Search Results - EGA European Genome-Phenome Archive

Comparison clinical recommendation MASTER and panel sequencing: RNA data

This dataset contains 19 case/control samples of RNA sequencing data. Sequencing was performed on Illumina HiSeq 4000 and NovaSeq 6000 using TruSeq Stranded mRNA Kit. The sequencing was always paired.

Dataset EGAD50000000625

miRNAseq of paired FL and tFL samples

This dataset contains miRNA-seq of paired FL and tFL samples (n=10 pairs) sequenced by Illumina NextSeq500. Libraries used in this miRNA-seq dataset were prepared with NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB,Catalog number: E7560S). RNAs used for library preparation were isolated from FFPE tissues using High Pure miRNA Isolation Kit (Roche,Catalog number: 05080576001). Data are uploaded as FASTQ format.

Dataset EGAD50000001385

RNAseq

Libraries for sixty-eight cases (23 EATL and 45 MEITL) were prepared starting from 1 µg of total RNA using the TruSeq Stranded total RNA Gold kit from Illumina (San Diego, California, USA) and were sequenced in three batches on a HiSeq 4000 machine from Illumina with an average output of 63 million reads per sample (range 49-126).

Dataset EGAD50000001619

WGS

A genome-wide approach based on next generation sequencing (NGS) is performed on trios ( Patient+ Father + Mother) with SAID in order to identify known and new gene variants associated with certain forms of the disease. Whole-genome sequencing (WGS) was performed on frozen PBMCs. DNA was extracted using Chemagic Prime ( Perkin Elmer) and quantified with nanodrop. The raw sequencing data is generated on the Novaseq 6000 using an S4 flowcell, with a sequencing depth of ~30X

Dataset EGAD50000002026

Clinical data of liver cancer patients from EuCanImage - Use case 1 Synthetic

This study is part of EuCanImage project. It contains the standardized clinical information following FHIR model. The data was collected together with MRI of patients diagnosed with liver cancer (HCC) and controls (non-HCC). All data is synthetic.

Study EGAS50000001444

A study on personalized medicine in genitourinary cancers using genetic biomarkers

We present a patient with MSI-high castration-resistant PC who showed a remarkable and durable response to pembrolizumab. Whole exome sequencing revealed approximate tumor mutation burden of 61 mutations/Mb as well as biallelic loss of MSH2.

Study JGAS000510

Transcriptome analysis of Familial dysautonomia patient cells treated with splice-regulating compounds

In order to investigate familial dysautonomia patient fibroblasts in response to splice-regulating compounds, cells were treated with RECTAS or TG003 and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

Study JGAS000170

exploration of biomarkers in colorectal cancer

Targeted therapies based on the molecular and histological features of cancer types are becoming standard practice. To understand the molecular basis of colorectal cancer, we performed CAGE (Cap Analysis of Gene Expression) to quantify promoter activities on 45 colorectal cancers.

Study JGAS000489

DNA methylation array analysis of pediatric T-cell acute lymphoblastic leukemia

Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is rare and its pathogenesis is poorly understood. To investigate epigenetic profiles of pediatric T-ALL, we performed DNA methylation array analysis in 79 cases of pediatric T-ALL.

Study JGAS000138

Transcriptome analysis of Fabry disease iPSC-derived cardiomyocytes treated with splice-regulating compound; RECTAS

In order to investigate transcriptome profiles in response to splice-regulating compounds, iPSC-derived cardyomyocytes were treated with RECTAS and transcriptome study was conducted by RNA-seq. Splicing profiles of cells in each condition were then analyzed.

Study JGAS000225

Genome-wide integrative analysis of pediatric pancreatoblastoma

Pancreatoblastoma is the most common pancreatic malignancy of young children, but its molecular pathogenesis remains poorly understood. To understand the molecular pathogenesis of pancreatoblastoma, we comprehensively analysed the whole exome sequencing, RNA sequencing, SNP array, and methylation array data of pancreatoblastoma.

