Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-sacgf-04-08-2014-08:35:16:587-100 - samples

ABSTRACT: This dataset contains the fastq sequencing data collected from bone marrow DNA of a chronic myeloid leukaemia patient at time of diagnosis.

PROVIDER: EGAD00001000967 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

A comparative analysis of algorithms for somatic SNV detection in cancer.

Roberts Nicola D ND Kortschak R Daniel RD Parker Wendy T WT Schreiber Andreas W AW Branford Susan S Scott Hamish S HS Glonek Garique G Adelson David L DL

Bioinformatics (Oxford, England) 20130709 18

<h4>Motivation</h4>With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four rece ...[more]

PMID: 23842810

Similar Datasets

Spatiotemporal dynamics of confirmed case distribution during the COVID-19 pandemic in China: data comparison between 2020/04-2020/08 and 2021/04-2021/08.

Project description: Not available

| S-EPMC10363524 | biostudies-literature

Transcription profiling of human indolent and aggressive forms of Chronic Myeloid Leukaemia (CML)

Project description:Title: Gene expression analysis of indolent and aggressive forms of Chronic Myeloid Leukaemia (CML). Description: Chronic Myeloid Leukaemia presents in chronic phase (CP) and terminates in 'blast crisis'. Despite a common abnormality, the duration of CP is variable. The aim is to compare the gene expression profiles of the indolent and aggressive forms of CML. All samples were taken within 3 months of first diagnosis. Indolent patients were defined by chronic phase CML, duration minimum 7 years. Aggressive patients were defined by chronic phase, duration maximum 3 years.

2013-01-30 | E-MIMR-17 | biostudies-arrayexpress

Profound Immune Alterations in the Murine CML Bone Marrow Microenvironment Revealed by Single Cell Ph- Macrophage Profiling and Secretory Proteomics

Project description:Macrophages are cells of the innate immune system fundamental to support normal haematopoiesis, fight infection, anti-cancer immunity and tumour progression. However, the function of macrophages in myeloid leukaemias remain largely unknown, due to difficulties in isolating non-transformed cells from the malignant ones. Here we use a state-of-the-art chimeric mouse of chronic myeloid leukaemia (CML) to study in the impact of the dysregulated bone marrow (BM) microenvironment on bystander macrophages. Utilising single cell RNA sequencing (scRNA seq) of Philadelphia chromosome (Ph) negative macrophages and secretome proteomics of murine c-kit+ stem/progenitor cells we have uncovered that macrophages exposed to a CML environment are altered transcriptionally and have reduced phagocytic function

2023-12-23 | PXD022366 | Pride

Treatment of CML CD34+ cells with EZH2 inhibitor GSK343

Project description:Transcriptional profiling by array of CML CD34+ cells to understand the response of chronic myeloid leukaemia stem cells to an EZH2 inhibitor, GSK343.

2016-11-01 | E-MTAB-2893 | biostudies-arrayexpress

Genomic profiling of Imatinib resistance in CD34+ cell populations from chronic myeloid leukaemia patients using Agilent-014698 Whole Human Genome 105K microarrays.

Project description:To ascertain genomic alterations associated with Imatinib resistance in chronic myeloid leukaemia, we performed high resolution genomic analysis of CD34+ cells from 25 Imatinib (IM) resistant and 11 responders CML patients. Using patients' T-cells as reference, we found significant association between number of acquired cryptic copy number alterations (CNA) and disease phase (p=0.036) or loss of IM response for patients diagnosed in chronic phase (CP) (p=0.04). Recurrent cryptic losses were identified on chromosomes 7, 12 and 13. On chromosome 7, recurrent deletions of the IKZF1 locus were detected, for the first time, in four patients in CP. Patients suffering from chronic myeloid leukaemia were compared using CD34+ cells and T cells as reference and hybridized on Agilent-014698 Whole Human Genome 105K microarrays.

2010-11-15 | E-GEOD-21986 | biostudies-arrayexpress

Transcriptional profiling of CML and normal, stem and progenitor haematopoietic cells.

Project description:Transcriptional profiling of four cell populations to understanding chronic myeloid leukaemia in humans. The populations are normal haematopoietic stem cells (HSC), normal progenitor cells (HPC), CML stem cells (LSC) and CML progenitor cells (LPC).

2016-05-26 | E-MTAB-2581 | biostudies-arrayexpress

Single cell RNA-seq analysis of haemopoietic stem cells and CML stem cells isolated from human peripheral blood

Project description:To identify differences in the transcriptomes of normal haemopoietic stem cells (HSC) and leukaemic stem cells (LSC) found in patients with chronic myeloid leukaemia (chronic phase) we performed single cell RNA-seq.

2023-12-19 | GSE218184 | GEO

IMMUNE LANDSCAPES PREDICT CHEMOTHERAPY RESISTANCE AND IMMUNOTHERAPY RESPONSE IN ACUTE MYELOID LEUKAEMIA

Project description:Immunological classifiers that predict patient outcome and therapeutic responses have been constructed through targeted immune gene expression profiling of diagnostic bone marrow samples from patients with acute myeloid leukaemia.

2020-06-03 | GSE134589 | GEO

IMMUNE SENESCENCE PHENOTYPES PREDICT CHEMOTHERAPY RESISTANCE IN ACUTE MYELOID LEUKAEMIA

2022-09-16 | GSE176100 | GEO

Characterisation of gene expression changes in T cells from patients presenting with AML compared with healthy T cells

Project description:Work previously published by our group has demonstrated that T cells from patients with chronic lymphocytic leukaemia (CLL) show differentially regulated genes compared with healthy T cells. This study was initiated to examine if these gene expression changes were unique to CLL T cells or common to an alternative leukaemia, acute myeloid leukaemia (AML). Keywords: Comparison of immune cells in health and disease

2009-05-20 | GSE14924 | 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