Sequenced cell-free DNA (cfDNA) datasets
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
Jump to: NucPosDB front page | stable nucleosomes of the human genome | experimental nucleosome maps in vivo | experimental cfDNA datasets | tools for analysis of nucleosome mapping experiments | tools for prediction of nucleosome maps from DNA sequence | tools for analysis of sequenced cfDNA
| Description | Organism | Medical condition | cfDNA source | Experimental method | Raw data | Processed data | Access | Year | Number of patients |
|---|---|---|---|---|---|---|---|---|---|
| Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns (Ma et al., 2017) | Homo sapiens | gastric cancer, lung cancer | blood plasma | whole genome sequencing | SRA438908 | all nucleosomes hg19 | stable nucleosomes hg19| stable nucleosomes hg38 | Open | 2017 | 5 |
| Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing (Ramesh et al., 2020) | Homo sapiens | prostate cancer, metastatic cancer, bone cancer, liver cancer, lung cancer | blood plasma | whole genome sequencing, exome sequencing | PRJNA554329 | all nucleosomes hg19 | stable nucleosomes hg19| stable nucleosomes hg38 | Open | 2020 | 23 |
| Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease (Butler et al., 2015) | Homo sapiens | breast cancer, metastatic cancer | blood plasma | exome sequencing | PRJEB8969 | all nucleosomes hg19| stable nucleosomes hg19| stable nucleosomes hg38 | Open | 2015 | 2 |
| Cell‐free DNA as a biomarker of ageing (Teo et al., 2018) | Homo sapiens | ageing | blood plasma | whole genome sequencing | GSE114511 | all nucleosomes hg19 | stable nucleosomes hg19| stable nucleosomes hg38 | Open | 2018 | 12 |
| 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages (Song et al., 2017) | Homo sapiens | healthy, liver cancer, breast cancer, lung cancer, pancreatic cancer, brain cancer, gastric cancer, colorectal cancer, hepatitis B | blood plasma | 5hmC-Seal sequencing | GSE81314 | all nucleosomes hg19 | stable nucleosomes hg19| stable nucleosomes hg38 | Open | 2017 | 121 |
| 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 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 cancer | blood plasma | whole genome sequencing | GSE71378 | all nucleosomes hg19 | stable nucleosomes hg19| stable nucleosomes hg38 | Open | 2016 | 60 |
| Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden (Peneder et al., 2021) | Homo sapiens | healthy, bone cancer | blood plasma | whole genome sequencing | EGAS00001005127 | processed aggregated data | Restricted | 2021 | 148 |
| 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 | Open | 2019 | 62 | |
| Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden (Zhu et al., 2021) | Homo sapiens | healthy, colorectal cancer, breast cancer | blood plasma | whole genome sequencing, targeted sequencing | EGAS00001004657 | Restricted | 2021 | 51 | |
| Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer (Keup et al, 2021) | Homo sapiens | breast cancer, metastatic cancer | blood plasma | targeted sequencing | PRJEB39331 | Open | 2021 | 26 | |
| Transcriptional Start Site Coverage Analysis in Plasma Cell-Free DNA Reveals Disease Severity and Tissue Specificity of COVID-19 Patients (Chen et al, 2021) | Homo sapiens | healthy, COVID-19 | blood plasma | whole genome sequencing | CNP0001059 | Restricted | 2021 | 4 | |
| Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients (Mouliere et al., 2021) | Homo sapiens | healthy, brain cancer | cerebrospinal fluid, blood plasma, urine | whole exome sequencing, whole genome sequencing, targeted sequencing | EGAS00001004355 | Restricted | 2021 | 36 | |
| A Study of Cell-Free DNA Fragmentation Pattern and Its Application in DNA Sample Type Classification (Chen et al., 2018) | Homo sapiens | brain cancer, metastatic cancer, breast cancer, lung cancer | cerebrospinal fluid, blood plasma | targeted sequencing, exome sequencing | PRJNA266729 | Restricted | 2018 | 57 | |
| Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer (Herberts et al., 2020) | Homo sapiens | prostate cancer, metastatic cancer | blood plasma | exome sequencing, targeted sequencing | EGAS00001004328 | Restricted | 2020 | 599 | |
| 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, tissue transplantation | blood plasma | bisulfite sequencing | GSE152648 | Open | 2019 | 24 | |
| Bayesian-based noninvasive prenatal diagnosis of single-gene disorders (Rabinowitz et al., 2019) | Homo sapiens | non-invasive prenatal testing | blood plasma | whole genome sequencing, whole exome sequencing | phs001659.v1.p1 | Restricted | 2019 | 9 | |
| Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution (Zeng et al., 2019) | Homo sapiens | healthy, liver cancer | blood plasma, blood serum | bisulfite sequencing, targeted sequencing | GSE112048 | Open | 2019 | 6 | |
| 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 | healthy, liver cancer | blood plasma | bisulfite sequencing | EGAS00001002728 | Restricted | 2018 | 8 | |
| Cell-free DNA methylation markers in diagnosis and prognosis of common cancer (Hao et al., 2017) | Homo sapiens | colon cancer | blood serum | bisulfite sequencing | GSE97923 | Open | 2017 | 773 | |
| Cell-free DNA methylation markers in diagnosis and prognosis of common cancers (Hao et al., 2017) | Homo sapiens | lung cancer | blood serum | bisulfite sequencing | GSE97932 | Open | 2017 | 654 | |
| ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs (Sadeh et al., 2020) | Homo sapiens | healthy, acute myocardial infarction, benign liver disease, metastatic cancer, colorectal cancer | blood plasma | ChIP-seq | zenodo.4277001 | Open | 2020 | 150 | |
| Chromosomal Instability in Cell-free DNA Is a Serum Biomarker for Prostate Cancer (Schütz et al., 2015) | Homo sapiens | healthy, prostate cancer, hyperplasia, prostatitis | blood serum | targeted sequencing | PRJEB7339 | Open | 2015 | 431 | |
| Circumventing intratumoral heterogeneity to identify potential therapeutic targets in hepatocellular carcinoma (Huang et al., 2017) | Homo sapiens | liver cancer | blood plasma | exome sequencing, targeted sequencing | EGAS00001002207 | Restricted | 2017 | 9 | |
| 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 sapiens | lung 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 cancer | blood plasma | targeted sequencing | EGAS00001002251 | Restricted | 2017 | 605 | |
| 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 sapiens | healthy, pancreatic cancer | blood serum | MBD-seq | GSE150468 | Open | 2020 | 4 | |
| Decoding genetic and epigenetic information embedded in cell free DNA with adapted SALP‐seq (Wu et al., 2019) | Homo sapiens | healthy, esophageal cancer | blood plasma | SALP-seq | GSE116345 | Open | 2019 | 20 | |
| 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 | whole genome sequencing | EGAS00001003695 | Restricted | 2019 | 30 | |
| 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 | whole genome sequencing | EGAS00001003255 | Restricted | 2018 | 13 | |
| 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 | targeted sequencing | EGAS00001003382 | Restricted | 2019 | 34 | |
| Direct detection of early-stage cancers using circulating tumor DNA (Phallen et al., 2019) | Homo sapiens | healthy, breast cancer, colorectal cancer, lung cancer, ovarian cancer | blood plasma | targeted sequencing | EGAS00001002577 | Restricted | 2019 | 238 | |
| DNA 5-hydroxymethylcytosines from cell-free circulating DNA as diagnostic biomarkers for human cancers (Li et al., 2017) | Homo sapiens | healthy, colorectal cancer, gastric cancer, pancreatic cancer, liver cancer, thyroid cancer, benign tumour | blood plasma | 5hmC-Seal sequencing | GSE89570 | Open | 2017 | 350 | |
| Dnase1l3 knockout causes aberrations in plasma DNA fragmentation (Serpas et al., 2019) | Mus musculus | Dnase1l3 knockout | blood plasma | whole genome sequencing | EGAS00001003174 | Restricted | 2019 | 41 | |
| Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment (Peter et al., 2020) | Homo sapiens | prostate cancer | blood plasma | MeDIP-seq | GSE152631 | Open | 2020 | 16 | |
| Enhanced detection of circulating tumor DNA by fragment size analysis (Mouliere et al., 2018) | Homo sapiens | ovarian cancer | blood plasma | whole genome sequencing | EGAS00001003258 | Restricted | 2018 | 200 | |
| Epigenetic analyses of methylation and nucleosome occupancy in cell-free DNA (Erger et al., 2020) | Homo sapiens | healthy, benign kidney disease | blood plasma, urine | whole genome sequencing | EGAS00001004370 | Restricted | 2020 | 21 | |
| Evaluation of commercial Guardant360 ctDNA test in metastatic prostate cancer (Taavitsainen et al., 2019) | Homo sapiens | prostate cancer, metastatic cancer | blood plasma | targeted sequencing | EGAS00001003352 | Restricted | 2019 | 24 | |
| 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 sapiens | prostate cancer | blood plasma | targeted sequencing | PRJEB12109 | Open | 2016 | 62 | |
