Search Results - EGA European Genome-Phenome Archive

Genome and transcriptome sequence data from a breast ductal carcinoma patient

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

Dataset EGAD00001010954

Genome and transcriptome sequence data from a uveal melanoma patient

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

Dataset EGAD00001010956

Genome and transcriptome sequence data from a leiomyosarcoma patient

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

Dataset EGAD00001010957

Genome and transcriptome sequence data from a ovarian serous carcinoma patient

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

Dataset EGAD00001010961

Genome and transcriptome sequence data from a carcinoma of unknown primary patient

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

Dataset EGAD00001010962

RNAseq of 25 sarcoma samples

100 bp paired-end fastq RNAseq files for 25 sarcoma samples. RNAseq data from exon capture library prep.

Dataset EGAD00001010839

The mutational status of 121 genes recurrently altered in B-cell lymphoma was examined in 55 of 56 diagnostic and 10 of 12 relapse samples using a custom targeted NGS panel. Libraries were generated from 150 ng of DNA using molecular-barcoded library adapters (ThruPLEX Tag- seq kit; Takara) coupled with a custom hybridization capture-based method (SureSelectXT Target Enrichment System Capture strategy, Agilent Technologies). The quality of the libraries was determined using the Bioanalyzer high sensitivity DNA kit (Agilent) and quantified by PCR using the KAPA library quantification kit (KAPA Biosystems). Finally, the libraries were pooled and sequenced in the MiSeq instrument (Illumina).

Dataset EGAD00001010842

Single-cell RNA-sequencing of nivolumab-treated glioblastoma

Single-cell RNA-sequencing of 8 patients, from primary and relapse tumour (total of 16 samples). Patients were treated with nivolumab prior to relapse surgery.

Dataset EGAD00001010843

Bulk RNA-sequencing of nivolumab-treated glioblastoma

Bulk RNA-sequencing of 30 relapse tumour samples. 20 patients were treated with nivolumab prior to relapse surgery, while 10 patients are control patients.

Dataset EGAD00001010844

PacBio medulloblastoma datasets

PacBio data from 5 medulloblastoma tumor-normal pairs. The data consists of BAM files aligned using NGMLR

Dataset EGAD00001010852

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 7a)

Whole genome sequencing data of 36 high-grade serous carcinoma (HGSC) patients (89 samples) sequenced with HiSeq X Ten.

Dataset EGAD00001010845

Linked-Read Medulloblastoma data

Linked-read data from 25 medulloblastomas and their matching control. Dataset consists of 25 group 4 medulloblastomas (G4) as well as 2 sonic hedgehog medulloblastomas (SHH-MB) samples and 2 group 3 medulloblastomas. The data consists of BAM files generated by the LongRanger pipeline developed by 10x Genomics

Dataset EGAD00001010849

RNA-Seq Medulloblastoma data

RNA-Seq data from 12 medulloblastoma samples, all group 4 medulloblastomas. The data consists of BAM files aligned using STAR

Dataset EGAD00001010850

Nanopore medulloblastoma data

Nanopore data from 3 medulloblastoma samples of which 2 are tumor-normal pairs sequenced with the MinIon and one is tumor only data sequenced on the PromethIon. The data consists of BAM files aligned using minimap2

Dataset EGAD00001010851

Whole exome and Transcriptome sequencing of treatment-naïve esophageal adenocarcinoma biopsies and matched peripheral blood mononuclear cells

Exome sequencing was performed on n=28 treatment-naïve esophageal adenocarcinoma (EACs). Three to four biopsies sampling different areas of each tumor were pooled before nucleic acid extractions to mitigate the elevated heterogeneity described for EAC. WES was performed on EAC biopsies at 120X average coverage, with autologous PBMCs used as germline controls at 80X average coverage. Libraries were prepared from 30 ng of input DNA using the SureSelect QXT Human All Exon V7 kit (Agilent Technologies) and sequenced on the NextSeq 550 (Illumina), 2x150 bp. BCL files were demultiplexed to FastQ files using bcl2fastq2 software (Illumina). Three paired end sequencing batches were analyzed independently (Batch1: samples 8, 10, 11, 12, 15, 17, 18; Batch2: samples 20, 24, 25, 26, 27, 29, 30, 31, 33, 34 ; Batch3: samples 35, 37, 39, 40, 41, 43, 45, 48, 54, 55, 57). RNA sequencing was performed on n=26 treatment-naïve esophageal adenocarcinoma (EACs). Three to four biopsies sampling different areas of each tumor were pooled before nucleic acid extractions to mitigate the elevated heterogeneity described for EAC. RNAseq libraries were prepared on 50 ng of total RNA (with RNA integrity index RIN >=7) with the TruSeq Stranded mRNA library preparation kit (Illumina) in accordance with low-throughput protocol. After PCR enrichment (15 cycles) and purification of adapter-ligated fragments, the concentration and length of DNA fragments were measured using D1000 Screen Tape System (Agilent), obtaining a median insert size of 311 nucleotides. Then, RNAseq libraries were sequenced using the Illumina NovaSeq platform, 1x100 bp, obtaining on average 100 million single reads per sample.

