Search Results - EGA European Genome-Phenome Archive

Clear cell renal cell carcinoma (HIPO-045)

Exome from EGAS00001001861

Dataset EGAD00001002166

Single Cell Genome Sequence for DLP+ library A98279A

Single Cell Genome Sequence for high grade serous ovarian carcinoma patient-derived xenograft SA1050A passage 1, patient SA1234 on DLP+ library A98279A

Dataset EGAD00001009486

Genomics of enteropathy-associated T cell lymphoma (EATL)

Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples.

Dataset EGAD00001003284

Genome and transcriptome sequence data from an adrenocortical carcinoma patient

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

Dataset EGAD00001003053

Genome and transcriptome sequence data from a solitary fibrous tumors (sarcoma) patient

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

Dataset EGAD00001003056

Genome and transcriptome sequence data from a metastatic adenoid cystic carcinoma of the palate patient

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

Dataset EGAD00001003065

Genome and transcriptome sequence data from an extraosseous osteosarcoma patient

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

Dataset EGAD00001003062

Genome and transcriptome sequence data from an osterosarcoma patient

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

Dataset EGAD00001003685

Genome and transcriptome sequence data from a metastatic rectal adenocarcinoma patient

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

Dataset EGAD00001003693

Paired RNA-Seq for Sarcoma tumors

Paired RNA-Seq of 199 samples of Sarcoma tumors. The sequencing was done mostly on HiSeq 4000 with Illumina TruSeq Stranded mRNA, ist was also done on NovaSeq 6000 using the same kit. Very few samples were sequenced on HiSeq X Ten with Illumina TruSeq RNA or Illumina TruSeq Stranded mRNA.

Dataset EGAD00001010256

Genome and transcriptome sequence data from an appendiceal adenocarcinoma patient

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

Dataset EGAD00001003066

Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4

Small cell carcinoma of the ovary of hypercalcemic type (SCCOHT) is an extremely rare, aggressive cancer affecting children and young women. We identified germline and somatic inactivating mutations in the SWI/SNF chromatin-remodeling gene SMARCA4 in 75% (9/12) of SCCOHT patients in addition to SMARCA4 protein loss in 82% (14/17) of SCCOHT tumors, but in only 0.4% (2/485) of other primary ovarian tumors. These data implicate SMARCA4 in SCCOHT oncogenesis.

Dataset EGAD00001000794

Single-cell Transcriptome for glioblastoma intra-tumoral heterogeneity

Single-Cell RNA Sequencing of 355 cells isolated from 7 tissue fragments of 3 patients corresponding to locally adjacent tumor, multifocal with recurrence and sections segregated by a marker of tumor cellularity (5-ALA).

Dataset EGAD00001002249

DLBCL Validation (FFPE) Cohort

miRNA-seq Cohort of 140 Formalin Fixed Paraffin Embedded Diffuse Large B-cell Lymphoma Patient Samples

Dataset EGAD00001001073

Genome and transcriptome sequence data from a pleural mesothelioma patient

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

Dataset EGAD00001003071

Whole genome sequencing on HiSeq platform of tumour-normal sample pairs from 183 melanoma cases

Aligned, merged and deduplicated BAM files from HiSeq whole genome sequencing of 366 samples: matched tumour-normal pairs from 183 melanoma cases comprising 48 primary melanomas, 15 cell lines, and 120 metastases. Sequencing was performed on the Illumina HiSeq 2000 and Xten platforms at Australian and Korean sequencing centres. Data was aligned to the human genome (GRCh37) using BWA-MEM.

Dataset EGAD00001003388

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

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

Dataset EGAD00001003073

Whole Genome Sequencing of a secondary myelodysplastic syndrome (MDS)

Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009); duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Sample derived from secondary myelodysplastic syndrome (MDS), arising after treatment for medulloblastoma in an 11-year old female Li-Fraumeni syndrome case (LFS-MB1; Rausch et al., 2012; matching WGS data available under EGAS00001000085).

Dataset EGAD00001000665

Dataset HCV positive lymphoma whole exome sequencing

This dataset contains 68 BAM files from matched normal-tumor pairs of HCV positive lymphoma analyzed by exome sequencing on Ilumina platform.

