5270 results for "*oma"

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• Genome and transcriptome sequence data from a unknown primary, cholangiocarcinoma patient

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

  Dataset EGAD00001015917

• Genome and transcriptome sequence data from a metastatic invasive ductal carcinoma of the breast patient

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

  Dataset EGAD00001015918

• Genome and transcriptome sequence data from a metastatic anal squamous cell carcinoma patient

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

  Dataset EGAD00001015919

• Genome and transcriptome sequence data from a cutaneous squamous cell carcinoma patient

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

  Dataset EGAD00001015920

• Genome and transcriptome sequence data from a wildtype glioblastoma patient

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

  Dataset EGAD00001015921

• Genome and transcriptome sequence data from a metastatic recurrence of pancreatic ductal adenocarcinoma patient

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

  Dataset EGAD00001015923

• Genome and transcriptome sequence data from a metastatic high grade neuroendocrine carcinoma patient

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

  Dataset EGAD00001015926

• Genome and transcriptome sequence data from a metastatic hepatocellular carcinoma patient

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

  Dataset EGAD00001015927

• Genome and transcriptome sequence data from a squamous cell carcinoma of the vulva patient

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

  Dataset EGAD00001015928

• Genome and transcriptome sequence data from a oligodendroglioma patient

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

  Dataset EGAD00001015929

• Genome and transcriptome sequence data from a recurrent salivary gland (myoepithelial carcinoma) patient

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

  Dataset EGAD00001015933

• Genome and transcriptome sequence data from a metastatic osteosarcoma patient

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

  Dataset EGAD00001015934

• Genome and transcriptome sequence data from a advanced endometrioid carcinoma (primary unknown) patient

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

  Dataset EGAD00001015938

• Genome and transcriptome sequence data from a metastatic melanoma patient

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

  Dataset EGAD00001015939

• Genome and transcriptome sequence data from a invasive metastatic adenocarcinoma, originating from extramammary paget’s disease patient

  Genome and transcriptome sequence data from a invasive metastatic adenocarcinoma, originating from extramammary paget’s disease patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001015940

• Genome and transcriptome sequence data from a histiocytic sarcoma patient

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

  Dataset EGAD00001015945

• Genome and transcriptome sequence data from a astrocytoma li fraumeni syndrome patient

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

  Dataset EGAD00001015946

• Genome and transcriptome sequence data from a metastatic melanoma patient

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

  Dataset EGAD00001015948

• Genome and transcriptome sequence data from a osteosarcoma patient

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

  Dataset EGAD00001015951

• 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 EGAD00001015952

• Genome and transcriptome sequence data from a renal cell carcinoma, non-clear cell patient

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

  Dataset EGAD00001015953

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

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

  Dataset EGAD00001015954

• Genome and transcriptome sequence data from a synovial sarcoma patient

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

  Dataset EGAD00001015985

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

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

  Dataset EGAD00001015955

• Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma patient

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

  Dataset EGAD00001015956

• Genome and transcriptome sequence data from a metastatic thymic carcinoma patient

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

  Dataset EGAD00001015958

• Genome and transcriptome sequence data from a osteosarcoma patient

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

  Dataset EGAD00001015959

• Genome and transcriptome sequence data from a malignant paraganglioma patient

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

  Dataset EGAD00001015960

• Genome and transcriptome sequence data from a vulvar squamous cell carcinoma patient

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

  Dataset EGAD00001015961

• 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

• 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

• PacBio medulloblastoma datasets

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

  Dataset EGAD00001010852

• 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

• RNA-seq analysis refines molecular subtypes of hepatocellular carcinoma

  This work aims to identify homogeneous and robust molecular subtypes in HCC based on a large, homogenous and well-annotated cohort. We performed RNA sequencing (RNA-seq) on 529 HCC from 461 patients collected mainly in France. Based on the consistency between genomic and transcriptomic data, we identified 9 robust HCC subtypes mainly based on driver mutations. We further characterized HCC subtypes using transcriptomic and clinicopathological features. Our study provided a robust molecular classification based on a large HCC dataset from a Western country, improving our understanding of the mechanisms of carcinogenesis and facilitating the development of genome-based precision medicine in HCC.

  Dataset EGAD00001015427

• WGS/WES analysis refines molecular subtypes of hepatocellular carcinoma

  This work aims to identify homogeneous and robust molecular subtypes in HCC based on a large, homogenous and well-annotated cohort. We performed whole genome/exome sequencing (WGS/WES) on 529 HCC from 461 patients collected mainly in France. Based on the genomic data, we identified 9 robust HCC subtypes primarily driven by key mutations. We further characterized these subtypes using genomic and clinicopathological features. Among the 9 subtypes, 5 belonged to chromosome instable tumors, while 3 belonged to chromosome stable tumors. Our subtypes were associated with prognosis and showed distinct distributions across features like etiology and gender. This study offers a comprehensive molecular classification of HCC, enhancing our understanding of hepatocarcinogenesis and supporting the development of genome-based precision medicine for liver cancer.

  Dataset EGAD00001015428

• Sequencing data for oesophageal and related samples - Zamani et al

  Data supporting: "Genomic and epidemiological similarities between phenotypically distinct esophageal adenocarcinoma suggest a single entity" Zamani et al

  Dataset EGAD00001015435

• RNA sequencing of Hepatoblastoma cell lines and drug-treated HepG2 xenograft tumors

  RNA sequencing was performed on 7 pediatric liver cancer cell lines, complementing a panel of 8 cell lines previously described (Hirsch, Cancer Discov. 2021) and on 16 HepG2 xenograft tumors treated with cisplatin, low-dose elimusertib, elimusertib at MTD, or elimusertib/cisplatin compared to vehicle-treated controls.

  Dataset EGAD00001015439