Search Results - EGA European Genome-Phenome Archive

Ovarian carcinoma

Genome-wide NanoRCS of cfDNA from ascites of Ovarian cancer patients

Dataset EGAD50000000219

Transcriptome of CD4+ T cells and CD8+ T cells in glioblastoma multiforme

Patients included in this study were over 18 years of age and had a histology-confirmed diagnosis of glioblastoma multiforme (GBM). Exclusion criteria were the previous administration of any anti-tumor therapy including radiation therapy. All patients gave written informed consent. The study was approved by the local ethics committee (TUM Medical school) and conducted following the Declaration of Helsinki. During resection of the tumors, tumor tissue and tissue from normal appearing brain within the operative channel was collected. Blood was drawn during the surgical procedure. Single cell suspensions were prepared from the tumor tissue, the normal appearing brain, and the blood. CD4+ T cells and CD8+ T cells were sorted by flow cytometry. Only patients with a complete set of specimens (CD4+ tumor infiltrating lymphocytes (TIL), CD8+ TIL, CD4+ T cells from normal appearing brain, CD8+ T cells from normal appearing brain, blood-derived CD4+ and CD8+ T cells) containing a minimum of 1000 cells in each sorted sample were further analyzed (n=9). Total RNA was isolated from sorted cell populations using the RNAeasy Plus micro kit (Qiagen, 74034). Quality and integrity of total RNA was controlled on a Bioanalyzer 2100 (Agilent Technologies). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (ThermoFisher Scientific, EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing, a TruSeq adapter was ligated and 3'-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to previous descriptions (Parekh et al., 2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read 1 and barcodes and UMIs in read 2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 59 cycles for the cDNA in read 1 and 16 cycles for the barcodes and UMIs in read 2. Data were processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCh38) was used for alignment. Transcript and gene definitions were used according to the Genecode Annotation Version 35.

Dataset EGAD50000000226

ScRNA-seq of human kidney immune cells of patients with ANCA-associated glomerulonephritis, Lupus Nephritis against a healthy nephrectomy control

ANCA-associated glomerulonephritis (AGN) associates with a high risk of end-stage kidneydisease. The role of kidney immune cells in local inflammation remains unclear. This study investigates kidney immune cell diversity and function. Kidney tissue from AGN patients (n=5) and a lupus nephritis (LN) patient (n=1) were aquired during a biopsy procedure for a clinical indication. Needle-core biopsies were obtained for histopathological examination, and an additional pass was performed to retrieve kidney tissue for scRNA-seq. Healthy kidney tissue (n=1) was obtained from a kidney that was surgically removed do tue due to a (non-invasive) papillary urothelial carcinoma. Immediately after collection, kidney tissue was processed into a single-cell suspension and sorted using a 4-color flow cytometry panel to isolate living, CD45+immune cells. To aid in the multi-omic characterization, surface markers and T and B cell repertoires were sequenced in 2 samples (1 AGN patient and the nephrectomy control). These samples were incubated with an oligo-antibody TotalSeq-C cocktail containing 130 unique cell surface antigens.

Dataset EGAD50000000229

Dataset for central nervous system glioma samples

This dataset contains VCF files for 124 central nervous system glioma samples for the study "Cerebrospinal fluid cfDNA sequencing for classification of central nervous system glioma"

Dataset EGAD50000000085

Dataset for WGS and RNA melanoma samples

This dataset contains WGS and RNA sequencing data for 4 melanoma samples. Sequencing was performed on Illumina Novaseq 6000 and Illumina HiSeq X. The sequencing was always paired.