Dataset EGAD00001009786

WGS files for CIC paper data

WGS files for CIC paper titled "Malignant progression of an ancestral bone marrow clone harboring a CIC-NUTM2A fusion in isolated myeloid sarcoma"

Dataset EGAD00001009787

RNASeq files for CIC paper data

RNASeq files for CIC paper titled "Malignant progression of an ancestral bone marrow clone harboring a CIC-NUTM2A fusion in isolated myeloid sarcoma"

Dataset EGAD00001009788

Analysis of tumor periphery and center-specific mutations in renal cell carcinoma

Renal cell carcinoma (RCC) is a genomically heterogeneous tumor. In the present project, the question whether intratumoral heterogeneity follows a zonal pattern indicating spatial niches was addressed. Whole exome sequencing of 16 paired samples from tumor periphery and center revealed a number of region-specific functional SNVs and Indels. Therefore, RCCs are not composed of evenly admixed tumor cells but show topological differences in their clonal composition.

Dataset EGAD00001002067

lymphoma plasma cfRNA

Dataset contains total RNA sequencing data from plasma of 65 different human donors: 30 diffuse large B-cell lymphoma (DLBCL) and 13 primary mediastinal large B-cell lymphoma (PMBCL) patients, and 22 cancer-free controls. Samples were sequenced on a NovaSeq 6000 and are provided in FASTQ format.

Dataset EGAD00001010259

Hodgkin Lymphoma Whole Genome Sequencing

Whole genome sequencing of 17 paired tumor-normal Hodgkin Lymphoma whole genomes. Bulk tumor (-T) and flow-sorted Reed Sternberg cell (-HRS) samples. Approximately 30x wgs normal depth, 40-50x wgs depth tumor samples.

Dataset EGAD00001009818

WGS data for medulloblastoma samples (ICGC)

WGS data of medulloblastoma tumor/control pairs.

Dataset EGAD00001003127

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

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

Dataset EGAD00001003612

Raw data for "Spatial and temporal transcriptomics of medulloblastoma with chromothripsis identifies multiple genetic clones that resist to treatment and lead to relapse"

FASTQ files from Illumina sequencing of 10x Visium experiments.

Dataset EGAD00001010260

Genome and transcriptome sequence data from a metastatic rhabdomyosarcoma patient

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

Dataset EGAD00001003668

Genetic landscape of Extranodal NK/T-cell lymphoma

Whole-exome sequence (WES) data of tumor-normal pairs from 40 ENKTCL patients and RNA sequence (RNA-seq) data of tumors from 20 ENKTCL patients.

Dataset EGAD00001009852

Merged analysis-ready bam files: HiSeq sequencing of matched tumour/normal DNA samples from Pancreatic Ductal Adenocarcinoma cases

Additional sequencing data for 173 donors in EGAS00001000154, a study of Pancreatic Ductal Adenocarcinoma. WGS libraries were used for high-cellularity cases, WXS sequencing to high depth on low-cellularity cases. HiSeq 2xxx platform was used in all cases. The analysis files associated with this dataset are merged, de-duplicated bams aligned against GRCh37, one tumour and one normal bam per donor.

Dataset EGAD00001002192

BLUEPRINT September 2016, ATAC-seq Mantle Cell Lymphoma from venous blood, on Genome GRCh38

ATAC-seq data for 5 sample(s) Mantle Cell Lymphoma from venous blood, on Genome GRCh38. 5 run(s), 5 experiment(s), 5 alignment(s). Part of BLUEPRINT (September 2016).

