Below is an interactive list of all available 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. (2016). Nucleosome positioning: resources and tools online. Briefings in Bioinformatics. 17, 745-757. |  Open access article

 

Cell-free DNA (cfDNA) datasets

DescriptionOrganismMedical conditioncfDNA sourceExperimental methodNCBI GEO IDEBI EGA IDRestricted access?YearNumber of patients
Shotgun sequencing of 5-hydroxymethylcysotine circulating cell-free DNA from the blood distinguishes solid tumor tissues of origin (Song et al., 2017)Homo sapiensglioblastoma, lung cancer, liver cancer, pancreatic cancerblood plasmahMe-Seal sequencingGSE81314no201779
Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic tumour DNAs for 23 well-characterised UBC patients (Togneri et al., 2016)Homo sapiensbladder cancerurinemicroarrayE-MTAB-3841no201523
High intensity sequencing of plasma cfDNA and WBC gDNA (Razavi et al., 2019)Homo sapiensmetastatic cancerblood plasmacfDNA-seqEGAD00001005302yes2019396
Improved SALP-seq method for construct next-generation sequencing library of cell free DNA (Wu et al., 2019)Homo sapiensesophageal cancerblood plasmaSALP-seqGSE116345no201920
Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin (Liu et al., 2019)Homo sapienshealthy, colorectal cancer, lung cancer, melanomablood plasmacfDNA-seqGSE124974yes2019102
Genome-wide analysis of cfDNA fragmentation patterns and nucleosome positioning in dual enzyme-digested NIPT quality control materials (DENQCMs) and maternal plasma (Zhang et al., 2019)Homo sapiensnoninvasive prenatal testingblood plasmacfDNA-seqGSE124686no20192
Sequencing of cfDNA derived from the plasma of individuals of different ages (Teo et al., 2019)Homo sapiensageingblood plasmacfDNA-seqGSE114511no201912
Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma (Arend et al., 2018)Homo sapiensovarian cancerblood plasmaIon Torrent panelGSE109934no201820
Genome profiling of free circulating tumor DNA by oncoscan and comparison to profiles in tumor biopsies evaluated by cytoscan ( Østrup et al., 2017)Homo sapiensmetastatic cancerblood plasmamicroarrayGSE85937no201713
Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma (Zhang et al., 2016)Homo sapienssepsisblood plasmacfDNA-seqGSE81178no20163
Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin (Snyder et al., 2016)Homo sapienslung cancer, colorectal cancer, liver cancer, breast cancer, autoimmune diseaseblood plasmacfDNA-seqGSE71378no201660
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, heart transplantationblood plasmaBisulfite sequencingGSE152648no201924
Comparison of the genome-wide DNA methylation status between FNA sample of pancreatic tumor and cfDNA samples from the same patients. MBD-sequencing (seq) was performed in paired samples of FNA and cfDNA from two patients. (Shinjo et al., 2020)Homo sapienspancreatic cancerblood serumMBD-seqGSE150468no20202
A direct comparison of two liquid biopsies: urine and blood in terms of how well they represent the prostate tumor methylome. (Silva et al., 2020)Homo sapiensprostate cancerurine, blood plasmaMethylation profiling by arrayGSE119260no202015
5-Hydroxymethylcytosines in Circulating Cell-free DNA Reveal Vascular Complications of Type 2 Diabetes (Yang et al., 2019)Homo sapienstype 2 diabetesblood plasma5hmC-Seal sequencingGSE125929no201962
Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (lung cancer) (Hao et al., 2017)Homo sapienslung cancerblood serumBisulfite sequencingGSE97932no2017654
Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (COAD) (Hao et al., 2017)Homo sapienscolon cancerblood serumBisulfite sequencingGSE97923no2017773
Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma (Chiuet al., 2019)Homo sapiensB-cell lymphomablood plasma5hmC-Seal sequencingGSE126676no201946
Genome-wide discovery and validation of diagnostic DNA methylation-based biomarkers for hepatocellular cancer detection in circulating cell free DNA (Hlady et al., 2019)Homo sapiensliver cancerblood plasmaMethylation profiling by arrayGSE129374no2019415
Genome-wide Mapping of 5-Hydroxymethylcytosines in Circulating Cell-free DNA as a Non-invasive Approach for Early Detection of Hepatocellular Carcinoma (Cat et al., 2019)Homo sapiensliver cancerblood plasma5hmC-Seal sequencingGSE112679no20192554
Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA (Liu et al., 2019)Homo sapienshealthy, non-malignant liver diseaseblood plasmaMCTA-seqGSE118690no201914
Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease (Moss et al., 2018)Homo sapienshealthyblood plasmaMethylation profiling by arrayGSE122126no201848
Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution (Zeng et al., 2019)Homo sapiensliver cancerblood plasma, blood serumCATCH-seqGSE112048no201918
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 pancreatic cancerblood plasmaMeDIP-seq, cfMeDIP-seqGSE79838no201824
Identification of cell-free DNA in gastric cancer patient (Bong, 2018)Homo sapiensgastric cancerblood serumaCGH arrayGSE108602no20182
