Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Minimally invasive classification of pediatric solid tumors using reduced representation bisulfite sequencing of cell-free DNA: a proof-of-principle study

ABSTRACT: This submission contains the data from https://www.biorxiv.org/content/10.1101/795047v2.full This dataset contains processed data of cell-free reduced representation bisulfite sequencing from 60 pediatric cancer samples, in order to classify them according to histopathological diagnosis. Files are provided in bismark coverage format. Samples were sequenced on a NextSeq 500.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Ruben Van Paemel

PROVIDER: E-MTAB-8770 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

Project description:In this study, we evaluated the effect of preservation agent on the effect of the methylation pattern of cell-free DNA. The methylation pattern was assessed with cell-free reduced representation sequencing (cf-RRBS). Blood was drawn from three healthy individuals (male and females between 24 and 50 years old). 15 tubes were drawn per healthy volunteer: 3x BD Vacutainer K2E EDTA spray tubes (REF 367525), 3x Streck Cell-Free DNA BCT tubes (catalogue number 218962), 3x PAXgene Blood ccfDNA tubes (catalogue number 768115), 3x Roche Cell-Free DNA Collection tubes (catalogue number 07785674001) and 3x Biomatrica LBgard blood tubes (SKU 68021-001), resulting in 45 samples in total. All 45 samples were sequenced on a NovaSeq6000. Samples are given as bismark coverage files (GRCh37).

2020-04-03 | E-MTAB-8858 | biostudies-arrayexpress

sWGS on paired cfDNA and tissue DNA from pediatric cancer patients

Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.

2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress

Genome-wide plasma cell-free DNA methylation profiling in pancreatic cancer patients using MeDIP-seq

Project description:We carried out a genome-wide cfDNA methylation profiling study of pancreatic ductal adenocarcinoma (PDAC) patients by Methylated DNA Immunoprecipitation coupled with high-throughput sequencing (MeDIP-seq). Compared with healthy individuals, 775 differentially methylated regions (DMRs) located in promoter regions were identified in PDAC patients with 761 hypermethylated and 14 hypomethylated regions; meanwhile, 761 DMRs in CpG islands (CGIs) were identified in PDAC patients with 734 hypermethylated and 27 hypomethylated regions (p-value < 35 0.0001). 143 hypermethylated DMRs were further selected which were located in promoter regions and completely overlapped with CGIs. A total of 8 probes from 8 genes were found to fairly distinguish PDAC patients from the healthy individuals, including TRIM73, FAM150A, EPB41L3, SIX3, MIR663, MAPT, LOC100128977 and LOC100130148.

2020-10-29 | E-MTAB-9678 | biostudies-arrayexpress

Machine learning-based detection of immune-mediated diseases from genome-wide cell-free DNA sequencing datasets

Project description:The early detection of tissue and organ damage associated with autoimmune diseases (AID) has been identified as key to improve long-term survival, but non-invasive biomarkers are lacking. Elevated cell-free DNA (cfDNA) levels have been observed in AID and inflammatory bowel disease (IBD), prompting interest to use cfDNA as a potential non-invasive diagnostic and prognostic biomarker. Despite these known disease-related changes in concentration, it remains impossible to identify AID and IBD patients through cfDNA analysis alone. By using unsupervised clustering on large sets of shallow whole-genome sequencing (sWGS) cfDNA data, we uncover AID- and IBD-specific genome-wide patterns in plasma cfDNA in both the obstetric and general AID and IBD populations. Supervised learning of the genome-wide patterns allows AID prediction with 50% sensitivity at 95% specificity. Importantly, the method can identify pregnant women with AID during routine non-invasive prenatal screening. Since AID pregnancies have an increased risk of severe complications, early recognition or detection of new onset AID can redirect pregnancy management and limit potential adverse events. This method opens up new avenues for screening, diagnosis and monitoring of AID and IBD.

2022-09-14 | E-MTAB-11607 | biostudies-arrayexpress

Genome-wide plasma cell-free DNA methylation profiling in lung cancer patients using MeDIP-seq

Project description:As a non-invasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma is raising increasing interest due to its diagnostic and biology applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. Through enriching methylated cfDNA fragments with MeDIP followed by deep sequencing, we aimed to characterize cfDNA methylome in cancer patients. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. MEDIPS package was used for the identification of differentially methylated regions (DMRs) between patients and normal ones. Overall, we identified 330 differentially methylated regions (DMRs) in gene promoter regions, 33 hypermethylation and 297 hypomethylation respectively, by comparing lung cancer patients and healthy individuals as controls. The 33 hypermethylation regions represent 32 genes. Some of the genes had been previously reported to be associated with lung cancers, such as GAS7, AQP10, HLF, CHRNA9 and HOPX. Taken together, our study provided an alternative method of cfDNA methylation analysis in lung cancer patients with potential clinical applications.

2019-03-31 | E-MTAB-7163 | biostudies-arrayexpress

Processed small RNA sequencing data of plasma samples from patients with esophageal adenocarcinoma or precursor lesions

Project description:In the past decades, the incidence of esophageal adenocarcinoma has increased dramatically in Western populations. Better understanding of disease etiology along with the identification of novel prognostic and predictive biomarkers are urgently needed to improve the dismal survival probabilities. Here, we performed comprehensive RNA (both coding and non-coding) profiling in various samples from 17 patients diagnosed with esophageal adenocarcinoma, high-grade dysplastic or non-dysplastic Barrett’s esophagus. Per patient, a blood plasma sample, and a healthy esophageal and disease tissue sample were included. In total, this comprehensive dataset consists of 102 RNA-seq libraries from 51 samples. The raw data for this study have been deposited to the controlled access archive EGA under submission EGAS00001004939.

2022-01-01 | E-MTAB-10004 | biostudies-arrayexpress

Processed mRNA capture sequencing data of plasma samples from patients with esophageal adenocarcinoma or precursor lesions

2022-01-01 | E-MTAB-10002 | biostudies-arrayexpress

Accurate multi-cancer detection using cell-free DNA shallow whole-genome sequencing data

Project description:Plasma DNA from 558 malignancies, 263 benign and borderline tumors and 367 healthy control samples were collected and subjected to random short-gun whole genome sequencing.

2022-07-03 | E-MTAB-10934 | biostudies-arrayexpress

Targeted next generation sequencing of cfDNA from lung cancer patients enrolled in the GALAXY-1 trial (NCT01348126)

Project description:We evaluated whether targeted next-generation sequencing (NGS) using the Ion Torrent Personal Genome Sequencer of cfDNA could identify prognostic or predictive factors for overall survival (OS) or progression free survival (PFS) within a large cohort of patients with advanced lung adenocarcinoma enrolled in the GALAXY-1 trial.

2018-01-10 | E-MTAB-5749 | biostudies-arrayexpress

Exposure of THP1 cells to plasma containing or lacking cfDNA

Project description:We aimed to clarify the cell-free DNA (cfDNA) physiological role. We exposed THP1 cells to plasma from healthy individuals with and without cfDNA and compared their transcriptomes and proteomes.

2020-12-01 | E-MTAB-8574 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data