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
| Description | Organism | Medical condition | cfDNA source | Experimental method | NCBI GEO ID | EBI EGA ID | Restricted access? | Year | Number 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 sapiens | healthy, hepatocellular carcinoma, breast cancer, lung cancer, pancreatic cancer, glioblastoma, gastric cancer, colorectal cancer, hepatitis B | blood plasma | hMe-Seal sequencing | GSE81314 | no | 2017 | 121 | |
| 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 sapiens | bladder cancer | urine | microarray | E-MTAB-3841 | no | 2015 | 23 | |
| High intensity sequencing of plasma cfDNA and WBC gDNA (Razavi et al., 2019) | Homo sapiens | healthy, breast cancer, lung cancer, prostate cancer | blood plasma | cfDNA-seq | EGAD00001005302 | yes | 2019 | 396 | |
| Improved SALP-seq method for construct next-generation sequencing library of cell free DNA (Wu et al., 2019) | Homo sapiens | healthy, esophageal cancer | blood plasma | SALP-seq | GSE116345 | no | 2019 | 20 | |
| Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin (Liu et al., 2019) | Homo sapiens | healthy, colorectal cancer, lung cancer, melanoma | blood plasma | cfDNA-seq | GSE124974 | yes | 2019 | 102 | |
| 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 sapiens | noninvasive prenatal testing | blood plasma | cfDNA-seq | GSE124686 | no | 2019 | 2 | |
| Sequencing of cfDNA derived from the plasma of individuals of different ages (Teo et al., 2019) | Homo sapiens | ageing | blood plasma | cfDNA-seq | GSE114511 | no | 2019 | 12 | |
| Molecular Response to Neoadjuvant Chemotherapy in High-Grade Serous Ovarian Carcinoma (Arend et al., 2018) | Homo sapiens | ovarian cancer | blood plasma | Ion Torrent panel | GSE109934 | no | 2018 | 40 | |
| Genome profiling of free circulating tumor DNA by oncoscan and comparison to profiles in tumor biopsies evaluated by cytoscan ( Østrup et al., 2017) | Homo sapiens | bile duct cancer, stomach cancer, pancreatic cancer, oesophageal cancer, lung cancer, colon cancer, breast cancer, cervical cancer | blood plasma | microarray | GSE85937 | no | 2017 | 13 | |
| Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma (Zhang et al., 2016) | Homo sapiens | sepsis | blood plasma | cfDNA-seq | GSE81178 | no | 2016 | 28 | |
| Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin (Snyder et al., 2016) | Homo sapiens | healthy, lung cancer, pancreatic cancer, breast cancer, lupus, colorectal cancer, prostate cancer, liver cancer, ovarian cancer, Crohn's disease, ulcerative colitis, melanoma, uterine cancer, head and neck cancer, bladder cancer, kidney cancer, testicular cancer, esophageal cancer | blood plasma | cfDNA-seq | GSE71378 | no | 2016 | 60 | |
| 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 sapiens | acute cellular rejection, heart transplantation | blood plasma | Bisulfite sequencing | GSE152648 | no | 2019 | 24 | |
| 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 sapiens | pancreatic cancer | blood serum | MBD-seq | GSE150468 | no | 2020 | 2 | |
| 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 sapiens | prostate cancer | urine, blood plasma | Methylation profiling by array | GSE119260 | no | 2020 | 8 | |
| 5-Hydroxymethylcytosines in Circulating Cell-free DNA Reveal Vascular Complications of Type 2 Diabetes (Yang et al., 2019) | Homo sapiens | type 2 diabetes | blood plasma | 5hmC-Seal sequencing | GSE125929 | no | 2019 | 62 | |
| Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (lung cancer) (Hao et al., 2017) | Homo sapiens | lung cancer | blood serum | Bisulfite sequencing | GSE97932 | no | 2017 | 654 | |
| Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (COAD) (Hao et al., 2017) | Homo sapiens | colon cancer | blood serum | Bisulfite sequencing | GSE97923 | no | 2017 | 773 | |
| Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma (Chiuet al., 2019) | Homo sapiens | B-cell lymphoma | blood plasma | 5hmC-Seal sequencing | GSE126676 | no | 2019 | 46 | |