Cell-free DNA modification dynamics in abiraterone acetate-treated prostate cancer patients ( Gordevičius et al., 2018)Homo sapiensprostate cancerblood plasmaMethylation profiling by arrayGSE108462no201833
Discovery of Methylated Circulating DNA Biomarkers For Comprehensive Non-Invasive Monitoring Of Treatment Response In Metastatic Colorectal Cancer (Barault et al., 2018)Homo sapienscolorectal cancerblood plasmaMethylation profiling by arrayGSE86078no2018181
DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers​ (Li et al., 2017)Homo sapienscolorectal cancer, gastric cancer, pancreatic cancer, liver cancer, thyroid cancerblood plasma5hmC-Seal sequencingGSE89570no2017260
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 sapiensbrain cancer, colon cancer, intestinal cancer, kidney cancer, liver cancer, lung cancer, pancreatic cancer, spleen cancer, gastric cancerblood plasmaBisulfite sequencingGSE79277no201759
Circulating-cell free DNA pooled samples for epigenome-wide discovery of methylation biomarkers for colorectal cancer screening (Gallardo-Gómez et al., 2018)Homo sapienscolorectal cancerblood serumMethylation profiling by arrayGSE110185no20186
Detection of mutational patterns in cell‐free DNA of colorectal cancer by custom amplicon sequencing (Herrmann et al., 2019)Homo sapienscolorectal cancerblood plasma cfDNA-seqEGAD00001004574yes2019189
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 sapienspediatric solid tumorsblood plasma, cerebrospinal fluidcf-RRBS sequencingEGAD00001005928yes202060
Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection (Ulz et al., 2019)Homo sapienscolon cancerblood plasmacfDNA-seqEGAD00001005343yes201941
Whole exome sequencing of cell-free DNA reveals temporo-spatial heterogeneity and identifies treatment-resistant clones in neuroblastoma (Chicard et al., 2017)Homo sapiensneuroblastomablood plasmacfDNA-seqEGAD00001003803yes2017146
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 sequencingEGAD00001006007yes202045
Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma (Yu et al., 2013)Homo sapiensnoninvasive prenatal testingblood plasmacfDNA-seqEGAS00001000439yes20131
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 plasmacfDNA-seqEGAD00001005070yes201950
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 plasmacfDNA-seqEGAD00001005737yes20208
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 plasmacfDNA-seqEGAD00001005339yes2019537
Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing (Chan et al., 2014)Homo sapienslupus erythematosusblood plasmaBisulfite sequencing, cfDNA-seqEGAD00001001093yes20142
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 cancerblood plasmacfDNA-seqEGAD00001004307yes201830
Enhanced detection of circulating tumor DNA by fragment size analysis (Mouliereet al., 2019)Homo sapienscolorectal cancer, bile duct cancer, lung cancer, ovarian cancer, breast cancer, brain cancer, renal cancer, pancreatic cancerblood plasmacfDNA-seqEGAD00001004939yes2019118
White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer (Leal et al., 2020)Homo sapiensgastric cancerblood plasmacfDNA-seqEGAD00001005750yes2020167
Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA (Che et al., 2020)Homo sapiensnoninvasive prenatal testingblood plasmacfDNA-seqEGAD00001004989yes202051
Inferring expressed genes by whole-genome sequencing of plasma DNA (Ulz et al., 2016)Homo sapiensbreast cancerblood plasmacfDNA-seqEGAS00001001754yes2016204
Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma (Huang et al., 2017)Homo sapiensliver cancerblood plasmacfDNA-seqEGAD00001003278yes2017124
Non-Invasive Cancer Diagnosis and Tissue-of-Origin Prediction Using Methylation Profiles of Cell-Free DNA (Kang et al., 2017)Homo sapienslung cancerblood plasmaBisulfite sequencingEGAD00001003168yes20179
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 sapiensliver cancerblood plasmaBisulfite sequencingEGAD00001004317yes201810
Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping (Vermeulen et al., 2017)Homo sapiensnoninvasive prenatal testingblood plasmacfDNA-seqEGAD00001003595yes201755
Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer (Herberts et al., 2020)Homo sapiensprostate cancerblood plasmacfDNA-seqEGAD00001006122yes2020114
Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer (Taavitsainen et al., 2019)Homo sapiensprostate cancerblood plasmacfDNA-seqEGAD00001004486yes201948
Needlestack: an ultra-sensitive variant caller for
multi-sample next generation sequencing data (Delhomme et al., 2020)
Homo sapienshealthyblood plasmacfDNA-seqEGAD00001005463yes2020125
Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer (Ulz et al., 2016)Homo sapiensprostate cancerblood plasmacfDNA-seqEGAD00001000364yes201650
Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer (Ritch et al., 2019)Homo sapiensprostate cancerblood plasmacfDNA-seqEGAD00001005474yes2019154
Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients (Mouliere et al., 2018)Homo sapiensbrain cancercerebrospinal fluid cfDNA-seqEGAD00001004425yes201813