Study JGAS000088

RNA-Seq for SF3B1 splicing signature

This dataset includes exome-captured RNA-Seq made with exome v8 (Agilent) - library preparation on a MAGNIS XT-HS2 starting from 100ng of RNA. RNA has been extracted from lymphocytes cultures from 2 probands with SF3B1 mutations and 14 controls. All 16 RNA-Seq were sequenced on a single HighOutput flowcell 2x75bp (NextSeq550). Raw fastq files have between 20 and 30M paired-reads.

Dataset EGAD50000002121

Bulk RNASeq of metastatic colorectal cancer organoids with ATOH1 knockout

Bulk RNA sequencing was performed on mCRC organoids subjected to cetuximab treatment, comparing ATOH1 knockout and control conditions. The dataset is intended to elucidate the contribution of ATOH1-regulated secretory cell population to cetuximab persistence mechanisms.

Study EGAS50000001421

Bulk RNASeq of metastatic colorectal cancer organoids treated with crenigacestat alone or in combination with cetuximab

Bulk RNA sequencing was performed on mCRC organoids cultured under untreated conditions or treated with crenigacestat alone or in combination with cetuximab. This dataset was generated to investigate the transcriptional changes associated with combination therapy and to compare these profiles with the adaptive responses observed following cetuximab monotherapy in the corresponding ATOH1 wild-type and knockout organoid models.

Dataset EGAD50000002061

Whole-genome sequencing study of uveal melanoma

Uveal melanoma is the most common primary intraocular cancer, characterized by metastasis-related mortality. Here, we explored whole-genome sequences from 40 primary uveal melanomas to illustrate the landscape of genomic mutations and investigate their association with prognosis.

Study EGAS50000001603

10X single-cell Multiome (RNA+ATAC) of bone marrow-derived HSPC

10X genomics chromium single-cell ATAC+RNA (Multiome) was use to prepare single-nucleus RNA- and ATAC-seq libraries, sequenced on an Illumina NovaSeq 6000 platform. BAM files are provided. Samples from 6 donors were sequenced after sorting for primitive HSPCs in 5 libraries; each library comprises a single donor, except one with cells from 1 male and 1 female donor.

Dataset EGAD50000002326

WGS data from PASS-01 trial

WGS data for pancreatic cancer samples (PASS-01 Trial; Knox et al., Journal of Clinical Oncology, 2025). The dataset includes tumour and normal cram files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=127 tumour/normal pairs)

Dataset EGAD50000002309

WNT7B-reporter organoids sorted

Transcriptomic data from pancreatic ductal adenocarcinoma (PDAC) organoids to investigate the role of WNT7B. This dataset includes: - Bulk mRNA sequencing of WNT7B-reporter pancreatic ductal adenocarcinoma (PDAC) organoids sorted for cells displaying low, medium and high expression of the reporter

Study EGAS50000001543

Bulk RNA sequencing data of high-grade serous ovarian cancer samples (set 18-19)

The dataset contains RNA sequencing data of 66 high-grade serous carcinoma (HGSC) patients sequenced with Novoseq 6000. The 155 samples are fresh frozen tissue samples that have been collected from different tissues and time points before and during treatment. The files provided are paired fastq files.

Dataset EGAD50000002370

Transcriptome analysis of human muscle/myofibers carrying the human nemaline myopathy type 6-associated KBTBD13-R408C variant.

This dataset contains mRNA-seq results from eleven samples from human donors, each sample being composed of 5-10 rebulked fiber type-specific myofibers. This sample set includes; 1) Three FT-I and three FT-IIa rebulked samples from control individuals 2) Three FT-I and two FT-IIa rebulked samples from NEM6 patients with a KBTBD13R408C variant (NP_001094832.1: p.Arg408Cys)

Dataset EGAD50000002408

Whole exome sequencing of virus-associated HCC

To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

Study EGAS00001000389

HER2_positive_Breast_Cancer_

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

Study EGAS00001000042

Genetic_factors_underlying_premature_MI_in_Greek_families_without_vessel_disease

The study will analyse by exome sequencing 8 Greek family members with an excess of potentially damaging mutations relating to premature MI and no vessel disease, to identify genetic factors underlying this condition. This is a follow on from project GPMI-NVD

Study EGAS00001000478

Alternative splicing in Shh-MB

We analyzed alternative splicing with Shh medulloblastoma. This dataset contains bam files of whole genome sequencing from 4 cases. Genomic DNA was isolated from both tumor and matched control specimens. We performed whole genome sequence on Illumina Hiseq.

