Search Results - EGA European Genome-Phenome Archive

Whole Genome Sequencing of Head and Neck Angiosarcoma

This dataset contains 55 Whole Genome Sequencing of the study titled Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma.

Dataset EGAD00001010140

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

Genome and transcriptome sequence data from a metastatic breast carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001004688

Leiomyosarcoma Whole Genome Sequencing

DNA was extracted from fresh frozen LMS material for 29 untreated tumors (24 primary tumors, 5 metastatic 13 relapses) and 13 tumors treated with radiation (7 primaries, 6 metastatic relapses). DNA from matched blood was used as a normal reference. Whole-genome sequencing was performed using established protocols on Illumina instruments.

Dataset EGAD00001007722

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0169_003

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0169_003 for Follicular lymphoma patient sample TFRI_Cont_4

Dataset EGAD00001010206

Patient-derived GBM cultures TMZ+BMP4 treated

Batch RNA sequencing of passages 5-7 of three patient-derived monolayer glioblastoma cultures in which TMZ and BMP4 synergize. 3 biological replicates, either untreated, only temozolomide, only BMP4 or temozolomide + BMP4

Dataset EGAD00001010163

Single cell epigenomic study of H3-K27M mutant diffuse midline glioma across age and location

This dataset contains the open chromatin profiles of 8 patient H3-K27M mutant DMGs utilizing the single-cell/nucleus assay for transposase-accessible chromatin using sequencing (snATAC-seq)

Dataset EGAD00001010170

10x Single Cell Gene Expression Library SCRNA10X_CS_CHIP0169_002

10x Single Cell Gene Expression library SCRNA10X_CS_CHIP0169_002 for Diffuse large B-cell lymphoma patient sample TFRIPAIR4_DLBCL

Dataset EGAD00001010228

DLP+ Single Cell Genomic Library A98203

DLP+ Single Cell Genomic Library A98203 for Diffuse large B-cell lymphoma patient sample TFRIPAIR8_DLBCL

Dataset EGAD00001010242

DLP+ Single Cell Genomic Library A98193

DLP+ Single Cell Genomic Library A98193 for Follicular lymphoma patient sample TFRI_Pair_6_FL

Dataset EGAD00001010241

DLP+ Single Cell Genomic Library A98205

DLP+ Single Cell Genomic Library A98205 for Follicular lymphoma patient sample TFRIPAIR9_FL

Dataset EGAD00001010243

DLP+ Single Cell Genomic Library A98221A

DLP+ Single Cell Genomic Library A98221A for Follicular lymphoma patient sample TFRIPAIR5_FL

Dataset EGAD00001010245

WES and RNA-seq data of 11 cancer patients with multiple cancer types

This dataset includes WES and RNAseq from 11 patients with metastatic melanoma, lung, kidney, and stomach cancers, enrolled in phase I clinical trials of TIL ACT (NCT03475134 & NCT04643574). WES was performed on matched cancer and healthy samples, whereas RNAseq was performed on cancer tissues, using Illumina HiSeq 2500/4000 and Illumina NextSeq 550 systems. Paired-end reads are provided in fastq format.

Dataset EGAD00001010169

Copy number profiles detected by shallow coverage WGS

We performed shallow coverage whole genome sequencing on 147 glioma samples and analyzed their copy number profile. The coverage of each sample is about 2. Data are presented as VCF files which describe the copy number segments and their log2 ratio.

Dataset EGAD00001005062

Dataset for Sarcoma-WGS linked from study EGAS00001004813

Sequencing data of 77 sarcoma tumor and control runs, which were uploaded to EGAS00001004813. The sequencing was always paired.

Dataset EGAD00001010257

Whole Exome Sequencing

The Whole Exome Sequencing dataset contains 30 whole exome sequencing files (tumor, germ line DNA) and phenotype metadata for 15 patients on the phase II clinical trial of neoadjuvant immune checkpoint blockade in high-risk resectable melanoma at MD Anderson Cancer Center (NCT02519322). Included are data from baseline samples.

Dataset EGAD00001004352

Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC)

Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC). RNA was extracted and sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocol. The sequencing was done using Illumina Novaseq 6000.

