Below is the repository of sequenced cell-free DNA (cfDNA) datasets. This collection is part of NucPosDB, a manually curated database of experimental nucleosome maps in vivo, cfDNA and computational tools related to nucleosome positioning

*How to cite: A publication describing NucPosDB is currently in preparation. Meanwhile please site this paper:
Teif V.B. and Clarkson C.T. (2019) Nucleosome Positioning. In Encyclopedia of Bioinformatics and Computational Biology (Ed.: S. Ranganathan, M. Gribskov, K. Nakai, and C. Schönbach), vol. 2, pp. 308–317. Oxford: Academic Press |Published version | Authors’ manuscript

 

Sequenced cell-free DNA (cfDNA) datasets

DescriptionOrganismMedical conditioncfDNA sourceExperimental methodRaw dataProcessed dataAccessYearNumber of patients
5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages (Song et al., 2017)Homo sapienshealthy, liver cancer, breast cancer, lung cancer, pancreatic cancer, brain cancer, gastric cancer, colorectal cancer, hepatitis Bblood plasma5hmC-Seal sequencingGSE81314hg19 readsOpen2017121
5-Hydroxymethylcytosines in Circulating Cell-free DNA Reveal Vascular Complications of Type 2 Diabetes (Yang et al., 2019)Homo sapienstype 2 diabetesblood plasma5hmC-Seal sequencingGSE125929Open201962
Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma (Chiu et al., 2019)Homo sapiensB-cell lymphomablood plasma5hmC-Seal sequencingGSE126676Open201948
Genome-wide mapping of 5-hydroxymethylcytosines in circulating cell-free DNA as a non-invasive approach for early detection of hepatocellular carcinoma (Cai et al., 2019)Homo sapienshealthy, liver cancer, hepatitis B, liver cirrhosis, benign tumourblood plasma5hmC-Seal sequencingGSE112679Open20192554
DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers​ (Li et al., 2017)Homo sapienshealthy, colorectal cancer, gastric cancer, pancreatic cancer, liver cancer, thyroid cancer, benign tumourblood plasma5hmC-Seal sequencingGSE89570Open2017350
Assessing the feasibility of using ventricle-specific methylation patterns in human cfDNA as an alternative biomarker for acute cellular rejection in cardiac transplantation (Pattar, 2019) Homo sapiensacute cellular rejection, tissue transplantationblood plasmabisulfite sequencingGSE152648Open201924
Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (Hao et al., 2017)Homo sapienslung cancerblood serumbisulfite sequencingGSE97932Open2017654
Cell-free DNA methylation markers in diagnosis and prognosis of common cancer (Hao et al., 2017)Homo sapienscolon cancerblood serumbisulfite sequencingGSE97923Open2017773
Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tissue-of-origin mapping from plasma DNA (Guo et al., 2017)Homo sapienshealthy, brain cancer, colon cancer, intestinal cancer, kidney cancer, liver cancer, lung cancer, pancreatic cancer, spleen cancer, gastric cancerblood plasmabisulfite sequencingGSE79277Open2017134
Non-Invasive Cancer Diagnosis and Tissue-of-Origin Prediction Using Methylation Profiles of Cell-Free DNA (Kang et al., 2017)Homo sapienslung cancer, benign tumourblood plasmabisulfite sequencingEGAS00001002211Restricted20179
CancerDetector: Ultrasensitive and Non-Invasive Cancer Detection at the Resolution of Individual Reads using Cell-free DNA Methylation Sequencing Data (Li et al., 2018)Homo sapienshealthy, liver cancerblood plasmabisulfite sequencingEGAS00001002728Restricted20188
Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin (Sun et al., 2019)Homo sapienscolorectal cancerblood plasmabisulfite sequencing, whole genome EGAS00001003117Open201911
Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing (Chan et al., 2014)Homo sapienshealthy, lupus erythematosusblood plasmabisulfite sequencing, whole genome sequencingEGAS00001000962Restricted201435
Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract (Burnham et al., 2018)Homo sapiensbacteriuriaurinebisulfite sequencing, whole genome sequencingphs001564.v1.p1., phs001564.v3.p1Restricted2018130
Integrated digital error suppression for ultrasensitive detection of circulating tumor DNA