Study EGAS00001003220

WTCCC2 People of the British Isles (POBI) genotypes

As part of the WTCCC2 project, approximately 2,900 individuals from the People of the British Isles (POBI) project were genotyped on the Illumina 1.2M array (2,912 samples) and the Affymetrix 6.0 array (2,930 samples).

Study EGAS00001000672

IBDCA_Edinburgh

In this experiment we have sequenced tumour normal pairs from patients presenting with CRC who have a prior history of inflammatory bowel disease. The idea is to identify driver mutations, new genes and novel pathways associated with the development of these malignancies.

Study EGAS00001001129

Predictor_RIO_TNBC

In this study, samples fom a window study of the PARP inhibitor rucaparib in patients with primary triple negative or BRCA1/2 related breast cancer (RIO trial) will be investigated. Samples will undergo whole genome sequence and analysis, including use of HR Predict.

Study EGAS00001002805

Triple_Negative_Breast_Cancer_sequencing

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

Study EGAS00001000161

Transposome_Bisulfite_Sequencing

DNA belonging to 16 tumour/normal samples were treated with bisulfite, then up to 5 different bisulfite PCRs were performed in each one of the samples. Amplicons form the same sample were pooled and submitted to sequencing on a MiSeq platform.

Study EGAS00001000751

Tumor suppressor miR-133a modulates the prostate cancer epigenome by repressing BAZ2A

Our study revealed a new subgroup of prostate tumors defined by the expression of a novel prognostic marker, BAZ2A, and the first time to show the establishment of CIMP via an microRNA-epigenetic interaction in prostate tumors.

Study EGAS00001000568

Exome sequencing of United Kingdom Brain Expression Consortium samples

The United Kingdom Brain Expression Consortium studies regulation of gene expression through common and rare variation. One of the main set of samples is compound by bulk brain tissue from 10 brain regions obtained from 134 controls.

Study EGAS00001002113

Myeloma WGS

Most patients with multiple myeloma (MM) die from progressive disease after relapse. To advance our understanding of MM evolution mechanisms, we performed whole-genome sequencing of 80 tumour-normal newly diagnosed pairs and 24 matched relapse tumours from the Myeloma XI trial.

Study EGAS00001004000

Whole exome sequencing of Congenital Cataract

Whole exome sequencing to identify potentially relevant mutations of congenital cataract in a Chinese girl. The novel PAX6 mutation (c.221G>A) is associated with congenital cataract, and the WFS1 mutation (c.2070_2079del) interactively aggravates this process.

Study EGAS00001005673

Subtype specific studies of breast cancer progression. Milan cohort.

The aim of this study is to compare DCIS and IBC in a subtype stratified manner in several genomic levels (gene expression, copy number, methylation).The data in this archive is supplementary to previously published data.

Study EGAS00001004390

Childhood cerebellar tumors mirror conserved fetal transcriptional programs

We used single-cell transcriptomics to study >60,000 cells from the developing murine cerebellum, and show that different molecular subgroups of childhood cerebellar tumors mirror the transcription of cells from distinct, temporally restricted cerebellar lineages.

Study EGAS00001003170

Overactivation of the IGF signalling pathway in osteosarcoma

Tumour samples (low coverage WGS) from 35 patients with osteosarcoma were included. All samples were re-evaluated by an experienced bone pathologist who conﬁrmed the diagnosis and a tumour content >50% per sample. All tumours represented conventional high-grade osteosarcomas.

Study EGAS00001004767

Targeted sequencing of brain AVM tissues

We previously identified somatic activating KRAS mutations in a majority of human arteriovenous malformations (AVMs), using whole exome sequencing. We have now performed targeted sequencing on AVMS, investigating genes in the RAS-MAPK pathway, angiogenesis and brain vascular disorders among others.

Study EGAS00001006729

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