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
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Description Organism Medical condition cfDNA source Experimental method Raw data Processed data Access Year Number of patients
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 hg19 reads Open 2017 121
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
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 Open 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 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 hg19 reads Open 2016 60
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
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, metastatic cancer, liver cancer, brain cancer blood plasma whole genome sequencing SRA438908 Open 2017 5
Cell‐free DNA as a biomarker of ageing
(Teo et al., 2018)Homo sapiens ageing blood plasma whole genome sequencing GSE114511 hg19 reads Open 2018 12
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
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 hg19 reads Open 2020 23
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 mutant, non-invasive prenatal testing 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
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 Open 2015 2
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, brain cancer, colon cancer, intestinal cancer, kidney cancer, liver cancer, lung cancer, pancreatic cancer, spleen cancer, gastric cancer blood plasma bisulfite sequencing 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 200
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