(Newman et al., 2016)		Homo sapienshealthy, lung cancerblood plasmaCAPP-SeqPRJNA311126Open2016172
Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution (Zeng et al., 2019)Homo sapienshealthy, liver cancerblood plasma, blood serumCATCH-seqGSE112048Open20196
Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA: a proof-of-principle study (Van Paemel
et al., 2020)		Homo sapienshealthy, pediatric solid tumoursblood plasma, cerebrospinal fluidcf-RRBS sequencingEGAS00001004194Restricted202059
Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome
(Van Paemel
et al., 2020)		Homo sapienshealthyblood plasmacf-RRBS sequencingEGAD00001006007, EGAS00001004271Restricted20203
ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs (Sadeh et al., 2020)Homo sapienshealthy, acute myocardial infarction, benign liver disease, metastatic cancer, colorectal cancerblood plasmacfChIP-seqzenodo.4277001Open2020150
Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment (Peter et al., 2020)Homo sapiensprostate cancerblood plasmacfMeDIP-seqGSE152631Open202016
Whole exome sequencing of cell-free DNA reveals temporo-spatial heterogeneity and identifies treatment-resistant clones in neuroblastoma (Chicard et al., 2017)Homo sapiensbrain cancerblood plasmaexome sequencingEGAS00001002705Restricted201719
Rapid Response of Stage IV Colorectal Cancer With APC/TP53/KRAS Mutations to FOLFIRI and Bevacizumab Combination Chemotherapy: A Case Report of Use of Liquid Biopsy (Hendricks et al., 2020)Homo sapienscolorectal cancerblood plasmaexome sequencingEGAS00001004088Restricted20201
Liquid biopsy by NGS: differential presence of exons (DPE) in cell‐free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer (Olmedillas‐López et al., 2018)Homo sapienscolorectal cancer, metastatic cancerblood plasmaexome sequencingEGAS00001002687Restricted201830
Needlestack: an ultra-sensitive variant caller for
multi-sample next generation sequencing data (Delhomme et al., 2020)		Homo sapienshealthyblood plasmaexome sequencingEGAS00001003989Restricted2020125
Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease (Butler et al., 2015)Homo sapiensbreast cancer, metastatic cancerblood plasmaexome sequencingPRJEB8969Open20152
Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma (Huang et al., 2017)Homo sapiensliver cancerblood plasmaexome sequencing, targeted sequencingEGAS00001002207Restricted20179
Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer (Herberts et al., 2020)Homo sapiensprostate cancer, metastatic cancerblood plasmaexome sequencing, targeted sequencingEGAS00001004328Restricted2020599
Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer (Ritch et al., 2020)Homo sapiensprostate cancer, metastatic cancerblood plasmaexome sequencing, targeted sequencingEGAS00001003899Restricted2020433
Comparison of the genome-wide DNA methylation status between FNA sample of pancreatic tumor and cfDNA samples from the same patients (Shinjo et al., 2020)Homo sapienshealthy, pancreatic cancerblood serumMBD-seqGSE150468Open20204
Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA (Liu et al., 2019)Homo sapienshealthy, benign liver diseaseblood plasmaMCTA-seqGSE118690Open201914
Methylome analysis of colorectal cancer cell line DNA (HCT116) and colorectal cancer patient derived xenografts (PDXs) using MeDIP-seq and cfMeDIP-seq (Shen et al., 2018)Homo sapiens, Mus musculus colorectal cancerblood plasmaMeDIP-seq, cfMeDIP-seqGSE79838Open20182
Epigenetic analyses of methylation and nucleosome occupancy in cell-free DNA (Erger et al., 2020)Homo sapienshealthy, benign kidney diseaseblood plasma, urinewhole genome sequencingEGAS00001004370Open202021
Decoding genetic and epigenetic information embedded in cell free DNA with adapted SALP‐seq (Wu et al., 2019)Homo sapienshealthy, esophageal cancerblood plasmaSALP-seqGSE116345Open201920
White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer (Leal et al., 2020)Homo sapiensgastric cancerblood plasmatargeted sequencingEGAS00001004114Restricted202050
