Search Results - EGA European Genome-phenome Archive

Mannheim Liquid Biopsy Unit, Heidelberg University & DKFZ

The dataset consists of sequenced cell free DNA (cfDNA) samples from colorectal cancer patients. The samples were sequenced on an Illumina MiSeq machine using a custom amplicon sequencing approach. These amplicons were designed to cover the most common mutation hotspots in colorectal cancer. The data include 138 cfDNA samples from 34 different patients. For each patient several samples are available derived from blood drawn at different time points during treatment. In addition the data include samples from 22 histology slides and 30 samples derived from HT29/HCT116 cell lines that were used as controls.

Dataset EGAD00001004574

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

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

Dataset EGAD00001004600

Metabolic reprogramming towards OXPHOS identifies a novel therapeutic target for mantle cell lymphoma

Metabolic reprogramming is linked to cancer cell growth and proliferation, metastasis, and therapeutic resistance in a multitude of cancers. Targeting dysregulated metabolic pathways to overcome resistance, an urgent clinical need in all relapsed/refractory cancers, remains difficult. Through genomics analysis of clinical specimens, we show that metabolic reprogramming towards oxidative phosphorylation (OXPHOS) and glutaminolysis is associated with therapeutic resistance to the Bruton’s tyrosine kinase inhibitor ibrutinib in mantle cell lymphoma (MCL), an incurable B-cell lymphoma with poor clinical outcomes. Inhibition of OXPHOS with a novel, clinically applicable small molecule, IACS-010759, which targets complex I of the mitochondrial electron transport chain, results in significant growth inhibition in vitro and in vivo in ibrutinib-resistant patient-derived cancer models. This work suggests that targeting metabolic pathways to subvert therapeutic resistance is a clinically viable approach to treat highly refractory malignancies.

Dataset EGAD00001004577

Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers

Dataset EGAD00001004585

MCO colorectal cancer genomics at UNSW

This dataset contains DNA sequencing data from 95 colorectal cancer and matched-normal samples. The dataset contains targeted deep sequencing of selected regulatory elements in 95 cancer and matched-normal samples, and data for one sample that was additionally whole-genome sequenced (cancer and matched-normal).

Dataset EGAD00001004582

A compendium of mutational signatures due to environmental exposures

Whole-genome-sequencing (WGS) of human tumours has revealed distinct mutation patterns that hint at the causative origins of cancer. We examined mutational-signatures in 324 WGS of human induced pluripotent stem cells (iPSCs) following exposure to known or suspected environmental carcinogens. 79 agents were tested with or without metabolic activation at concentrations that produced measurable cytotoxicity; 41 yielded characteristic substitution mutational signatures. Some exhibit similarity with signatures found in human tumours. Additionally, 6 agents produced double-substitution signatures and 8 produced indel signatures. Investigating mutation asymmetries across genome topography reveals fully functional mismatch and transcription-coupled repair pathways in iPSCs. Primary adducts induced by environmental carcinogens can be resolved by disparate repair/replicative pathways, resulting in an assortment of signature outcomes even for a single mutagen. This compendium of experimentally-induced mutational-signatures permits further exploration of roles of environmental agents in cancer aetiology, and underscores how human stem cell DNA is directly vulnerable to environmental agents.

Dataset EGAD00001004583

Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

The dataset includes multi-region exome sequencing (MSeq) of four resected treatment naïve mismatch repair deficient gastro-esophageal cancers. Paired-end sequencing was performed on the Illumina HiSeq 2500 or NovaSeq 6000 with a target depth of 200X. Seven primary tumor regions along with tumor-adjacent non malignant tissue were subjected to MSeq. An additional two lymph node metastases were also included from each of two cases.

Dataset EGAD00001004594

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Mannheim Liquid Biopsy Unit, Heidelberg University &amp; DKFZ

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

Metabolic reprogramming towards OXPHOS identifies a novel therapeutic target for mantle cell lymphoma

Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers

MCO colorectal cancer genomics at UNSW

A compendium of mutational signatures due to environmental exposures

Extreme intratumor heterogeneity and driver evolution in mismatch repair deficient gastro-esophageal cancer

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic leiomyosarcoma patient

Genome and transcriptome sequence data from a osteosarcoma patient

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

Genome and transcriptome sequence data from a metastatic basal cell carcinoma of frontal scalp patient

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

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

Genome and transcriptome sequence data from a metastatic mmmt of the endometrium patient

Genome and transcriptome sequence data from a lung cancer patient

Genome and transcriptome sequence data from a anorectal gastrointestinal stromal tumor patient

Genome and transcriptome sequence data from a ganglioglioma of the left temporal lobe patient

Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of the cheek patient

Genome and transcriptome sequence data from a metastatic rectosigmoid cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a breast cancer patient

Genome and transcriptome sequence data from a double-hit lymphoma patient

Genome and transcriptome sequence data from a metastatic gastric cancer patient

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

Genome and transcriptome sequence data from a leiomyosarcoma patient

Genome and transcriptome sequence data from a metastatic follicular thyroid carcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic melanoma patient

Genome and transcriptome sequence data from a low grade chondrosarcoma (bronchus) patient

Genome and transcriptome sequence data from a metastatic colorectal carcinoma patient

Genome and transcriptome sequence data from a metastatic choroidal melanoma patient

Genome and transcriptome sequence data from a metastatic pancreatic cancer patient

Genome and transcriptome sequence data from a metastatic colorectal cancer patient

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

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

Genome and transcriptome sequence data from a metastatic colon cancer patient

Genome and transcriptome sequence data from a clear cell carcinoma of the left ovary patient

Genome and transcriptome sequence data from a follicular lymphoma patient

Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic uveal melanoma patient

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

Genome and transcriptome sequence data from a metastatic spindle cell sarcoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic breast cancer patient

Genome and transcriptome sequence data from a metastatic lung adenocarcinoma patient

Genome and transcriptome sequence data from a lung adenocarcinoma patient

Mannheim Liquid Biopsy Unit, Heidelberg University & DKFZ