Search Results - EGA European Genome-Phenome Archive

RNAseq

RNAseq of pancreatic cancer organoids.

Dataset EGAD00001010834

Melanoma PEACE Dataset

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

Dataset EGAD00001010877

Genome and transcriptome sequence data from a multifocal glioblastoma multiforme tumor patient

Genome and transcriptome sequence data from a multifocal glioblastoma multiforme patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

Dataset EGAD00001015281

Genome and transcriptome sequence data from a progressive facial plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a progressive facial plexiform neurofibroma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

Dataset EGAD00001015282

The dataset for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

The dataset for Single molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer includes 57 BAM files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from individuals with and without cancer.

Dataset EGAD00001010891

Clonal selection after gene therapy in sickle cell disease

While gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD), the occurrence of myeloid malignancies in clinical trials has prompted concern. To interrogate potential mechanisms underlying increased cancer risk, we used hematopoietic stem cell (HSC) clonal tracking by whole genome sequencing (WGS) to map the somatic mutation and clonal landscape of 2,592 gene modified as well as unmodified single stem and progenitor cells from six SCD patients undergoing gene therapy (7-26 years old, average 12.7× depth). Pre-GT phylogenetic trees in SCD were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified. However, an increased frequency of driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) were seen in both genetically modified and unmodified cells suggested positive selection of mutant clones during gene therapy. This work sheds light on the mutation landscape and HSC clonal dynamics in gene therapy for SCD and highlights enhanced fitness of some HSCs harboring pre-existing driver mutations following gene therapy. Future studies should define the long-term fate of mutant clones including any contribution to expansions associated with myeloid neoplasms.

Dataset EGAD00001010914

The dataset for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

The dataset for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes includes 444 BAM files from whole genome next-generation sequencing on the Illumina NovaSeq 6000. The samples analyzed include plasma samples from individuals with and without cancer.

Dataset EGAD00001010931

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

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

Dataset EGAD00001010940

Genome and transcriptome sequence data from a myoepithelioma patient

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

Dataset EGAD00001010938

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 EGAD00001010939

Genome and transcriptome sequence data from a squamous cell carcinoma patient

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

Dataset EGAD00001010941

Genome and transcriptome sequence data from a non-small cell lung carcinoma patient

Genome and transcriptome sequence data from a non-small cell lung carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001010942

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 sequence data from a metastatic rectal carcinoma patient

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

Dataset EGAD00001010972

Genome sequence data from a metastatic paraganglioma patient

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

Dataset EGAD00001010985

Genome and transcriptome sequence data from a unknown - likely pancreatobiliary / intrahepatic cholangiocarcinoma in liver patient

Genome and transcriptome sequence data from a unknown - likely pancreatobiliary / intrahepatic cholangiocarcinoma in liver patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001010989

Genome and transcriptome sequence data from a metastatic ovarian cancer patient

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

Dataset EGAD00001011005

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

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

Dataset EGAD00001011021

Genome and transcriptome sequence data from a rectal adenocarcinoma patient

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

Dataset EGAD00001011040

Genome and transcriptome sequence data from a thymoma patient

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

Dataset EGAD00001011039

47 urothelial cancer patients WES and 38 RNAseq

We performed a global mutational landscape analysis using tumor samples from the 47 urothelial cancer patients included in MATCH-R or MOSCATO studies, with advanced metastatic disease and WES available (RNAseq is included for 38 patient samples).

Dataset EGAD00001011063

Organoid Derivation Project - GRCh38 - RNAseq (2023-06-22)

Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

Dataset EGAD00001011092

Organoid Derivation Project - GRCh38 - WGS (2023-06-22)

Sequencing of tissue samples and their derived organoids from oesophageal, pancreatic and colorectal cancer patients. . This dataset contains all the data available for this study on 2023-06-22.