Sensitive Monogenic Non-invasive Prenatal Diagnosis by Targeted Haplotyping (Vermeulen et al., 2017)Homo sapiensnon-invasive prenatal testingblood plasmatargeted sequencingEGAS00001002622Restricted201720
Clinical application of targeted NGS of circulating tumor DNA in identifying tumor-specific mutations and uncovering clinical actionable targets in a variety of solid tumors in large patient cohorts (Shu et al., 2017)Homo sapienslung cancer, breast cancer, colorectal cancer, uterine cancer, colon cancer, ovarian cancer, thymic cancer, esophageal cancer, soft tissue cancer, liver cancer, metastatic cancer, pancreatic cancer, gastric cancerblood plasmatargeted sequencingEGAS00001002251Restricted2017605
Targeted next generation sequencing of cfDNA from lung cancer patients enrolled in the GALAXY-1 trial (Rakhit, 2018)Homo sapienslung cancerblood plasmatargeted sequencingPRJEB20969Open2018259
Detection of mutational patterns in cell‐free DNA of colorectal cancer by custom amplicon sequencing (Herrmann et al., 2019)Homo sapienscolorectal cancerblood plasma targeted sequencingEGAS00001003382Restricted201934
Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA (Che et al., 2020)Homo sapiensnon-invasive prenatal testingblood plasmatargeted sequencingEGAS00001003634Restricted20209
Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer (Taavitsainen et al., 2019)Homo sapiensprostate cancer, metastatic cancerblood plasmatargeted sequencingEGAS00001003352Restricted201924
Monitoring clonal evolution and resistance to EGFR blockade in the blood of metastatic colorectal cancer patients (Siravegna et al., 2015)Homo sapienscolorectal cancer, metastatic cancerblood plasmatargeted sequencingPRJEB9202Open2015100
Functional analysis of androgen receptor mutations that confer anti-androgen resistance identified in circulating cell-free DNA from prostate cancer patients (Lallous et al., 2016)Homo sapiensprostate cancerblood plasmatargeted sequencingPRJEB12109Open201662
White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer (Leal et al., 2020)Homo sapiensgastric cancerblood plasmatargeted sequencingEGAS00001004114Open202050
A Study of Cell-Free DNA Fragmentation Pattern and Its Application in DNA Sample Type Classification (Chen et al., 2018)Homo sapiensbrain cancer, metastatic cancer, breast cancer, lung cancercerebrospinal fluid, blood plasmatargeted sequencing, exome sequencingPRJNA266729Open201857
Direct detection of early-stage cancers using circulating tumor DNA (Phallen et al., 2019)Homo sapienshealthy, breast cancer, colorectal cancer, lung cancer, ovarian cancerblood plasmaTEC-Seq, targeted sequencingEGAS00001002577Open2019238
Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution (Abbosh et al., 2017)Homo sapienslung cancerblood plasmawhole exome sequencingEGAS00001002247Open2017100
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors (Adalsteinsson et al., 2017)Homo sapienshealthy, breast cancer, prostate cancer, metastatic cancerblood plasmawhole exome sequencing, whole genome sequencingphs001417.v1.p1Open2017545
High intensity sequencing of plasma cfDNA and WBC gDNA (Razavi et al., 2019)Homo sapienshealthy, breast cancer, lung cancer, prostate cancerblood plasmawhole genome sequencingEGAS00001003755Restricted2019196
Generation of highly biomimetic quality control materials for noninvasive prenatal testing based on enzymatic digestion of matched mother-child cell lines
(Zhang et al., 2019)		Homo sapiensnon-invasive prenatal testingblood plasmawhole genome sequencingGSE124686Open20192
Cell‐free DNA as a biomarker of ageing
(Teo et al., 2018)		Homo sapiensageingblood plasmawhole genome sequencingGSE114511hg19 readsOpen201812
Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin (Snyder et al., 2016)Homo sapienshealthy, lung cancer, pancreatic cancer, breast cancer, lupus erythematosus, colorectal cancer, prostate cancer, liver cancer, ovarian cancer, inflammatory bowel disease, melanoma, uterine cancer, head and neck cancer, bladder cancer, kidney cancer, testicular cancer, esophageal cancerblood plasmawhole genome sequencingGSE71378hg19 readsOpen201660