Dataset EGAD00001010172

t(14,18) negative diffuse follicular lymphoma with 1p36 deletion

Whole Exome Sequencing reads consisting of BAM paired end reads from Follicular Lymphoma samples.

Dataset EGAD00001004386

Genomic Analysis of Anaplastic Thyroid Carcinoma

This dataset includes WGS & WTS alignment data generated from 1 ATC tumor, its matched peripheral blood specimen and 3 authenticated ATC cell lines, THJ-16T, THJ-21T and THJ-29T. In addition, it includes WTS data from extra 4 unique anaplastic cell lines, ACT-1, C643, HTh7 and T238.

Dataset EGAD00001001321

Paired Exome sequencing of Sarcoma tumor and control

Paired Exome sequencing of Sarcoma tumor and control of 10 samples (5 tumor/control pairs). The sequencing was done on Illumina Hiseq 4000 and Agilent Sureselect V5+UTRs kit.

Dataset EGAD00001010278

71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients

Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. We performed 71 Whole-exome sequencing of Esophageal Squamous Cell Carcinoma on Chinese Patients.

Dataset EGAD00001001926

Shallow WGS of neuroblastoma cell lines with large-scale chromosomal deletions induced through CRISPR-Cas9

Shallow WGS of neuroblastoma cell lines with large-scale deletions induced through CRISPR-Cas9 and matching controls. Deletion of 11q was induced in the cell line SKNSH and loss of 6q was induced in the cell line NMB.

Dataset EGAD00001007758

Genome and transcriptome sequence data from a breast invasive ductal carcinoma patient

Genome and transcriptome sequence data from a breast invasive ductal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001004654

GBM whole tumor transcriptomic analysis before-after standard chemoradiation or chemoradiation+tumor treating fields (TTFields)

Glioblastoma Patient samples were acquired before and after standard chemoradiation or standard chemoradiation+TTFields (Novo-TTF100) treatment. The set includes paired before-after samples of 6 control patients (chemoradiation) and 6 TTFields+chemoradiation patients.

Dataset EGAD00001007782

Whole exome and targeted sequencing data from glioblastoma multiforme samples

Whole exome and targeted sequencing data from 11 glioblastoma multiforme patients. A total of 70 tumour specimens and 11 blood samples were used for whole exome sequencing (WES) using the Agilent SureSelectXT Human All Exon V5 Kit. Two custom targeted sequencing panels were designed using the using Agilent’s Haloplex (TES1) or Agilent SureSelect XT2 technology (TES2). Libraries were sequenced on an Illumina HiSeq2500

Dataset EGAD00001004420

2014 Lung squamous cell carcinoma WES analysis result

This data is belong to 2014 Lung squamous patients' exome data which is aligned to human reference(human_g1k_v37.fasta). There are 104 paired tumor/normal samples from SMC. All samples has passed QC and re-calibration steps while aligning to reference.

Dataset EGAD00001003960

A Protein Neddylation Inhibitor MLN4924 Suppresses Patient-Derived Glioblastoma Cells via Inhibition of ERK and AKT Signaling

To identify what factors cause a different reactivity to MLN4924, 15 cells were categorized into high, intermediate, and low MLN4924 resistance groups based on the half-maximal inhibitory concentration (IC50) of MLN4924. PDC1, PCD2, PDC3, PDC4, and PDC5 showed high MLN4924 sensitivity, whereas PDC12, PDC13, PDC14, and PDC15 showed low MLN4924 sensitivity. Whole-transcriptome sequencing of these 9 patient-derived glioblastoma stem cells was performed.

Dataset EGAD00001005709

RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells

RNAseq on 20 samples of multiple myeloma patients and 3 normal plasma cells. RNAseq was performed using 200 ng of total RNA by GATC Biotech. Directional libraries were performed after mRNA selection by polyA selection using UTP method. RNA-seq libraries were sequenced on HiSeq2500 Illumina machine using 100bp paired-end reads. Reads alignment was performed using the STAR aligner (version 2.4.0f1) and human genome hg19 as reference.

