Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Fragment Enrichment of Circulating Tumor DNA with Low-Frequency Mutations

PROVIDER: PRJNA562379 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10064500.fastq.gz	Fastqsanger.gz
	SRR10064500_1.fastq.gz	Fastqsanger.gz
	SRR10064500_2.fastq.gz	Fastqsanger.gz
	SRR10064501.fastq.gz	Fastqsanger.gz
	SRR10064501_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 315

Similar Datasets

Rattus norvegicus

Project description:Fragment Length of Circulating Tumor DNA

| PRJNA326160 | ENA

Project description:Comparison of target enrichment platforms for circulating tumor DNA detection

| PRJNA577992 | ENA

Enhanced detection of circulating tumor DNA by fragment size analysis

Project description:Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on sensitivity for detecting genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for non-invasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 cancer patients using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90–150 bp, and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90–150 bp improved detection of tumor DNA, with more than 2-fold median enrichment in >95% of cases, and more than 4-fold enrichment in > 10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with AUC> 0.99 compared to AUC < 0.80 without fragmentation features. Increased identification of cfDNA from patients with glioma, renal, and pancreatic cancer was achieved with AUC > 0.91, compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection. This could reduce the required depth of cfDNA sequencing for clinical applications, earlier diagnosis and study of tumor biology.

| EGAS00001003258 | EGA

Evaluation of RAS gene status in circulating tumor DNA for colorectal cancer patients with RASg gene mutation

Project description:Primary outcome(s): the allele frequency of RAS gene mutation in circulating tumor DNA

| 2653459 | ecrin-mdr-crc

Detection of duplication mutations in coding regions in normal lung and lung tumor in wild-type (WT) and FEN1 A159V mutant mice

Project description:Faithful and efficient Okazaki fragment maturation is the key to maintain the genome integrity. In addition, this process is coupled with deposition of histone proteins. Therefore, functional deficiency in Okazaki fragment maturation may cause duplication mutations. We conduct WES of normal lung and lung tumor from WT and A159V/WT mice to define the duplication mutations caused by defective Okazaki fragment maturation.

2021-11-01 | GSE181154 | GEO

4T1 RNA-Seq

Project description:Background: the transcription of tumor mutations from DNA into RNA has implications for biology, epigenetics and clinical practice. It is not clear if mutations are in general transcribed and, if so, at what proportion to the wild-type allele. Here, we examined the correlation between DNA mutation allele frequency and RNA mutation allele frequency. Methods: we sequenced the exome and transcriptome of tumor cell lines with large copy number variations, identified heterozygous single nucleotide mutations and absolute DNA copy number, and determined the corresponding DNA and RNA mutation allele fraction. Results: we found that 99% of the DNA mutations in expressed genes are expressed as RNA. Moreover, we found a high correlation between the DNA and RNA mutation allele frequency. Exceptions are mutations that cause premature termination codons and therefore activate nonsense-mediated decay. Beyond this, we did not find evidence of any wide-scale mechanism, such as allele-specific epigenetic silencing, preferentially promoting mutated or wild-type alleles. Conclusion: taken together, our data strongly suggest that genes are equally transcribed from all alleles, mutated and wild-type, and thus transcribed in proportion to their DNA allele frequency.

2014-03-05 | E-MTAB-2383 | biostudies-arrayexpress

Long Fragment enrichment

Project description:Long Fragment enrichment

| PRJEB12651 | ENA

Best timing of EGFR re-challenge by monitoring the mutant allele of KRAS/NRAS in liquid biopsy

Project description:Primary outcome(s): The dynamics of the positive RAS mutations rate by circulating tumor DNA analysis using OncoBEAM RAS CRC KIT

| 2651470 | ecrin-mdr-crc

Less invasive diagnostics for identification and monitoring of cancer associated mutations in blood

Project description:Primary outcome(s): Quantitative detection and monitoring of genetic mutations in tumor-associated genes, such as oncogenic KRAS, in circulating plasma DNA.

| 2628163 | ecrin-mdr-crc

Transcriptomic profile of CD8+ circulating tumor-reactive lymphocytes (CTRL) isolated by MHC multimers

Project description:Circulating tumor-reactive lymphocytes (CTRL) present in blood circulation at a very low frequency. We efficiently isolated them based on high-performance microfluidics and MHC multimer binding assay. Using an ultra-low input bulk RNAseq workflow, we systematically characterize the transcriptomic profile of tumor-reactive lymphocytes and identified novel biomarkers for multimer-free isolation. Two animal models were studied - B16 melanoma model and CT-26 colon cancer model.

2023-04-09 | GSE227345 | GEO

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