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 | glioblastoma, lung cancer, liver cancer, pancreatic cancer | blood plasma | hMe-Seal sequencing | GSE81314 | no | 2017 | 79 | |
| 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 | metastatic 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 | 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 | 20 | |
| 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 | metastatic 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 | 3 | |
| Cell-free DNA comprises an in vivo, genome-wide nucleosome footprint that informs its tissue(s)-of-origin (Snyder et al., 2016) | Homo sapiens | lung cancer, colorectal cancer, liver cancer, breast cancer, autoimmune disease | 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 | 15 | |
| 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 |