Dataset EGAD50000000093

Single-Cell RNA Sequencing of Primary High Grade Serous Carcinoma

CD45- Single Cell RNA Sequencing data on 8 High Grade Serous Carcinoma Primary Tumors

Dataset EGAD50000000098

Tumor reactive γδ T cells contribute to a complete response to PD-1 blockade in a Merkel cell carcinoma patient

Single cell RNA and TCR sequencing of γδ T cells FACS sorted from peripheral blood of two Merkel cell carcinoma patients

Dataset EGAD50000000137

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 10)

Whole genome sequencing data of 56 high-grade serous carcinoma (HGSC) patients (208 samples) sequenced with Novoseq 6000

Dataset EGAD50000000275

GLASS-NL Transcriptomic data

This dataset contains RNA-sequencing data of 169 IDH-mutant astrocytoma samples included in the GLASS-NL cohort

Dataset EGAD50000000408

Whole exome sequencing of preneoplasia lung adenocarcinoma

Multi-region exome sequencing of 271 pulmonary nodules and matched adjacent lung tissue including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=49), adenocarcinoma in situ (AIS, N=42), minimally invasive adenocarcinoma (MIA, N=37), invasive lung adenocarcinoma (ADC, N=86) and adjacent lung tissues (Normal, N=57).

Dataset EGAD50000000397

Whole genome sequencing of preneoplasia lung adenocarcinoma

Whole genome sequencing of 42 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=5), adenocarcinoma in situ (AIS, N=7), minimally invasive adenocarcinoma (MIA, N=6) and invasive lung adenocarcinoma (ADC, N=8) and adjacent lung tissues (Normal, N=16).

Dataset EGAD50000000396

RNAseq of preneoplasia lung adenocarcinoma

RNA sequencing of 168 pulmonary samples including lung preneoplasia atypical adenomatous hyperplasia (AAH, N=38), adenocarcinoma in situ (AIS, N=22), minimally invasive adenocarcinoma (MIA, N=19) and invasive lung adenocarcinoma (ADC, N=38) and adjacent lung tissues (Normal, N=62).

Dataset EGAD50000000395

PRADO trial - Personalized response-directed surgery and adjuvant therapy after neoadjuvant ipilimumab plus nivolumab in stage III melanoma

The dataset includes WES sequencing data on PRE- treatment biopsies of lymph node metastasis (n=79) The technology used for sequencing is llumina HiSeq. The PRADO trial tested a personalized response-directed treatment approach based on the pathologic response after neoadjuvant ipilimumab plus nivolumab in stage III melanoma patients. In patients achieving a major pathologic response, in their index lymph node (the largest lymph node metastasis at baseline), therapeutic lymph node dissection (TLND) and adjuvant therapy were omitted. Patients with partial response underwent TLND only, whereas patients with pathologic non-response underwent TLND and adjuvant systemic therapy ± synchronous radiotherapy.

Dataset EGAD50000000393

Medulloblastoma dataset

This dataset contains a tumor + normal DNA sequence data and tumor RNA seq data for a medulloblastoma patient.

Dataset EGAD50000000384

RNA sequencing

For RNA sequencing: All sample numbers starting with 6717 are tumor samples which has been sequenced using transcriptomics (see BAM files). It concerns biopsies of metastatic lesions from patients with BRAFV600 mutated melanoma, obtained before, during and after the study treatment (see samples metadata). RNA sequencing is performed using the Illumina Novaseq 6000 system.

Dataset EGAD50000000383

DNA sequening

The dataset consist of DNA and RNA sequencing results and metadata of the samples. All sample numbers starting with 6716 are tumor samples which has been sequenced using WES (see BAM files). It concerns biopsies of metastatic lesions from patients with BRAFV600 mutated melanoma, obtained before, during and after the study treatment (see samples metadata) and in some cases blood for germline mutation analysis. Sequencing is performed using the Illumina Novaseq 6000 system.

Dataset EGAD50000000382

WES

Whole Exome Sequencing data from Lauss et al Nat Comm 2024. Molecular patterns of resistance to immune checkpoint blockade in melanoma.

Dataset EGAD50000000380

TCRseq

TCRseq data from Lauss et al Nat Comm 2024: Molecular patterns of resistance to immune checkpoint blockade in melanoma.

Dataset EGAD50000000379

Single-cell RNA-seq of immune cell subsets isolated from human tumors (Kaptein et al., 2024)

Single-cell RNA-seq profiling of effector (KLRG1+ PD1-), transitional (KLRG1+ PD1-intermediate), dysfunctional (CD39+ PD1+) and memory (IL7Rα+) CD8 T cells isolated from 4 human tumors (1 melanoma, 1 renal carcinoma and 2 ovarian carcinoma). Respective cell populations were identified and isolated using FACS. FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on individual CD8 T cell subsets across the 4 different samples.