Dataset EGAD00001007813

Next gen seq of eye cancers (2019-08-14)

Retinoblastoma (RB), the commonest eye cancer in children was the first cancer for which a genetic cause was identified: the Rb1 gene is a tumour suppressor gene that is mutated in RB. The Rb1 gene defect alone does not predict the clinical outcome. We propose to study other possible mechanisms: 1. Stepwise further mutations occur in RB, increasing its carcinogenesis. We will sequence the whole genome in RB tissue, and relate the different genes expressed to the treatments used. 2. Extracellular matric proteins contribute to a tumour permissive environment for RB to continue to grow. This includes Samll Leucine Rich Proteoglycans (SLRP), a family of 15 secreted extracellular matrix proteins involved in eye development. 3. Cancer stem cells (CSC), a subpopulation of treatment resistant cells, drive RB tumours, and whether these stem cells can be manipulated for new therapies. The aim of this study is to assist finding targeted diagnostic techniques and treatments for RB. . This dataset contains all the data available for this study on 2019-08-14.

Dataset EGAD00001005251

Whole exome and RNA sequencing data from the OXIRI phase 1b clinical trial in Asian pancreatic ductal adenocarcinoma (PDAC) patients

This dataset contains 8 samples, each of which has paired-end WXS fastq files for Tumour and Normal samples, as well as RNA-Seq fastq file.

Dataset EGAD00001008632

scRNA-seq and scATAC-seq data of bone marrow

17 scRNA-seq and 16 scATAC-seq datasets on bone marrows derived from 16 patients. The sequencing dataset consists of 5 samples without bone marrow infiltration, defined as controls (C1, C2, C3, C4, and C5) and 11 neuroblastoma infiltrated bone marrow samples from patients with MYCN amplification (M1, M2, M3, M4), ATRX mutations (A1, A2), and cases lacking either alteration (S1, S2, S3, S4, S5).

Dataset EGAD00001008635

Genomic characterisation of SDH deficient renal cell carcinoma - WGS

SDH deficient renal cell carcinomas are a rare and recently defined subtype of kidney cancer, often associated with an inherited mutation in one of the SDH gene subunits. This dataset sought to understand the genomic events that underpin tumour formation, from putative cell of origin, characterisation of the tumour microenvironment, to the genomic evolution of these rare tumours. We performed whole genome and RNA sequencing of 4 patients with SDH deficient renal cell carcinomas, including one patient who had an additional paraganglioma. An addition patient in this cohort had the initial diagnosis revised to a clear cell renal cell carcinoma.

Dataset EGAD00001008469

RNA-seq data for 67 patient cohort

This dataset includes RNA-seq data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)

Dataset EGAD00001008648

G-SAM: Transcriptional Evolution of Glioblastomas Treated With Standard of Care

Collection of mostly matching primary and recurrent glioblastoma RNA-seq sample pairs, also matching with an earlier DNA sequencing study

Dataset EGAD00001007860

WGS data for 67 patient cohort

This dataset includes WGS data of samples from our paper titled "Dynamic phenotypic heterogeneity and the evolution of multiple RNA subtypes in Hepatocellular Carcinoma: The PLANET study." (National Science Review, nwab192. https://doi.org/10.1093/nsr/nwab192)

Dataset EGAD00001008647

A new subgroup of hepatocellular adenomas with sonic hedgehog pathway activation

Using sequencing and gene expression analyses, we identified a subgroup of HCA characterized by fusion of the INHBE and GLI1 genes and activation of sonic hedgehog pathway. Molecular subtypes of HCAs associated with different patients’ risk factors for HCA, disease progression, and pathology features of tumors. This classification system might be used to select treatment strategies for patients with HCA. Related Publication: Molecular Classification of Hepatocellular Adenoma Associates With Risk Factors, Bleeding, and Malignant Transformation Nault, Jean-CharlesLaurent, Christophe et al. Gastroenterology , Volume 152 , Issue 4 , 880 - 894.e6 http://dx.doi.org/10.1053/j.gastro.2016.11.042

Dataset EGAD00001003092

RNA-sequencing of six Pilocytic astrocytoma tumors

Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

Dataset EGAD00001003143

Congenital mesoblastic nephroma and infantile fibrosarcoma

The genetic basis of many rare childhood cancers remains unknown. These include a spectrum of infant soft tissue tumors without canonical gene fusions, encompassing congenital mesoblastic nephroma (CMN) of the kidney and infantile fibrosarcoma (IFS). Here, we integrated whole genome and transcriptome sequencing and identified diagnostic markers and novel therapeutic strategies.