| 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 sapiens | liver cancer | blood plasma | Methylation profiling by array | GSE129374 | no | 2019 | 415 | |
| 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 sapiens | liver cancer | blood plasma | 5hmC-Seal sequencing | GSE112679 | no | 2019 | 2554 | |
| Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA (Liu et al., 2019) | Homo sapiens | healthy, non-malignant liver disease | blood plasma | MCTA-seq | GSE118690 | no | 2019 | 14 | |
| Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease (Moss et al., 2018) | Homo sapiens | healthy | blood plasma | Methylation profiling by array | GSE122126 | no | 2018 | 48 | |
| Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution (Zeng et al., 2019) | Homo sapiens | liver cancer | blood plasma, blood serum | CATCH-seq | GSE112048 | no | 2019 | 18 | |
| 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 cancer | blood plasma | MeDIP-seq, cfMeDIP-seq | GSE79838 | no | 2018 | 24 | |
| Identification of cell-free DNA in gastric cancer patient (Bong, 2018) | Homo sapiens | gastric cancer | blood serum | aCGH array | GSE108602 | no | 2018 | 2 | |
| Cell-free DNA modification dynamics in abiraterone acetate-treated prostate cancer patients ( Gordevičius et al., 2018) | Homo sapiens | prostate cancer | blood plasma | Methylation profiling by array | GSE108462 | no | 2018 | 33 | |
| Discovery of Methylated Circulating DNA Biomarkers For Comprehensive Non-Invasive Monitoring Of Treatment Response In Metastatic Colorectal Cancer (Barault et al., 2018) | Homo sapiens | colorectal cancer | blood plasma | Methylation profiling by array | GSE86078 | no | 2018 | 181 | |
| DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers (Li et al., 2017) | Homo sapiens | colorectal cancer, gastric cancer, pancreatic cancer, liver cancer, thyroid cancer | blood plasma | 5hmC-Seal sequencing | GSE89570 | no | 2017 | 260 | |
| 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 sapiens | brain cancer, colon cancer, intestinal cancer, kidney cancer, liver cancer, lung cancer, pancreatic cancer, spleen cancer, gastric cancer | blood plasma | Bisulfite sequencing | GSE79277 | no | 2017 | 59 | |
| Circulating-cell free DNA pooled samples for epigenome-wide discovery of methylation biomarkers for colorectal cancer screening (Gallardo-Gómez et al., 2018) | Homo sapiens | colorectal cancer | blood serum | Methylation profiling by array | GSE110185 | no | 2018 | 6 | |
| Detection of mutational patterns in cell‐free DNA of colorectal cancer by custom amplicon sequencing (Herrmann et al., 2019) | Homo sapiens | colorectal cancer | blood plasma | cfDNA-seq | EGAD00001004574 | yes | 2019 | 189 | |
| 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 sapiens | pediatric solid tumors | blood plasma, cerebrospinal fluid | cf-RRBS sequencing | EGAD00001005928 | yes | 2020 | 60 | |
| Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection (Ulz et al., 2019) | Homo sapiens | colon cancer | blood plasma | cfDNA-seq | EGAD00001005343 | yes | 2019 | 41 | |
| Whole exome sequencing of cell-free DNA reveals temporo-spatial heterogeneity and identifies treatment-resistant clones in neuroblastoma (Chicard et al., 2017) | Homo sapiens | neuroblastoma | blood plasma | cfDNA-seq | EGAD00001003803 | yes | 2017 | 146 | |
| Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome (Van Paemel et al., 2020) | Homo sapiens | healthy | blood plasma | cf-RRBS sequencing | EGAD00001006007 | yes | 2020 | 45 | |
| Noninvasive Prenatal Molecular Karyotyping from Maternal Plasma (Yu et al., 2013) | Homo sapiens | noninvasive prenatal testing | blood plasma | cfDNA-seq | EGAS00001000439 | yes | 2013 | 1 | |
| Detecting and Tracking Circulating Tumour DNA Copy Number Profiles during First Line Chemotherapy in Oesophagogastric Adenocarcinoma (Davidson et al., 2019) | Homo sapiens | esophageal cancer, gastric cancer | blood plasma | cfDNA-seq | EGAD00001005070 | yes | 2019 | 50 | |