Dataset EGAD50000000376

A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial)

This dataset is related to the NeoBCC trial and includes 12 human tissue samples

Dataset EGAD50000000371

Single-cell RNA-seq of immune cells from human tumor fragments after 48 hour culture ex vivo (Kaptein et al., 2024)

Single-cell RNA-seq profiling of immune cells from human ovarian carcinoma, renal carcinoma and melanoma samples after 48h of ex vivo culture using the patient-derived tumor fragment platform (5 samples total). Samples were cultured in various conditions, including: untreated, CD8-IL2v-treated, CD8-IL2v + LCKi -treated, aPD1-treated, CD8-IL2v + aPD1 -treated, Untargeted IL2-treated, aCD3-treated and aCD3 + CD8-IL2-treated . FASTQ files contain gene expression data, feature barcode antibody capture or TCR data on immune cells from all conditions combined per patient.

Dataset EGAD50000000377

Longitudinal 3'RNA-Seq data from MEMORI trial

80 bam files generated from 3'RNAseq of tumour biopsies from oesophageal adenocarcinoma. Samples were collected within the clinical MEMORI trial.

Dataset EGAD50000000357

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 8b)

Whole genome sequencing data of 19 high-grade serous carcinoma (HGSC) patients (48 samples) sequenced with MGISEQ-2000

Dataset EGAD50000000177

RNA-Seq data from tumor samples collected from 12 UTSW translocation renal cell carcinoma (tRCC) patients.

This study investigates differentially expressed genes associated with the progression of translocation renal cell carcinoma (tRCC) by analyzing RNA-Seq data from 23 tumor samples obtained from 12 patients. The samples were collected from affiliated hospitals of the University of Texas Southwestern Medical Center (UTSW), including Parkland Hospital and Children’s Medical Center. RNA isolated from tumor samples was sequenced using the Illumina platform.

Dataset EGAD50000000172

WES data from tumors and matching controls collected from 11 UTSW translocation renal cell carcinoma (tRCC) patients.

This study investigates translocation renal cell carcinoma (tRCC) to identify mutations contributing to tRCC progression. The analysis relies on Whole Exome Sequencing (WES) data obtained from 11 patients treated at University of Texas Southwestern Medical Center (UTSW) affiliated hospitals, including Parkland Hospital and Children’s Medical Center. Tumor samples and their corresponding normal DNA were sequenced using the Illumina platform.

Dataset EGAD50000000171

Dataset for RNA sequencing of Glioblastoma samples

This dataset contains 10x scRNA sequencing of glioblastoma samples. Sequencing was performed on a Illumina HiSeq 4000. The sequencing was always paired.

Dataset EGAD50000000081

Agilent Sarcoma cohort

Dataset EGAD50000000073

RNAseq and ATACseq data, derived from HGSC cell lines pre- and post- treatment with an epigenetic compound

These data consist of transcriptome and chromatin accessibility data (RNAseq and ATACseq respectively) derived from five High-Grade Serous Ovarian Carcinoma (HGSC) cell lines. HGSC lines included PEO1, PEO4, PEA2, OVCAR5 and OVCAR8. Samples were taken pre- and post-treatment with a novel epigenetic compound, HKMTi-1-005, which targets the activity of two histone methyltransferases, EZH2 and G9a.

Dataset EGAD50000000064

Epigenomic dataset of Human Hepatocellular Carcinoma for EpiHK

This dataset is generated for EpiHK. It contains Histone PTM ChIP-seq, WGBS, RNA-seq of 7 Human Hepatocellular Carcinoma and 7 tumor adjacent normal tissue sample.

Dataset EGAD50000000058

The Dynamic Immune Behavior of Primary and Metastatic Ovarian Carcinoma

Single-cell RNA-seq data of prospectively collected normal ovarian tissue sample from 1 healthy individual and tumor tissue samples with or without chemotherapy from 19 HGSOC patients.