| 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 sapiens | non-invasive prenatal testing | blood plasma | whole genome sequencing | GSE124686 | Open | 2019 | 2 | |
| Genome-scale DNA methylation analysis of tissue-of-origin of plasma cell-free DNA (Liu et al., 2019) | Homo sapiens | healthy, benign liver disease | blood plasma | MCTA-seq | GSE118690 | Open | 2019 | 14 | |
| 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 sapiens | healthy, liver cancer, hepatitis B, liver cirrhosis, benign tumour | blood plasma | 5hmC-Seal sequencing | GSE112679 | Open | 2019 | 2554 | |
| 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 | bisulfite sequencing, whole genome sequencing | EGAD00001006007, EGAS00001004271 | Restricted | 2020 | 3 | |
| High intensity sequencing of plasma cfDNA and WBC gDNA (Razavi et al., 2019) | Homo sapiens | healthy, breast cancer, lung cancer, prostate cancer | blood plasma | whole genome sequencing | EGAS00001003755 | Restricted | 2019 | 196 | |
| Identification of hypermutation and defective mismatch repair in ctDNA from metastatic prostate cancer (Ritch et al., 2020) | Homo sapiens | prostate cancer, metastatic cancer | blood plasma | exome sequencing, targeted sequencing | EGAS00001003899 | Restricted | 2020 | 433 | |
| 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 | healthy, colorectal cancer, lung cancer | blood plasma | RRBS | GSE79277 | Open | 2017 | 134 | |
| Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection (Ulz et al., 2019) | Homo sapiens | healthy, colorectal cancer, prostate cancer | blood plasma | whole genome sequencing | EGAS00001003206 | Restricted | 2019 | 39 | |
| Inferring expressed genes by whole-genome sequencing of plasma DNA (Ulz et al., 2016) | Homo sapiens | healthy, breast cancer, metastatic cancer | blood plasma | whole genome sequencing | EGAS00001001754 | Restricted | 2016 | 285 | |
| Integrated digital error suppression for ultrasensitive detection of circulating tumor DNA (Newman et al., 2016) | Homo sapiens | healthy, lung cancer | blood plasma | CAPP-Seq | PRJNA311126 | Open | 2016 | 172 | |
| Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients (Jiang et al., 2015) | Homo sapiens | healthy, liver cancer, hepatitis B, liver cirrhosis | blood plasma | whole genome sequencing | EGAS00001001024 | Restricted | 2015 | 225 | |
| 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, metastatic cancer | blood plasma | exome sequencing | EGAS00001002687 | Restricted | 2018 | 30 | |
| Liver- and Colon-Specific DNA Methylation Markers in Plasma for Investigation of Colorectal Cancers with or without Liver Metastases (Gai et al., 2018) | Homo sapiens | tissue transplantation | blood plasma | bisulfite sequencing, whole genome sequencing | EGAS00001003116 | Restricted | 2018 | 14 | |
| 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 cancer | blood plasma | MeDIP-seq | GSE79838 | Open | 2018 | 2 | |
| 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 | healthy, pediatric solid tumours | blood plasma, cerebrospinal fluid | bisulfite sequencing, whole genome sequencing | EGAS00001004194 | Restricted | 2020 | 59 | |
| 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 | whole genome sequencing | EGAS00001003611 | Restricted | 2019 | 481 | |
| Monitoring clonal evolution and resistance to EGFR blockade in the blood of metastatic colorectal cancer patients (Siravegna et al., 2015) | Homo sapiens | colorectal cancer, metastatic cancer | blood plasma | targeted sequencing | PRJEB9202 | Open | 2015 | 100 | |
| Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients (Martignano et al., 2021) | Homo sapiens | healthy, lung cancer | blood plasma | whole genome sequencing | EGAS00001004975 | Restricted | 2021 | 11 | |
| Needlestack: an ultra-sensitive variant caller for multi-sample next generation sequencing data (Delhomme et al., 2020) | Homo sapiens | healthy | blood plasma | exome sequencing | EGAS00001003989 | Restricted | 2020 | 125 | |
| Non-Invasive Cancer Diagnosis and Tissue-of-Origin Prediction Using Methylation Profiles of Cell-Free DNA (Kang et al., 2017) | Homo sapiens | lung cancer, benign tumour | blood plasma | bisulfite sequencing | EGAS00001002211 | Restricted | 2017 | 9 | |
| Non-invasive prenatal diagnosis by genome-wide haplotyping of cell-free plasma DNA (Che et al., 2020) | Homo sapiens | non-invasive prenatal testing | blood plasma | targeted sequencing | EGAS00001003634 | Restricted | 2020 | 9 | |