Detecting and Tracking Circulating Tumour DNA Copy Number Profiles during First Line Chemotherapy in Oesophagogastric Adenocarcinoma (Davidson et al., 2019)Homo sapiensesophageal cancer, gastric cancerblood plasmawhole genome sequencingEGAS00001003695Restricted201930
Modeling Cancer Risk from Genomic Data: cfDNA profiles of healthy individuals reflect nucleosomal patterns of white blood cells, while patients with cancer have altered fragmentation profiles (Cristiano, 2019)Homo sapienshealthy, breast cancer, colorectal cancer, lung cancer, ovarian cancer, pancreatic cancer, gastric cancer, bile duct cancerblood plasmawhole genome sequencingEGAS00001003611Restricted2019481
Enhanced detection of circulating tumor DNA by fragment size analysis (Mouliere et al., 2018)Homo sapiensovarian cancerblood plasmawhole genome sequencingEGAS00001003258Restricted2018200
Inferring expressed genes by whole-genome sequencing of plasma DNA (Ulz et al., 2016)Homo sapienshealthy, breast cancer, metastatic cancerblood plasmawhole genome sequencingEGAS00001001754Restricted2016285
Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer (Ulz et al., 2016)Homo sapiensprostate cancer, metastatic cancer, non-invasive prenatal testingblood plasmawhole genome sequencingEGAS00001000451Restricted201653
Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients (Mouliere et al., 2018)Homo sapiensbrain cancercerebrospinal fluid whole genome sequencingEGAS00001003255Restricted201813
Non-invasive whole genome sequencing of a human fetus (Kitzman et al, 2012)Homo sapiensnon-invasive prenatal testingblood plasmawhole genome sequencingphs000500.v1.p1Restricted20121
Quantitative characterization of tumor cell-free DNA shortening (Guo et al., 2020) Homo sapiensgastric cancer, lung cancerblood plasmawhole genome sequencingPRJNA328281,
SRP078170		Open2020610
WGS of human pooled plasma cfDNA sampled from GI diseased individuals (Spisák et al., 2013)Homo sapienshealthy, adenoma, colorectal cancer, inflammatory bowel diseaseblood plasmawhole genome sequencingERP002472Open2013200
Potential of cell-free DNA as a screening marker for parasite infections in dog (Akter et al., 2019)Canis lupus familiarisparasitic infectionblood plasmawhole genome sequencing DRA006208, DRP004267, PRJDB6396Open201914
Chromosomal Instability in Cell-free DNA Is a Serum Biomarker for Prostate Cancer (Schütz et al., 2015)Homo sapienshealthy, prostate cancer, hyperplasia, prostatitisblood serumwhole genome sequencingPRJEB7339Open2015431
Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection (Ulz et al., 2019)Homo sapienshealthy, colorectal cancer, prostate cancerblood plasmawhole genome sequencingEGAS00001003206Restricted201939
Non-invasive prenatal molecular karyotyping from maternal plasma (Yu et al., 2013)Homo sapiensnon-invasive prenatal testingblood plasmawhole genome sequencingEGAS00001000439Restricted20136
The next-generation sequencing (NGS) technologies related assessments of circulating tumor DNA (ctDNA) in both primary brain tumors and metastatic brain tumors (Liang et al., 2020)Homo sapiensmetastatic cancer, brain cancerblood plasmawhole genome sequencingPRJCA002535Restricted202028
Dnase1l3 knockout causes aberrations in plasma DNA fragmentation (Serpas et al., 2019)Mus musculusmutant, non-invasive prenatal testingblood plasmawhole genome sequencingEGAS00001003174Open201941
Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients (Jiang et al., 2015)Homo sapienshealthy, liver cancer, hepatitis B, liver cirrhosisblood plasmawhole genome sequencingEGAS00001001024Open2015225
Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing (Ramesh et al., 2020)Homo sapiensprostate cancerblood plasmawhole genome sequencing, exome sequencingPRJNA554329hg19 readsOpen202023
Bayesian-based noninvasive prenatal diagnosis of single-gene disorders (Rabinowitz et al., 2019)Homo sapiensnon-invasive prenatal testingblood plasmawhole genome sequencing, whole exome sequencingphs001659.v1.p1Restricted20199