from plasma WGS",
      "burden": "66 subjects; approximately 13.4 GiB in five archives",
      "access": "Open processed coordinates, CC BY 4.0; raw data controlled",
      "best_use": "Immediate length, coverage, endpoint, hotspot and WPS software benchmark",
      "not_for": "Clinical specificity or pan-cancer validation"
    },
    {
      "name": "FinaleMe ULP-WGS prostate/breast cohort",
      "accession": "Zenodo 7779198",
      "url": "https://zenodo.org/records/7779198",
      "composition": "77 records but only 42 donor groups: 43 CRPC prostate, 22 metastatic breast and 12 healthy records",
      "assay": "Approximately 0.1x b37 fragment-coordinate files",
      "burden": "Verified 1.895 GB archive; 77 gzip members",
      "access": "Open processed coordinates, CC BY 4.0",
      "best_use": "Donor-grouped ultra-low-pass feature and domain-shift stress test with explicit batch baselines",
      "not_for": "Early detection; repeated donor records and healthy-batch confounding prohibit ordinary sample splits"
    },
    {
      "name": "1000 Genomes germline reference data",
      "accession": "IGSR / 1000 Genomes Project",
      "url": "https://www.internationalgenome.org/data",
      "composition": "Population germline genomes from cellular DNA, not matched plasma cfDNA cancer/control specimens",
      "assay": "Whole-genome germline sequencing across populations and technologies",
      "burden": "Large, but reference panels and selected files can be staged selectively",
      "access": "Open under source-specific terms",
      "best_use": "Population allele frequencies, ancestry checks, mappability/CNA technical controls and germline masking",
      "not_for": "Primary cancer-versus-normal cfDNA training or biological sensitivity estimates"
    },
    {
      "name": "Snyder plasma nucleosome-footprint cohort",
      "accession": "GSE71378 / SRP061633",
      "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71378",
      "composition": "60 paired-end runs: 48 cancers, 8 inflammatory noncancers, and four healthy-labelled records; one healthy record is pooled plasma",
      "assay": "Public paired-end plasma WGS with very heterogeneous depth",
      "burden": "Full study about 601 GB compressed; recommended six-run plumbing subset about 8.5 GB",
      "access": "Public INSDC records; cite original study and retain source terms",
      "best_use": "Raw alignment, duplicate, insert-size, WPS and downsampling invariance tests",
      "not_for": "Training an MCED classifier or estimating specificity"
    },
    {
      "name": "DELFI discovery cohort",
      "accession": "EGAS00001003611 / EGAD00001005339",
      "url": "https://ega-archive.org/datasets/EGAD00001005339",
      "composition": "Classifier cohort 208 untreated cancers across seven types and 215 healthy controls",
      "assay": "1-2x, 100-bp paired-end cfDNA WGS",
      "burden": "About 4.4 TB; EGA metadata show a 537/538-sample discrepancy that must be reconciled",
      "access": "Controlled EGA DAC/DUA; no redistribution",
      "best_use": "Reproduce the published regional fragmentation baseline and develop models inside grouped folds",
      "not_for": "Final independent or prospective validation"
    },
    {
      "name": "LUCAS lung and benign-control cohort",
      "accession": "EGAS00001005340 / EGAD00001007796",
      "url": "https://ega-archive.org/datasets/EGAD00001007796",
      "composition": "129 lung cancers and 158 noncancer development samples; external 46 cancers and 385 controls",
      "assay": "1-2x, 100-bp paired-end cfDNA WGS",
      "burden": "872 BAMs, approximately 4.5 TB",
      "access": "Controlled EGA DAC/DUA; no redistribution",
      "best_use": "Locked lung-cancer and benign-condition external challenge",
      "not_for": "Pan-cancer generalization by itself"
    },
    {
      "name": "Mouliere fragment-size cohorts",
      "accession": "EGAD00001004939 / EGAD00001006132",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC6483061/",
      "composition": "344 plasma samples from 200 patients across 18 cancers plus 65 healthy individuals",
      "assay": "Low-pass WGS around 0.4x",
      "burden": "Approximately 933 GB across the two controlled datasets",
      "access": "Controlled; restrictive ovarian data-use policy",
      "best_use": "Fragment-size and CNA method reproduction",
      "not_for": "Early-stage MCED sensitivity because disease is mainly advanced"
    },
    {
      "name": "FinaleDB processed fragmentome collection",
      "accession": "FinaleDB",
      "url": "https://finaledb.gitbook.io/finaledb-documentation/faq",
      "composition": "Uniformly processed coordinates and tracks for 2,579 datasets, 2,505 samples and 23 conditions",
      "assay": "Derived fragment coordinates and feature tracks from many source studies",
      "burden": "Feature-level downloads can be small; source studies vary",
      "access": "Research availability does not provide one uniform commercial license; source terms control",
      "best_use": "Rapid feature prototyping and hard-negative exploration",
      "not_for": "Redistribution or product training without source-by-source permission"
    },
    {
      "name": "Prospective early gastric cancer WGS",
      "accession": "HRA005926 / PRJCA020703",
      "url": "https://ngdc.cncb.ac.cn/gsa-human/browse/HRA005926",
      "composition": "Development 110 stage I-II gastric cancers and 139 noncancers; validation 73 cancers and 94 noncancers",
      "assay": "cfDNA WGS with size, CNA, nucleosome and SNV features",
      "burden": "Not exposed before authorization",
      "access": "Controlled, HDAC003271",
      "best_use": "Locked early-stage single-cancer external challenge",
      "not_for": "Pan-cancer specificity"
    },
    {
      "name": "SPOT-MAS public bisulfite cohort",
      "accession": "PRJNA929650",
      "url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA929650",
      "composition": "239 breast cancers and 278 healthy controls",
      "assay": "Paired-end bisulfite sequencing",
      "burden": "517 SRA experiments; about 1.26 TB",
      "access": "Public SRA",
      "best_use": "Adjacent methylation-plus-fragment modeling experiments",
      "not_for": "Direct validation of ordinary low-pass WGS because bisulfite conversion changes sequence and fragment distributions"
    },
    {
      "name": "ichorCNA metastatic ULP-WGS cohort",
      "accession": "phs001417.v1.p1",
      "url": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001417.v1.p1",
      "composition": "Longitudinal metastatic breast/prostate cancers and controls",
      "assay": "Ultra-low-pass WGS around 0.1x",
      "burden": "Controlled dbGaP",
      "access": "Controlled dbGaP",
      "best_use": "CNA and tumor-fraction algorithm validation",
      "not_for": "Interpreting the reported approximately 3% favorable-CNA threshold as early-cancer clinical LoD"
    }
  ],
  "recommended_snyder_subset": [
    {"run": "SRR2130052", "sample": "IH03", "class": "independent healthy", "compressed_mb": 1404},
    {"run": "SRR2130005", "sample": "IC05", "class": "lung adenocarcinoma", "compressed_mb": 1050},
    {"run": "SRR2130002", "sample": "IC02", "class": "ovarian cancer", "compressed_mb": 1521},
    {"run": "SRR2130010", "sample": "IC11", "class": "colorectal cancer", "compressed_mb": 1681},
    {"run": "SRR2130020", "sample": "IC21", "class": "pancreatic ductal adenocarcinoma", "compressed_mb": 1406},
    {"run": "SRR2129994", "sample": "IA01", "class": "Crohn disease hard negative", "compressed_mb": 1445}
  ]
}