Dataset EGAD00001003885

HERBY trial WES

Whole exome sequencing of non-brainstem paediatric high grade glioma from the HERBY phase II randomised trial. DNA from 86 cases was subjected to Illumina paired end whole exome sequencing using a customised SureSelect Human All Exon V6 capture set. Germline DNA from whole blood was sequenced for 83 cases. 26 cases were sequenced from both fresh frozen tissue and FFPE material, 10 were sequenced from only fresh frozen material and 50 from only FFPE. Data is provided as bwa aligned BAM files

Dataset EGAD00001004036

DNA (exome) sequencing of uveal melanoma metastases

DNA (exome) sequencing of uveal melanoma metastases.

Dataset EGAD00001007911

RNA-seq data from a variety of pediatric brain tumors

RNA-seq (n=52) data from a variety of pediatric brain tumors including ependymoma (PFA, PFB, Ste, spinal), medulloblastoma (G3, G4, SHH), high grade glioma (H3K27 and H3-WT), pilocytic astrocytoma, and more. Raw data provided as FASTQ. Data generated on Illumina HiSeq2500.

Dataset EGAD00001007915

BLUEPRINT release August 2014, Bisulfite-Seq for Multiple myeloma

Bisulfite-Seq data for 2 Multiple myeloma sample(s). 16 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT release August 2014. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

Dataset EGAD00001000934

RNASeq read files of glioblastoma PDX samples

This dataset contains 46 fastq files of paired-end RNA sequencing of an Illumina®️ TrueSeq stranded mRNA library of 23 glioblasoma PDX samples.

Dataset EGAD00001010196

Whole exome sequencing of SU- DIPG-XIII from different sites

Whole exome sequencing of diffuse intrinsic pontine glioma (DIPG) cells isolated from the pons and from a sub-ventricular zone site of spread within the frontal lobe from the same individual (SU- DIPG-XIII)

Dataset EGAD00001003563

Whole Exome and Target Sequencing Data in 75 Samples from 5 Hepatocellular Carcinoma Patients.

Whole Exome and Target Sequencing Data in 75 Samples from 5 Hepatocellular Carcinoma Patients. The sequencing was performed by Illumina HiSeq 4000. Background and aims: Intratumoral heterogeneity (ITH) challenges identifying mutations with target therapy potential whereas circulating cell-free DNAs (cfDNAs) could reflect nearly the entire mutation spectrum in given tumors. We investigated how to minimize the limit of ITH for profiling hepatocellular carcinoma (HCC).Methods: Thirty-two multi-regional HCC samples from five patients were subjected to whole exome sequencing (WES) and targeted deep sequencing (TDS). ITH extent was measured by the average percentage of non-ubiquitous mutations (present in parts of tumor regions). Matched cfDNAs were also analyzed by WES and TDS. Profiling efficiencies of single tumor specimen and cfDNA were compared and the one better depicted mutational landscape was selected to screen therapeutic targets.Results: We found variable extents of ITH in HCCs and observed branched and parallel evolution patterns. ITH level decreased at higher sequencing depth of TDS than that measured by WES (28.1% vs 34.9%, P < 0.01) but it remained unchanged upon additional samples analyzed. TDS of single tumor specimen detected an average of 70% the total mutations in HCC. Although more mutations were detected in cfDNA under TDS than WES, an average of 47.2% total HCC mutations uncovered by cfDNA suggested tissue outperform cfDNA and the latter may serve as alternative in profiling HCC genome. Consequently, TDS of single tumor tissue in 66 patients and cfDNAs in four unresectable HCCs identified 38.6% (26/66 and 1/4) patients bearing therapeutic targets.Conclusions: TDS of single tumor specimen could largely circumvent ITH to uncover mutations indicative of target therapy in HCC.

Dataset EGAD00001003278

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