Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Large cancer fingerprint screening for detection of MRD

ABSTRACT: Large cancer fingerprint screening for detection of MRD

PROVIDER: PRJNA605873 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Large cancer fingerprint screening for detection of MRD

Project description:Large cancer fingerprint screening for detection of MRD

| PRJNA605872 | ENA

MRD Screening Of Human B ALL

Project description:MRD screening in Human B-ALL: monitoring B-cell repertoires in longitudinal samples of patients.

2015-09-04 | E-ERAD-391 | biostudies-arrayexpress

New markers for minimal residual disease detection in acute lymphoblastic leukemia

Project description:To identify new markers for minimal residual disease (MRD) detection in acute lymphoblastic leukemia (ALL), we compared genome-wide gene expression of lymphoblasts from 270 patients with newly diagnosed childhood ALL to that of normal CD19 CD10 B-cell progenitors (n=4). Expression of 30 genes differentially expressed by > 3-fold in at least 25% of cases of ALL (or 40% of ALL subtypes) was tested by flow cytometry in 200 B-lineage ALL and 61 nonleukemic BM samples, including samples containing hematogones. Of the 30 markers, 22 (CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, CD49f) were differentially expressed in up to 81.4% of ALL cases; expression of some markers was associated with the presence of genetic abnormalities. Results of MRD detection by flow cytometry with these markers correlated well with those of molecular testing (52 follow-up samples from 18 patients); sequential studies during treatment and diagnosis-relapse comparisons documented their stability. When incorporated in 6-marker combinations, the new markers afforded the detection of 1 leukemic cell among 105 BM cells. These new markers should allow MRD studies in all B-lineage ALL patients, and substantially improve their sensitivity.

2011-04-20 | GSE28497 | GEO

High dimensional association detection in large-scale genomic data

Project description:High dimensional association detection in large-scale genomic data

| PRJNA656702 | ENA

EpiPanGI Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers

Project description:EpiPanGI Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers

| PRJNA628686 | ENA

Detection of Y chromosome

Project description:PCR based detection of Y-chromosome compared against results obtained by CGH microarrrays in Preimplantation Genetic Screening

2017-04-05 | GSE97386 | GEO

Circulating microRNA screening of high-risk individuals enrolled in COSMOS lung cancer screening trial.

Project description:Lung cancer is the leading cause of cancer death worldwide. Low-dose computed tomography screening (LDCT) was recently shown to anticipate the time of diagnosis, thus reducing lung cancer mortality. We identifed a serum microRNA signature (the miR-Test) that could identify the optimal target population for LDCT screening. Here, we performed a large-scale validation study of the miR-Test in high-risk individuals enrolled in the Continuous Observation of Smoking Subjects (COSMOS) lung cancer screening program. RT-qPCR of circulating microRNA purified from serum samples. Trizol-LS and miRNEASY Mini kit (Qiagen) were used for miRNA purification. Custom TaqManÂ® Low Density Array microRNA Custom Panel (Life Technologies) was used to screen serum circulating microRNA.

2016-02-29 | E-GEOD-76462 | biostudies-arrayexpress

Enhanced detection of MRD with cfDNA Fragmentomics.

Project description:The circulating tumor DNA (ctDNA) mutation-based approach shows limited performance in minimal residual disease (MRD) detection, especially for landmark MRD detection at an early-stage cancer after surgery. Here, we describe a cell-free DNA (cfDNA) fragmentomics-based method in MRD detection of resectable non-small cell lung cancer using whole genome sequencing, and the cfDNA-fragmentomics showed a great sensitivity in predicting prognosis.

| EGAS00001007192 | EGA

Large-scale production of human iPSC-derived macrophages for drug screening

Project description:Large-scale production of human iPSC-derived macrophages for drug screening

| PRJNA628531 | ENA

Screening for copy-number alterations and LOH in CLL - a comparative study of four microarray platforms

Project description:Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation, although this was compensated by high density of elements. Affymetrix detected a higher degree of CNAs compared to Illumina, while the latter showed a lower noise level and higher detection rate in the LOH analysis. Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested. 10 chronic lymphocytic leukemia (CLL) samples was analyzed using four different high-resolution platforms: 32K BAC arrays, 185K Agilent oligonucleotide arrays, 250K Affymetrix SNP arrays and 317K Illumina SNP arrays.

2008-12-10 | E-GEOD-13557 | 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