| 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 sapiens | colorectal cancer | blood plasma | cfDNA-seq | EGAD00001005737 | yes | 2020 | 8 | |
| 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 sapiens | healthy, breast cancer, colorectal cancer, lung cancer, ovarian cancer, pancreatic cancer, gastric cancer, bile duct cancer | blood plasma | cfDNA-seq | EGAD00001005339 | yes | 2019 | 537 | |
| Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing (Chan et al., 2014) | Homo sapiens | lupus erythematosus | blood plasma | Bisulfite sequencing, cfDNA-seq | EGAD00001001093 | yes | 2014 | 2 | |
| 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 sapiens | colorectal cancer | blood plasma | cfDNA-seq | EGAD00001004307 | yes | 2018 | 30 | |
| Enhanced detection of circulating tumor DNA by fragment size analysis (Mouliereet al., 2019) | Homo sapiens | colorectal cancer, bile duct cancer, lung cancer, ovarian cancer, breast cancer, brain cancer, renal cancer, pancreatic cancer | blood plasma | cfDNA-seq | EGAD00001004939 | yes | 2019 | 118 | |
| White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer (Leal et al., 2020) | Homo sapiens | gastric cancer | blood plasma | cfDNA-seq | EGAD00001005750 | yes | 2020 | 167 | |
| Noninvasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA (Che et al., 2020) | Homo sapiens | noninvasive prenatal testing | blood plasma | cfDNA-seq | EGAD00001004989 | yes | 2020 | 51 | |
| Inferring expressed genes by whole-genome sequencing of plasma DNA (Ulz et al., 2016) | Homo sapiens | breast cancer | blood plasma | cfDNA-seq | EGAS00001001754 | yes | 2016 | 204 | |
| Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma (Huang et al., 2017) | Homo sapiens | liver cancer | blood plasma | cfDNA-seq | EGAD00001003278 | yes | 2017 | 124 | |
| Non-Invasive Cancer Diagnosis and Tissue-of-Origin Prediction Using Methylation Profiles of Cell-Free DNA (Kang et al., 2017) | Homo sapiens | lung cancer | blood plasma | Bisulfite sequencing | EGAD00001003168 | yes | 2017 | 9 | |
| 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 sapiens | liver cancer | blood plasma | Bisulfite sequencing | EGAD00001004317 | yes | 2018 | 10 | |
| Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping (Vermeulen et al., 2017) | Homo sapiens | noninvasive prenatal testing | blood plasma | cfDNA-seq | EGAD00001003595 | yes | 2017 | 55 | |
| Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer (Herberts et al., 2020) | Homo sapiens | prostate cancer | blood plasma | cfDNA-seq | EGAD00001006122 | yes | 2020 | 114 | |
| Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer (Taavitsainen et al., 2019) | Homo sapiens | prostate cancer | blood plasma | cfDNA-seq | EGAD00001004486 | yes | 2019 | 48 | |
| Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data (Delhomme et al., 2020) | Homo sapiens | healthy | blood plasma | cfDNA-seq | EGAD00001005463 | yes | 2020 | 125 | |
| Whole-genome plasma sequencing reveals focal amplifications as a driving force in metastatic prostate cancer (Ulz et al., 2016) | Homo sapiens | prostate cancer | blood plasma | cfDNA-seq | EGAD00001000364 | yes | 2016 | 50 | |
| Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer (Ritch et al., 2019) | Homo sapiens | prostate cancer | blood plasma | cfDNA-seq | EGAD00001005474 | yes | 2019 | 154 | |
| Detection of cell-free DNA fragmentation and copy number alterations in cerebrospinal fluid from glioma patients (Mouliere et al., 2018) | Homo sapiens | brain cancer | cerebrospinal fluid | cfDNA-seq | EGAD00001004425 | yes | 2018 | 13 | |
| 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 sapiens | glioma, metastatic brain cancer | blood plasma | cfDNA-seq | PRJCA002535 | no | 2020 | 29 | |
| Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment () | Homo sapiens | prostate cancer | blood plasma | cfMeDIP-seq | GSE152631 | no | 2020 | 16 |