Search Results - EGA European Genome-Phenome Archive

Breast_Cancer_Whole_Genome_Sequencing

We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Study EGAS00001000210

Triple_Negative_Breast_Cancer_RNA_Sequencing

We propose to definitively characterise the somatic genetics of triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Study EGAS00001000377

Moles

In this project we have sequenced the exome of skin moles (melanocytic naevi) and also normal skin from young and old people. We are interested in looking at the clonality of these lesions and the burden of UV mutations

Study EGAS00001000789

Multisite_Primary_Breast_Cancer

DNA extracted from multiple biopsies taken from different areas of primary breast tumours will be subjected to targeted re-sequencing and analysed in order to assess intra-tumour heterogeneity with respect to mutations in a selection of cancer related genes.

Study EGAS00001000891

GWAS and Meta-analysis on Frontal Fibrosing Alopecia in two European Populations

Summary statistics of a GWAS meta-analysis for frontal fibrosing alopecia (FFA). A total of 7,039,930 genotyped and imputed variants were used for 1,044 European severe FFA cases and 4,145 matched population controls.

Study EGAS00001003460

BLUEPRINT Epigenetic characterization of megakaryocytes and erythroblasts

Megakaryocytes and erythroblasts derive from the same progenitor cell type but carry out very different functions. In order to understand how the different functional phenotypes arise we have characterised the epigenetic landscape of these cells.

Study EGAS00001001641

BCL11B enhancer hijacking defines a subtype of lineage ambiguous stem cell leukemia

Hijacking of primitive hematopoietic enhancers, or generation of a neo-enhancer by genomic amplification, results in deregulation of BCL11B as the defining feature of a subset of T/myeloid leukemia

Study EGAS00001004810

arrayCGH for copy number profiling on tumor DNA from pediatric cancer tissue samples

This dataset contains arrayCGH (HumanCytoSNP 850k and HumanCytoSNP v12.1) data from tumor DNA samples of various pediatric cancer entities. Files are provided in IDAT format and as text files processed with GenomeStudio 2.0.

Study EGAS00001005197

G3BP2-KIT drives leukemia amenable to kinase inhibition in Ph-like ALL

We describe a patient with Ph-like ALL, in which leukemic cells harbored an in-frame fusion between the GTPase-activating protein (SH3 domain)-binding protein 2 (G3BP2) and the KIT proto-oncogene.

Study EGAS00001005181

eccDNA in maternal plasma

We developed a new bioinformatics method for detecting the eccDNA in plasma. We revealed that the biological properties between eccDNA and linear DNA are different. eccDNA could be potentially provided as a new class of circulating biomarker.

Study EGAS00001003827

COIN CRC GWAS data

Genotype data from the COIN and COIN-B trials of advanced/metastatic colorectal cancer. Data provided in plink format, and has been quality controlled. Control data used was from the WTCCC2 project National Blood Donors (NBS) Cohort (EGAD00000000024).

Study EGAS00001005421

Molecular programs of melanoma brain metastases (MBM)

We performed paired-end whole transcriptome sequencing of fresh frozen or intraoperative brain metastases of therapeutically treated stage IV melanoma patients. In addition, we analysed the epigenetic landscape of tumors usind Illumina 850k bead chip technology.

Study EGAS00001005976

Dedifferentiated_Melanoma

De- and transdifferentiation of melanoma is a rare histopathological phenomenon that has not be characterised genetically. In this project we plan to sequence the genomes of de and transdifferentiated cases so as to define their genetic make-up.

Study EGAS00001003471

NLG-LBC-05 ctDNA

Correlative analysis of circulating tumor DNA (ctDNA) in aggressive large B-cell lymphoma patients treated in NLG-LBC-05 phase II trial. Whole genome and targeted sequencing was applied to longitudinal plasma cell-free DNA and diagnostic tumor tissues.

Study EGAS00001005835

RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

This experiment consists of RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 10) or with vehicle (N = 10).

Study EGAS00001006583

Comprehensive de novo variant discovery with HiFi long-read sequencing

We performed whole-genome sequencing of 8 trios with intellectual disability using Pacbio HiFi long-reads. We then called variants with PBSV and Deepvariant. We filtered for high-quality de novo variants and validated them.

Study EGAS00001006479

10X 3' V2 data of single immune cells in hepatocellular carcinoma

The immune microenvironment of hepatocellular carcinoma (HCC) is poorly characterized. Combining two single-cell RNA sequencing technologies, we produced transcriptomes of CD45+ immune cells for HCC patients from five immune-relevant sites: tumor, adjacent liver, hepatic lymph node (LN), blood, and ascites. This is the droplet data of this study

Dataset EGAD00001005961

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