Dataset EGAD00001011093

Evaluation of somatic mutations in cervicovaginal samples as a non-invasive method for the detection and molecular classification of endometrial cancer

Dataset EGAD00001011123

RNASeq data from one small cell prostate cancer patient (4 samples from 3 time points)

RNASeq data from one small cell prostate cancer patient - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points. mRNA was selected using the Magnetic mRNA Isolation Module (NEB) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

Dataset EGAD00001011154

10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0163_001

10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0163_001 for Triple negative breast cancer patient-derived xenograft SA609X7XB03505

Dataset EGAD00001011219

10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0206_002

10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0206_002 for Triple negative breast cancer patient-derived xenograft SA535X10XB03696

Dataset EGAD00001011235

10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0014_001

10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0014_001 for Triple negative breast cancer patient-derived xenograft SA604X6XB01979

Dataset EGAD00001011251

10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0015_001

10x Single Cell Gene Expression library SCRNA10X_SA_CHIP0015_001 for Triple negative breast cancer patient-derived xenograft SA604X6XB01979

Dataset EGAD00001011252

RNA-seq data from the tumor samples of head and neck cancer patients

This dataset contains paired-end RNA sequencing data (2x50 bp) from the primary tumors and the recurrences/metastases of 6 head and neck cancer patients.

Dataset EGAD00001011279

Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer

Dataset consists of 216 samples, with each sample having a BAM, BAI and VCF file.

Dataset EGAD00001011297

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a angiosarcoma patient, generated as part of the BC Cancer Agency's Pediatric Personalized Onco-Genomics study

Dataset EGAD00001015290

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

neoALTTO

RNAseq fastq files for 254 samples for the neoALTTO study of lapatinib, trastuzumab or combination in HER2+ breast cancer patients. Those are pre-treatment baseline samples.

Dataset EGAD00001011354

An MTOR mutation hitchhikes through renal embryogenesis, driving multifocal, multiphenotypic tumours - RNA

Embryogenesis is a vulnerable time. Mutations in developmental cells can result in the seeding of cells predisposed to disease within mature organs, creating a field effect. We characterise an embryonic cancer mutation that drives multifocal, multiphenotypic renal tumours in a 14-year-old girl. Their shared MTOR mutation, absent from normal tissues, increases protein flexibility which enables a FAT domain hinge to dramatically increase mTORC1 activity. Developmental mutations, not usually detected in traditional genetic screening, have vital clinical importance in guiding prognosis, targeted treatment, and family screening decisions for paediatric tumours.

Dataset EGAD00001011646

RNA-sequencing of Human Thyroid cancer cell lines

RNA-sequencing data of 5 human thyroid cancer cell lines cultured in control conditions

Dataset EGAD00001011677

Somatic mutant selection is altered by prior NOTCH1 mutation in ageing esophageal epithelium

Authors: Charlotte King1, Emilie Abbie1, Joanna C. Fowler1, Irina Abnizova1, Roshan K. Sood1, Swee Hoe Ong1, Michael W. J. Hall1,2, Faye Lynch-Williams3, Benjamin A. Hall4, Philip H. Jones1,2,5 Abstract: In cancer evolution, genome alterations often occur in a specific order, implying selection depends on the prior clonal genotype 1-3. It is unknown if similar constraints operate in normal epithelia. Here, we mapped mutations in normal mid-esophagus of aged UK subjects. Mutant NOTCH1 clones colonized most of the epithelium by age 60 and above 70 tissue was saturated with mutants under strong competitive selection. Mutant TP53 was more strongly selected in donors over 60 years of age. Samples predominantly mutant for NOTCH1 showed increased selection of NOTCH2 mutants and weaker selection of mutant TP53 compared with samples that were mostly NOTCH1 wild type. In mouse esophagus lacking Notch1 we observed strong selection of mutant Notch2 and other genes not selected in wild type esophagus. In normal ageing esophagus, the first driver mutation may change the trajectory of subsequent somatic evolution by altering mutant selection.