Dataset EGAD50000000057

singel cell RNAseq dataset for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

This dataset contains 16 fastq files of raw single-cell RNAsequencing data from 6 patients with Extramedullary multiple myeloma used for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

Dataset EGAD50000000053

WES dataset used for the study "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

This dataset contains 72 paired fastq files of raw Whole exome sequencing data from 14 patients with Extramedullary myeloma, 8 paired samples from the same patients at the time of Newly diagnosed myeloma, and the corresponding normal samples

Dataset EGAD50000000052

Berlin Pediatric Sarcoma PDX Whole Exome Sequencing dataset

Fastq files of 18 pediatric sarcoma PDX WXS samples. Each sample was sequenced on 2 Lanes.

Dataset EGAD50000000065

Bulk RNAseq dataset for "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

This dataset contains 84 paired fastq files of Bulk RNAseq collected from 14 patients with Extramedullary multiple myeloma, 14 patients with newly diagnosed multiple myeloma and 14 patients with Relapsed/refractory multiple myeloma

Dataset EGAD50000000051

CGMH-OCCC-WES

CGMH-OCCC-WES data (tumor-normal paired) from 104 patients with ovarian clear cell carcinoma.

Dataset EGAD50000000048

Single-cell multi-omic analysis of control and glioblastoma samples from the brain and border regions.

Single-cell RNA-sequencing. Some samples were analyzed using CITE-Seq and samples were multiplexed and run on the same 10X reaction

Dataset EGAD50000000045

Methylome profiling of Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) and a patient derived cell-line model

Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1 using the twist human methylome panel.

Dataset EGAD50000000040

Evaluating potential drug candidates for the treament of Henamgiopericytoma on patient derived cell line models

Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. This study established and characterized a novel SFT/HPC patient-derived cell line called SFT-S1. Potential drug candidates that could be repurposed for the treatment of SFT/HPC were screened. Screening was performed through RNA-Seq

Dataset EGAD50000000039

Whole genome sequencing of Sinonasal hemangiopericytoma and patient derived cell line model

Solitary fibrous tumor/Hemangiopericytoma (SFT/HPC) is a rare subtype of soft tissue sarcoma associated with NAB2-STAT6 gene fusions. In this study, a novel SFT/HPC was characterized using whole genome sequencing.

Dataset EGAD50000000038

Efficacy of two different FGFR-inhibitors in a patient with extrahepatic cholangiocarcinoma harboring an FGFR2 mutation

Cholangiocarcinomas (CCAs) is a type of cancer with few effective systemic therapies. Elucidation of the molecular landscape of the disease from genomic studies based on next generation sequencing (NGS) has contributed to the introduction of new targeted therapies. One of these treatments consists of a class of small molecules that target members of the FGFR family of receptor tyrosine kinases. These drugs are effective and have been approved for cholangiocarcinomas with fusions or rearrangements of FGFR genes. In contrast, the role of these inhibitors in cholangiocarcinomas with mutations in FGFR genes is less well defined. We report here a patient with a cholangiocarcinoma bearing a FGFR2 p.Ser252Trp mutation. The patient was treated with two different FGFR inhibitors, as the first caused ocular toxicity. She obtained clinical benefit from both. This case illustrates the efficacy of FGFR inhibitors on cholangiocarcinoma with specific point mutations. This is the first case to report the clinical benefit of these drugs in FGFR2 p.Ser252Trp mutation. Clinical benefit can be sustained, as seen in our patient. Our case also shows that FGFR inhibitors-induced adverse effects, such as ocular toxicities, may not recur after re-challenge with an alternative drug of the same class.

Dataset EGAD50000000021

Methylation Array data for: Three-dimensional patient-derived models of glioblastoma retain intra-tumoral heterogeneity

3 sets of matched patient-derived-organoids (PDOs),Â -neurospheres (PDNs), and parent glioblastoma tissue (9 samples total) underwent methylation array analysis. 200ng of each sample DNA extracted via a commercial kit (Qiagen) and loaded onto the Illumina EPIC v2.0 array. Data is provided as raw red and green .idat files.

Dataset EGAD00010002745

N2M2 methylation array data

Methylation profiling of 228 samples, using the approach described in "Molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation (N2M2/NOA-20 phase I/IIa umbrella trial)"

Dataset EGAD00010002747

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