Dataset EGAD00001010876

Melanoma PEACE Dataset

Dataset for the initial melanoma PEACE paper in Cancer Discovery, March 2023.

Dataset EGAD00001010877

Paired RNA-Seq data of 65 samples of chemo-naïve and post-chemotherapy pancreatic ductal adenocarcinoma (PDAC)

130 runs/ 65 samples of paired RNA-Seq data of chemo-naïve and post-chemotherapy pancreatic ductal adenocarcinoma (PDAC). The sequencing was done on Novaseq 6000 with Illumina TruSeq stranded mRNA Kit.

Dataset EGAD00001010883

Targetable NOTCH1 rearrangements in reninoma

Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

Dataset EGAD00001010887

Targetable NOTCH1 rearrangements in reninoma - WGS

Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

Dataset EGAD00001010888

Targetable NOTCH1 rearrangements in reninoma - RNA

Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

Dataset EGAD00001010889

Whole transcriptome sequencing of 78 follicular lyphoma tumours

This data set includes RNAseq from 77 follicular lymphoma tumours. All tumours were fresh frozen. Libraries were constructed by enriching for poly-A transcripts and sequenced as 75bp paired end reads on an Illumina HiSeq 2500 instrument.

Dataset EGAD00001010894

Human tumor bulk RNA-seq

We profiled 7 patient neuroblastoma-FOXR2 tumor samples by bulk RNA-seq. The raw fastqs are provided.

Dataset EGAD00001010901

Human tumor single-cell mutiome

We profiled 1 patient neuroblastoma-FOXR2 tumor sample by single-cell multiome RNA + ATAC. The raw fastqs are provided.

Dataset EGAD00001010902

Human tumor single-nuclei RNA-seq

We profiled 4 patient neuroblastoma-FORX2 tumor samples by single-nuclei RNA-seq using 10X Chromium 3'. The raw fastqs are provided.

Dataset EGAD00001010903

Exploration of neuroblastoma xenograft models for tumor extracellular RNA profiling in murine blood plasma

Total RNA sequencing (SMARTer Stranded Total RNA-Seq Kit v2) data of extracellular RNA (exRNA) from liquid biopsies of neuroblastoma xenograft models.

Dataset EGAD00001010905

Machine Learning Guided Signal Enrichment for Plasma Tumor-burden Monitoring Dataset

Includes 4 Datasets: 1. 35 Control Plasma WGS samples sequenced on NovaSeq V1.0 Chemistry at the New York Genome Center. Denoted by CTRL-2XX naming scheme. 2. Plasma WGS from 17 patients with Small Cell Lung Cancer. Samples extracted at either Pretreatment or Postoperative at weeks 2 or 3. Denoted by SCLC-XX naming scheme. 3. Plasma WGS from a synthetic mixing study of a high-burden melanoma plasma sample with plasma bag, at estimated tumor concentrations of 10e-3, 10e-4, 10e-5, and 10e-6 for 2 replicates. Denoted by SM-repX naming scheme. 4. Assorted Plasma, Tumor, and Normal WGS from patients with NSCLC expressing high-burden for use in model training. Denoted by NSCLC-2XX naming scheme.

Dataset EGAD00001011352

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 9 part 1)

Whole genome sequencing data of 6 high-grade serous carcinoma (HGSC) patients (11 samples) sequenced with MGISEQ-2000

Dataset EGAD00001011353

Single-cell RNA-seq of peripheral blood mononuclear cells in classic Hodgkin lymphoma

Abstract: Classic Hodgkin lymphoma (cHL) is a largely MHC class I-negative tumor with recurrent 9p24.1/ PD-L1/ PD-L2 copy gains and the highest reported response rates to PD-1 blockade. We utilized scRNA sequencing to characterize the peripheral immune response to PD-1 blockade and more broadly define non-CD8+ dependent mechanisms of immune evasion in cHL. Peripheral blood mononuclear cells were obtained from 20 patients with relapsed/refractory (R/R) cHL treated with PD-1 blockade (nivolumab) on the CheckMate 205 clinical trial (paired samples from cycle 1 day 1 [C1D1] and cycle 4 day 1 [C4D1]), 11 patients with newly diagnosed, previously untreated cHL and 13 healthy donors.

Dataset EGAD00001011360

Single-cell RNA-seq data of angioimmunoblastic T-cell lymphoma

Dataset EGAD00001011361

Bulk RNA-seq osteosarcoma

We profiled 23 patient osteosarcoma tumor samples by bulk RNA-seq. The raw fastqs are provided.