Dataset EGAD00001002918

THE GENOMIC LANDSCAPE OF ACTINIC KERATOSIS

Actinic keratoses (AK) are lesions of epidermal keratinocyte dysplasia and are precursors for invasive cutaneous squamous cell carcinoma (CSCC). Identifying the specific genomic alterations driving progression from normal skin-AK-invasive CSCC is challenging due to the massive ultraviolet radiation-induced mutational burden characteristic at all stages of this progression. Here, we report the largest AK whole exome sequencing study to date and perform mutational signature and candidate driver gene analysis on these lesions. We demonstrate in 37 AK, from both immunosuppressed and immunocompetent patients, that there are significant similarities to CSCC in terms of mutational burden, copy number alterations, mutational signatures and patterns of driver gene mutations. We identify 44 significantly mutated AK driver genes and confirm that these genes are similarly altered in CSCC. We identify the azathioprine mutational signature in all AK from patients exposed to the drug, providing further evidence for its role in keratinocyte carcinogenesis. CSCC differ from AK in having higher levels of intra-sample heterogeneity. Alterations in signaling pathways also differ, with immune-related signaling and TGF-β signaling significantly more mutated in CSCC. Integrating our findings with independent gene expression datasets confirms that dysregulated TGF-β signaling may represent an important event in AK-CSCC progression.

Dataset EGAD00001006894

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

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

Dataset EGAD00001003673

Whole-exome sequencing of 20 samples of actinic keratosis (10s) and cutaneous squamous cell carcinoma (10s)

Whole-exome sequencing of 20 samples of actinic keratosis (10) and cutaneous squamous cell carcinoma (10) was performed to investigate a potential relationship between DNA methylation-based subtypes and genetic mutation patterns. 7 samples were shown to belong to the stem cell-like subclass (4 AK and 2 SCC), 12 - to the keratinocyte-like subtype (6 AK and 6 SCC) and one SCC sample is unclassified (was not included in the methylation analysis). Exome regions were captured using Agilent Low Input Exome-Seq Human v5 kit and sequenced on Illumina Hiseq4000 with paired-end 100-nucleotide reads.

Dataset EGAD00001003765

Bulk RNAseq of Neuroblastoma patient's tumors

This dataset contains 9 bulk RNAseq of neuroblastoma patient's tumors used to compare with derived PDXs and/or single-cell data in the Thirant C et al, Nature Communications, 2023. They were intially produced for the Berlanga P., Cancer Discovery, 2022.

Dataset EGAD00001010287

Genome and transcriptome sequence data from a lung adenocarcinoma patient

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

Dataset EGAD00001004699

Genome and transcriptome sequence data from a superficial pleomorphic liposarcoma patient

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

Dataset EGAD00001002616

Genome and transcriptome sequence data from a small cell/neuroendocrine carcinoma of the lung patient

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

Dataset EGAD00001002617

Anaplastic Meningioma WGS-X10

Anaplastic meningiomas are a rare, malignant variant of meningioma. At present there is no effective treatment for this cancer. The aim of the study is to identify somatic mutations in anaplastic meningiomas. We plan to sequence a set of 500 known cancer genes in 50 anaplastic meningioma and corresponding peripheral blood DNA samples. Bioinformatics will be used to analyse the results to assess the probability of these mutations being causal and so likely of critical importance for the tumour growth. Identification of these mutations will guide selection of appropriate compounds to effectively treat the disease.

Dataset EGAD00001001267

Clonal expansion of mutated cell population in bladder urothelium (2018-08-03)

1cm biospies of from patients undergoing bladder cystectomy will be collected. The underlying muscle and stroma will be removed and the remaining epithelia dissected into small sequential areas which will be sent for ultra-deep exome sequencing using a panel of known cancer and viral genes. Sequence analysis using similar methods to Martincorena I et al (Science 2015, 348:880) will provide an idea of the somatic mutational landscape in these patient samples. Individual patient muscle samples will also be sequenced as a reference. . This dataset contains all the data available for this study on 2018-08-03.

Dataset EGAD00001004274

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 EGAD00001002593

Genome and transcriptome sequence data from a metastatic colorectal adenocarcinoma patient

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

Dataset EGAD00001002622

Gut microbiome from melanoma patients

Metagenomics shotgun sequencing was conducted on fecal samples from the Australian patients enrolled in the OpACIN-neo clinical trial (n = 38). Metagenomic shotgun sequencing was performed utilizing the same DNA from the same preparations as for the 16S rRNA gene analysis. Individual libraries were prepared using Nextera XT, and sequencing was performed on the Illumina NovaSeq 6000 S1 (2 x 150bp; Xp workflow).

Dataset EGAD00001010028

4859 results for "*oma"

in 23.22 milliseconds.