| Non-invasive prenatal molecular karyotyping from maternal plasma (Yu et al., 2013) | Homo sapiens | non-invasive prenatal testing | blood plasma | whole genome sequencing | EGAS00001000439 | Restricted | 2013 | 6 | |
| Non-invasive whole genome sequencing of a human fetus (Kitzman et al, 2012) | Homo sapiens | non-invasive prenatal testing | blood plasma | whole genome sequencing | phs000500.v1.p1 | Restricted | 2012 | 1 | |
| Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin (Sun et al., 2019) | Homo sapiens | colorectal cancer | blood plasma | bisulfite sequencing, whole genome sequencing | EGAS00001003117 | Restricted | 2019 | 11 | |
| Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution (Abbosh et al., 2017) | Homo sapiens | lung cancer | blood plasma | whole exome sequencing | EGAS00001002247 | Restricted | 2017 | 100 | |
| Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing (Chan et al., 2014) | Homo sapiens | healthy, lupus erythematosus | blood plasma | bisulfite sequencing, whole genome sequencing | EGAS00001000962 | Restricted | 2014 | 35 | |
| Potential of cell-free DNA as a screening marker for parasite infections in dog (Akter et al., 2019) | Canis lupus familiaris | parasitic infection | blood plasma | whole genome sequencing | DRA006208, DRP004267, PRJDB6396 | Open | 2019 | 14 | |
| Prognostic implications of 5-hydroxymethylcytosines from circulating cell-free DNA in diffuse large B-cell lymphoma (Chiu et al., 2019) | Homo sapiens | B-cell lymphoma | blood plasma | 5hmC-Seal sequencing | GSE126676 | Open | 2019 | 48 | |
| 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 | exome sequencing | EGAS00001004088 | Restricted | 2020 | 1 | |
| Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors (Adalsteinsson et al., 2017) | Homo sapiens | healthy, breast cancer, prostate cancer, metastatic cancer | blood plasma | whole exome sequencing, whole genome sequencing | phs001417.v1.p1 | Restricted | 2017 | 545 | |
| Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends (Chan et al., 2016) | Homo sapiens | non-invasive prenatal testing | blood plasma | whole genome sequencing | EGAS00001001882 | Restricted | 2016 | 2 | |
| Sensitive Monogenic Non-invasive Prenatal Diagnosis by Targeted Haplotyping (Vermeulen et al., 2017) | Homo sapiens | non-invasive prenatal testing | blood plasma | targeted sequencing | EGAS00001002622 | Restricted | 2017 | 20 | |
| Statistical analysis of mutant allele frequency level of circulating cell-free DNA and blood cells in healthy individuals (Xia et al., 2017) | Homo sapiens | healthy, kidney cancer, pancreatic cancer, liver cancer, breast cancer, lung cancer, uterine cancer, psoriasis, Hashimoto's disease, hepatitis B | blood plasma | targeted sequencing | PRJNA384491, SRP105315 | Open | 2017 | 826 | |
| Targeted next generation sequencing of cfDNA from lung cancer patients enrolled in the GALAXY-1 trial (Rakhit, 2018) | Homo sapiens | lung cancer | blood plasma | targeted sequencing | PRJEB20969 | Open | 2018 | 259 | |
| 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 | metastatic cancer, brain cancer | blood plasma | whole genome sequencing | PRJCA002535 | Open | 2020 | 28 | |
| Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract (Burnham et al., 2018) | Homo sapiens | bacteriuria | urine | bisulfite sequencing, whole genome sequencing | phs001564.v1.p1., phs001564.v3.p1 | Restricted | 2018 | 130 | |
| Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma (Zhang et al., 2016) | Homo sapiens | sepsis, tissue transplantation | blood plasma | whole genome sequencing | GSE81178 | Open | 2016 | 7 | |
| WGS of human pooled plasma cfDNA sampled from GI diseased individuals (Spisák et al., 2013) | Homo sapiens | healthy, adenoma, colorectal cancer, inflammatory bowel disease | blood plasma | whole genome sequencing | ERP002472 | Open | 2013 | 24 samples (pooled from 200 patients) | |
| 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 | targeted sequencing | EGAS00001004114 | Restricted | 2020 | 50 | |
| Whole exome sequencing of cell-free DNA reveals temporo-spatial heterogeneity and identifies treatment-resistant clones in neuroblastoma (Chicard et al., 2017) | Homo sapiens | brain cancer | blood plasma | exome sequencing | EGAS00001002705 | Restricted | 2017 | 19 | |
| Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing (Heitzer et al., 2013) | Homo sapiens | prostate cancer | blood plasma | whole genome sequencing | EGAS00001000451 | Restricted | 2016 | 53 |