Search Results - EGA European Genome-Phenome Archive

Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA Associated Pancreatic Cancer in the Clinical and Pre-clinical Setting

Whole genome sequencing data for germline BRCA pancreatic cancer

Dataset EGAD00001011129

Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial). Panel sequencing data from baseline FFPE biopsies were used to perform a comprehensive genomic profiling of CUP metastases. Combined targeted next-generation sequencing of patient-specific hotsport mutations and shallow whole genome sequencing of baseline and follow-up liquid biopsy samples were used to analyze ctDNA and to evaluate response to immunei checkpoint inhibitor treatment. In some cases, whole exome sequencing of peripheral blood mononuclear cells was performed to screen for potential CHIP and germline mutations.

Dataset EGAD00001011130

Total RNA sequencing data from the Triple Negative Trial (TNT)

BAM files from total RNA sequencing of samples from breast cancer patients in the TNT trial. Data includes 186 primary tumour samples and 13 matched recurrence samples.

Dataset EGAD00001011141

Exome sequencing data from two small cell prostate cancer patients

Exome sequencing data from two small cell prostate cancer patients - 4 cancer samples (FFPE) from Patient 1 collected at 3 different time points and 2 cancer samples (FFPE) from Patient 2 collected at 1 time point. Exonic DNA was enriched using the TruSeq Exome Kit (Illumina) and sequenced on the Illumina NextSeq 500 as 75bp paired end reads (total read length 150bp).

Dataset EGAD00001011149

Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

Sample cohort (n=48) is consisted of healthy, atrophic gastritis and gastric cancer patients. Some of the gastric cancer patients samples are collected at the separate time points: -1 before the operation; -2 after the operation; -3 during the control visit. For the hybridisation capture of the genes unique 15 gastric cancer-related gene panel was developed and very deep sequencing using TruSight Oncology Unique Molecular Identifier (UMI) Reagents (Illumina) was used.

Dataset EGAD00001011153

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

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

Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

We performed whole genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and regional lymph nodes of five treatment-naive patients with locally advanced disease who underwent radical prostatectomy. Whole genome sequencing was performed as 150bp paired end reads on the Illumina NovaSeq 6000 platform.

Dataset EGAD00001011174

cfDNA methylation profiling in Metastatic Cancer and Cancer of Unknown Primary

This study contains methyl-binding domain sequencing and shallow whole genome sequencing from circulating cell-free DNA (cfDNA) for 143 patients with metastatic cancer of known type, 41 patients with Cancer of Unknown Primary (CUP) and 27 non-cancer controls.

Dataset EGAD00001011178

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - wgs

Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

Dataset EGAD00001011181

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - 0.25mm punches targeted

Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

Dataset EGAD00001011182

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - nanoseq

Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

Dataset EGAD00001011183

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - 2mm targeted

Ageing epithelial tissues, including the esophagus, are progressively colonized by somatic mutant clones, some carrying mutations linked to cancer. However, whether normal epithelial mutational landscapes that evolve over decades can be altered by short term interventions such as cancer treatment is not known. Here we sequenced normal esophageal epithelium removed from patients after 5-8 weeks of therapy for esophageal cancer. Some patients had no prior treatment (NT), while others had 8 weeks of 5 Fluorouracil (5-FU) containing chemotherapy (FLOT) or 4 weeks of chemotherapy and radiation directed at the tumor (CROSS). Despite the brief duration of therapy, we observed treatment specific differences in the selection of mutant clones. The median size of mutant TP53 and PPM1D clones in the CROSS group was double that in the other groups. Mutants of the tumor suppressor SPOP were selected in CROSS but not FLOT or NT patients. In FLOT patients we found positive selection of activating MTOR mutations, consistent with the hypothesis that these mutants confer 5-FU resistance. Sequencing densely mutated normal epithelia after cancer reveals treatment specific selection of mutations with potential therapeutic impact.

Dataset EGAD00001011184

HiSeq Colorectal Cancer Dataset

Set of 19 patients afflicted with colorectal cancer with matching preoperative and postoperative blood plasma, PBMC, and tumor biopsy sequencing data. Originally referenced by Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat Med. 2020, Zviran et. al.

Dataset EGAD00001011186

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma - RNA-Seq

This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.

Dataset EGAD00001011192

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma - Ribo-Seq

This study aims to investigate the dysregulation of RNA translation and identify functional non-canonical open reading frames (ORFs) as potential targets for medulloblastoma treatment. The study involves ribosome profiling and RNAseq of medulloblastoma tissues and cell lines to observe the translation of non-canonical ORFs. Multiple CRISPR-Cas9 screens will be used to identify functional non-canonical ORFs implicated in medulloblastoma cell survival.

Dataset EGAD00001011193

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Spectrum of Response to Platinum and PARP Inhibitors in Germline BRCA Associated Pancreatic Cancer in the Clinical and Pre-clinical Setting

Sequencing data from a phase II study of nivolumab and ipilimumab in recurrent or refractory cancer of unknown primary (CheCUP trial)

Total RNA sequencing data from the Triple Negative Trial (TNT)

Exome sequencing data from two small cell prostate cancer patients

Cell-free DNA sequencing data of healthy control, atrophic gastritis, and gastric cancer patients’ blood

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

Colorectal cancer organoid-stroma biobank cohort

Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole genome sequencing with histopathological features

cfDNA methylation profiling in Metastatic Cancer and Cancer of Unknown Primary

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - wgs

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - 0.25mm punches targeted

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - nanoseq

Cancer treatment re-shapes the somatic mutational landscape of normal esophagus - 2mm targeted

HiSeq Colorectal Cancer Dataset

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma - RNA-Seq

Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma - Ribo-Seq

10x Single Cell Gene Expression Library SCRNA10X_SA_CHIP0063_000

Genome and transcriptome sequence data from a metastatic thymic carcinoma patient

Genome and transcriptome sequence data from a colorectal cancer patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of the salivary gland patient

Genome and transcriptome sequence data from a metastatic lymphoepithelial carcinoma of the parotid gland patient

Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient

Genome and transcriptome sequence data from a primary unknown patient

Genome and transcriptome sequence data from a metastatic duodenal carcinoma patient

Genome and transcriptome sequence data from a hepatic cholangiocarcinoma patient

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

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

Genome and transcriptome sequence data from a melanoma patient

Genome and transcriptome sequence data from a metastatic rectal cancer patient

Genome and transcriptome sequence data from a metastatic breast carcinoma (er positive) patient

Genome and transcriptome sequence data from a paget disease of the vulva patient

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic ovarian cancer patient

Genome and transcriptome sequence data from a poorly differentiated adenocarcinoma of the pancreas patient

Genome and transcriptome sequence data from a inflammatory myofibroblastic lung tumor patient

Genome and transcriptome sequence data from a colorectal adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic pancreatic neuroendocrine tumour patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of lung patient

Genome and transcriptome sequence data from a metastatic pancreatic neuroendocrine adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic cholangiocarcinoma patient

Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

Genome and transcriptome sequence data from a metastatic esophageal adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic adenocarcinoma of colon patient

Genome and transcriptome sequence data from a metastatic thymic carcinoma patient

Genome and transcriptome sequence data from a metastatic nasopharyngeal carcinoma patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a metastatic pancreatic neuroendocrine tumour patient

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

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

Genome and transcriptome sequence data from a melanoma patient