Dataset EGAD00001015258

The long term effects of chemotherapy on normal blood - Nanoseq dataset

In developed countries, ~10% of individuals are exposed to systemic chemotherapy for cancer and other diseases. Many chemotherapeutic agents act by increasing DNA damage in cancer cells, hence triggering cell death. However, there is limited understanding of the extent and consequences of collateral DNA damage to normal tissues. To investigate the impact of chemotherapy on mutation burdens and cell population structure of a normal tissue we sequenced blood cell genomes from 23 individuals, aged 3-80 years, treated with a range of chemotherapy regimens. Substantial additional mutation loads with characteristic mutational signatures were imposed by some chemotherapeutic agents, but there were differences in burden between different classes of agent, different agents of the same class and different blood cell types. Chemotherapy also induced premature changes in the cell population structure of normal blood, similar to those of normal ageing. The results constitute an initial survey of the long-term biological consequences of cytotoxic agents to which a substantial fraction of the population is exposed during the course of their disease management, raising mechanistic questions and highlighting opportunities for mitigation of adverse effects.

Dataset EGAD00001015340

Sequencing data for "Replication timing alterations are associated with mutation acquisition during tumour evolution in breast and lung cancer"

Repli-seq data for "Replication timing alterations are associated with mutation acquisition during tumour evolution in breast and lung cancer"

Dataset EGAD00001015363

To profile the landscape of sebaceous tumours_WES

Sebaceous tumours are a rare cutaneous cancer with potential for aggressive behaviour. However, limited information is available on these cancers with few published cases. Here we wish to exome sequence these cancers to define the first genomic landscape for this malignancy. We will extract DNA from formalin-fixed, paraffin-embedded (FFPE) cores. Cores may be obtained from lesional and non-lesional tissues of primaries as well as matching metastases. The extracted DNA will be used for exome sequencing. Please note that the dataset was last revised on October 16, 2025.

Dataset EGAD00001015367

DNA WGS Short Read Sequence (Illumina NovaSeq) for manuscript titled: "Performance of Somatic Structural Variant Calling in Lung Cancer using Oxford Nanopore Sequencing Technology"

Dataset EGAD00001015399

DNA WGS Long Read Sequence (PromethION) for manuscript titled: "Performance of Somatic Structural Variant Calling in Lung Cancer using Oxford Nanopore Sequencing Technology"

Dataset EGAD00001015400

Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER

Dataset EGAD00001015411

Somatic mutation in edited cholangiocyte organoids

Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

Dataset EGAD00001015456

HCA Organoids | Colon - Cancer, WES

HCA Organoids | Colon - Cancer, Whole Exome Sequencing (WES)

Dataset EGAD00001015548

The earliest stages of neoplastic transformation in Familial Adenomatous Polyposis

The succession of somatic genetic events associated with the conversion of a normal colorectal epithelial cell into a colorectal carcinoma constitutes a paradigmatic model of cancer development. Familial Adenomatous Polyposis (FAP) is caused by constitutional inactivating mutations in APC, the central gatekeeper gene of colorectal cancer, and is associated with a substantially increased lifetime-risk of colorectal cancer. To investigate the earliest stages of neoplastic change due to APC inactivation, we microdissected and individually whole genome sequenced 279 histologically normal and abnormal colorectal crypts from 15 individuals with FAP. Histologically normal crypts generally exhibited similar mutation burdens and mutational signatures to normal crypts from wild-type individuals of the same age, with 1/110 carrying a somatic inactivating APC mutation. By contrast, 9/18 aberrant crypt foci carried somatic APC mutations and exhibited modestly increased burdens of some mutational signatures found in normal crypts. 12/13 diminutive adenomatous polyps (less than 5mm diameter) showed somatic APC mutations and carried substantially increased mutation loads of most mutational signatures present in normal crypts. Phylogenetic trees of crypts from aberrant crypt foci and adenomatous polyps revealed that some had acquired their initiating somatic APC mutations decades previously during the first few years of life. The results catalogue the changes in somatic mutation rates, mutational processes and “driver” mutations in cancer genes during the earliest stages of colorectal neoplastic transformation initiated by APC inactivation and highlight the long periods of clonal evolution required for a cancer to develop.

Dataset EGAD00001015471

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