Dataset EGAD00001011371

Whole genome sequencing data of high-grade serous ovarian cancer samples (set 9 part 2)

Whole genome sequencing data of 35 high-grade serous carcinoma (HGSC) patients (112 samples) sequenced with Illumina Novoseq 6000

Dataset EGAD00001011368

WES raw data set for the study "Genomic profiling of localized (lFL) and systemic follicular lymphoma (sFL) reveals novel insights into FL pathogenesis"

221 patient samples including 164 initial tumor (TI) samples (53/164 fresh frozen TI samples, and 111/164 formalin-fixed paraffin-embedded (FFPE) TI samples), 22 paired matched normal samples, and 35 unpaired normal samples from healthy donors; FASTQ file format, Agilent SureSelect Human All Exon V6 Kit (Agilent Technologies, Inc., Santa Clara, California, USA)

Dataset EGAD00001011369

Exome sequencing of osteosarcoma, blood and saliva

We profiled 31 osteosarcoma tumor patient samples, 18 blood and 1 saliva control samples by exome sequencing, for a total of 50 samples. The raw fastqs are provided.

Dataset EGAD00001011370

Whole genome sequencing of osteosarcoma and blood

We profiled 2 patient osteosarcoma tumor samples as well as the blood of the same patients by whole genome sequencing, for a total of 4 samples. The raw fastqs are provided.

Dataset EGAD00001011372

Germline BAMs from patients with both uveal and cutaneous melanoma

Germline BAMs from blood/saliva samples from patients diagnosed with both uveal and cutaneous patients. Reads have been aligned, deduplicated and recalibrated.

Dataset EGAD00001011676

Complex structural variation patterns in pediatric solid tumors WGS

Paired tumor-normal whole genome sequencing data from primary tumors of patients diagnosed with neuroblastoma, Ewing sarcoma, Wilms tumor, hepatoblastoma and rhabdomyosarcoma

Dataset EGAD00001011378

WES data for study of the microenviroment of angioimmunoblastic T-cell lymphoma

Exome sequencing data for study of the microenviroment of angioimmunoblastic T-cell lymphoma

Dataset EGAD00001011581

WXS Tumor Samples Javelin head and neck 100

We performed Whole Exome (WXS) and RNASeq sequencing on samples obtained from the phase 3 randomized, double-blinded, placebo-controlled study in patients with locally advanced squamous cell carcinoma of the head and neck JAVELIN Head and Neck 100 (NCT02952586). There are 471 WXS Tumor samples and 346 RNASeq tumor samples. All tumor samples have matching normal samples.

Dataset EGAD00001011680

Low-coverage whole-genome sequencing of cancer and healthy plasma circulating DNA

Plasma samples from patients with melanoma (stage II/III/IV) and breast cancer (stage IV) as well as healthy individuals were subjected to low-coverage whole-genome sequencing (less than 10x average depth). This dataset contains raw fastq files from 39 breast cancer, 127 melanoma and 42 healthy control plasma samples.

Dataset EGAD00001011817

CHEWIE ctDNA in Rhabdomyosarcoma

Targeted DNA based panel of multiple ctDNA samples from 10 patients througout clinical care to assess treatment response. The panel is custom-designed and property of UGS, IC.

Dataset EGAD00001011127

Genomic and immune signatures predict clinical outcome in newly diagnosed multiple myeloma treated with immunotherapy regimens

In this study we performed whole genome sequencing on matched tumor-normal CD138+ bone marrow mononuclear cells from 60 patients with newly diagnosed multiple myeloma treated with daratumumab, carfilzomib, lenalidomide, and dexamethasone (NCT03290950-MANHATTAN trial). In addition, we performed 5’-single-cell RNA-sequencing (10X Genomics) coupled with V(D)J sequencing and capture of the surface protein markers (TotalSeq-C, Biolegend) of the CD138- bone marrow mononuclear cells to interrogate the composition of the immune microenvironment at baseline and after eight cycles of induction therapy in 22 patients with newly diagnosed multiple myeloma. Samples were multiplexed using hashtag oligo.

Dataset EGAD00001011132

Whole exome sequencing data of Hispanic hepatocellular carcinoma

The paired-end reads were aligned to the human reference genome (hg19) with decoy sequences (as used in the 1000 Genomes Project) using BWA (v0.7.5a) software. The duplicate reads were marked and subsequently removed using Picard (v1.140) (https://broadinstitute.github.io/picard/) and SAMtools (v0.1.19), respectively. Local realignment around insertions/deletions (indels) and base quality recalibration were performed using GATK (v3.6).

Dataset EGAD00001011158

Colorectal cancer organoid-stroma biobank cohort

In colorectal cancers (CRC) the tumor microenvironment plays a key role for prognosis and therapy efficacy. Patient-derived tumor organoids (PDTOs) show enormous potential for preclinical testing, however, purely epithelial cultures features including the ‘consensus molecular subtypes’ (CMS) are largely eradicated. To better reflect the cell type heterogeneity, we established the CRC organoid-stroma biobank of matched PDTOs and cancer-associated fibroblasts (CAFs) from 30 patients. Whole exome sequencing and transcriptome analysis in various in vitro and in vivo contexts was performed to study the influence of the TME on the CRC phenotype.

Dataset EGAD00001011173

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