Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1300941 | ENA |
REPOSITORIES: ENA
Similar 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
Project description:To analyse the host responses of Bama mini-pigs to ASFV infection, we chose the spleen and inguinal lymph nodes from Bama mini-pigs infected with ASFV at a dose of 103 HAD50 and the mock group for transcriptomic analysis.
2022-10-14 | GSE215197 | GEO
Project description:The genome-wide analysis of cfDNA fragmentation patterns in DENQCMs and maternal plasma was performed by deep sequencing using Illumina Novaseq to confirm their biological characteristics. We first performed deep whole genome sequencing of the cfDNA extracted from DENQCMs and maternal plasma cfDNA. Then we analyzed the sequencing data and compared various characteristics of cfDNA fragmentation patterns, such as dinucleotide composition, nucleosome protection length, and nucleosome occupancy based on a windowed protection score (WPS), to the submitter-provided processed data from a healthy individual IH01 (GEO accession GSM1833276).
2019-01-05 | GSE124686 | GEO
Project description:Nucleosomes are the basic unit of packaging of eukaryotic chromatin, and nucleosome positioning can differ substantially between cell types. Here, we sequence 14.5 billion plasma-borne cell-free DNA (cfDNA) fragments (700-fold coverage) to generate genome-wide maps of in vivo nucleosome occupancy. We identify 13 million local maxima of nucleosome protection, spanning 2.53 gigabases (Gb) of the human genome, whose positions and spacings correlate with nuclear architecture, gene structure and gene expression. We further show that short cfDNA fragments - poorly recovered by standard protocols - directly footprint the in vivo occupancy of DNA-bound transcription factors such as CTCF. The sequence composition of cfDNA has previously been used to noninvasively monitor cancer, pregnancy and organ transplantation, but a key limitation of this paradigm is its dependence on genotypic differences to distinguish between contributing tissues. We show that nucleosome spacing in gene bodies and cis-regulatory elements, inferred from cfDNA in healthy individuals, correlates most strongly with transcriptional and epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how in vivo nucleosome footprints can be used to infer the cell types that contribute to circulating cfDNA in pathological states such as cancer. Because it does not rely on genotypic differences, this strategy may enable the noninvasive cfDNA-based monitoring of a much broader set of clinical conditions than is currently possible. Sequencing of cfDNA libraries from healthy individuals, pooled healthy individuals and individuals with disease for the identification of nucleosomes and protection from other DNA binding proteins.
2015-11-04 | E-GEOD-71378 | biostudies-arrayexpress
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
Project description:This study selected cooperative pigs and Baoma pigs as the experimental subjects. By integrating the whole-transcriptome sequencing technology, the ceRNA network related to cold stress-induced anti-injury in the livers of cooperative pigs was screened. The aim was to reveal the molecular mechanism of maintaining liver functional homeostasis in cooperative pigs under cold stress conditions, and to provide new theoretical basis and technical support for cold resistance breeding and liver injury protection of livestock.
2025-07-01 | GSE295210 | GEO
Project description:Cell free DNA (cfDNA) in human plasma carries abundant information on physiological condition, especially in cancer patients such as esophageal cancer. Next-generation sequencing (NGS) as a rapidly developed technology could decode the information effectively. As a key step of NGS, using existing methods to construct cfDNA sequencing libraries is limited by several shortcomings. In this study, we developed a new NGS library construction method for highly degraded DNA, cfDNA as example, based on Single strand Adaptor Library Preparation (SALP). With the high ligation efficiency of single strand adaptor (SSA) which overhangs 3 random bases at 3' end of a double-strand DNA, the new method could construct the sequencing library with high sensitivity without using specific enzymes except T4 DNA ligase and Taq polymerase. With the special designed barcode T adaptor (BTA), multiple libraries constructed from different samples can be amplified in unbiased strategy and facility to compare. Using this method, this study successfully sequenced and compared totally 20 cfDNA samples derived from esophageal cancer patients and healthy people in whole genome scale. This study also compared the chromatin state between cancer patients and healthy people using cfDNA, identified the significant difference between different health condition. Our findings extend the application of cfDNA beyond the analysis with degraded DNA fragments itself, to the transcription regulation level, which also provide an important clue for biopsy of esophageal cancer and other diseases.
2019-04-12 | GSE116345 | GEO
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