Search Results - EGA European Genome-Phenome Archive

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

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 EGAD00001011645

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

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

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 EGAD00001011647

RNA-sequencing of Human Thyroid cancer cell lines

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

Dataset EGAD00001011677

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

Circulating tumor DNA, pathological and immunologic responses to neoadjuvant nivolumab or nivolumab plus relatlimab and chemoradiotherapy in resectable esophageal/gastroesophageal junction cancer

The dataset for the study “Circulating tumor DNA, pathological and immunologic responses to neoadjuvant nivolumab or nivolumab plus relatlimab and chemoradiotherapy in resectable esophageal/gastroesophageal junction cancer” includes 173 bam files from hybrid capture targeted error-correction next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 32 individuals with esophageal/gastroesophageal junction cancer, who received immunotherapy-containing regimens.

Dataset EGAD00001011822

Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

The dataset for the study Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer includes 207 bam files from hybrid capture targeted error-correction next-generation sequencing (TEC-Seq) from plasma cell-free DNA and matched white blood cell DNA from 30 individuals with non-small cell lung cancer, alongside 46 bam files from whole exome sequencing of tumor and matched normal DNA for 21 individuals with non-small cell lung cancer who received immunotherapy-containing regimens.

Dataset EGAD00001011991

Shallow-whole genome sequencing for copy numbers in resectable gastric cancer treated with surgery alone

Dataset EGAD00001011994

The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

Telomere fusions (TFs) can trigger the accumulation of oncogenic alterations leading to malignant transformation and drug resistance. Despite their relevance in tumour evolution, our understanding of the patterns and consequences of TFs in human cancers remains limited. Here, we characterize the rates and spectrum of somatic TFs across >30 cancer types using whole-genome sequencing data. TFs are pervasive in human tumours with rates varying markedly across and within cancer types. In addition to end-to-end fusions, we find novel patterns of TFs that we mechanistically link to the activity of the alternative lengthening of telomeres (ALT) pathway. We show that TFs can be detected in the blood of cancer patients, which enables cancer detection with high specificity and sensitivity even for early-stage tumours and cancers of high unmet clinical need. Overall, we report a novel genomic footprint that enables characterization of the telomere maintenance mechanism of tumours and liquid biopsy analysis.

Dataset EGAD00001012101

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

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

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

RNA-sequencing of Human Thyroid cancer cell lines

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

Circulating tumor DNA, pathological and immunologic responses to neoadjuvant nivolumab or nivolumab plus relatlimab and chemoradiotherapy in resectable esophageal/gastroesophageal junction cancer

Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer

Shallow-whole genome sequencing for copy numbers in resectable gastric cancer treated with surgery alone

The ALT pathway generates telomere fusions that can be detected in the blood of cancer patients

Geographic variation of mutagenic exposures in kidney cancer genomes – sequence data (Mutographs)

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a craniopharyngioma tumor patient

Genome and transcriptome sequence data from a NHL large B cell tumor patient

Genome and transcriptome sequence data from a malignant granular cell tumor tumor patient

Genome and transcriptome sequence data from a papillary thyroid carcinoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a aggressive fibromatosis tumor patient

Genome and transcriptome sequence data from a pineoblastoma tumor patient

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

Genome and transcriptome sequence data from a neuroblastoma tumor patient

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

Genome and transcriptome sequence data from a plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a diffuse intrinsic pontine glioma tumor patient

Genome and transcriptome sequence data from a acute lymphoblastic leukemia tumor patient

Genome and transcriptome sequence data from a ewing sarcoma tumor patient

Genome and transcriptome sequence data from a ependymoma tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a NUT midline carcinoma tumor patient

Genome and transcriptome sequence data from a angiosarcoma tumor patient

Genome and transcriptome sequence data from a pre-B all (2nd relapse in CNS) tumor patient

Genome and transcriptome sequence data from a gliomatosis cerebri anaplastic astrocytoma tumor patient

Genome and transcriptome sequence data from a osteosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a metastatic alveolar rhabdomyosarcoma tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a minimally invasive adenocarcinoma tumor patient

Genome and transcriptome sequence data from a aggressive fibromatosis tumor patient

Genome and transcriptome sequence data from a aggressive fibromatosis tumor patient

Genome and transcriptome sequence data from a glioblastoma tumor patient

Genome and transcriptome sequence data from a neurofibromatosis type 1 tumor patient

Genome and transcriptome sequence data from a papillary thyroid carcinoma tumor patient

Genome and transcriptome sequence data from a relapsed wilms tumor tumor patient

Genome and transcriptome sequence data from a plexiform neurofibroma tumor patient

Genome and transcriptome sequence data from a metastatic osteosarcoma tumor patient

Genome and transcriptome sequence data from a embryonal rhabdomyosarcoma of the nasopharynx tumor patient

Genome and transcriptome sequence data from a diffuse aarge B-cell lymphoma (relapse) tumor patient

Genome and transcriptome sequence data from a neuroblastoma tumor patient

Genome and transcriptome sequence data from a malignant rhabdoid tumour tumor patient

Genome and transcriptome sequence data from a relapsed osteosarcoma tumor patient