Search Results - EGA European Genome-Phenome Archive

Genome and transcriptome sequence data from a adenocarcinoma of the liver patient

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

Dataset EGAD00001004706

Genome and transcriptome sequence data from a metastatic pancreatic adenocarcinoma patient

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

Dataset EGAD00001004705

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 peripheral T-cell lymphoma patient

Genome and transcriptome sequence data from a peripheral T-cell lymphoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001004696

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 EGAD00001004695

Genome and transcriptome sequence data from a metastatic carcinoma to paraspinal mass with primary unknown patient

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

Dataset EGAD00001004693

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

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

Dataset EGAD00001004692

Genome and transcriptome sequence data from a angiosarcoma patient

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

Dataset EGAD00001004690

Genome and transcriptome sequence data from a metastatic breast carcinoma patient

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

Dataset EGAD00001004688

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 EGAD00001004685

Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

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

Dataset EGAD00001004716

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

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

Dataset EGAD00001004714

Melanoma-Til Study RNAseq

In this study, mutations present in a series of human melanomas (stage IV disease) will be determined, using autologous blood cells to obtain a reference genome. From each of the samples that are analyzed, tumour-infiltrating T lymphocytes have also been isolated. This offers a unique opportunity to determine which (fraction of) mutations in human cancer leads to epitopes that are recognized by T cells. The resulting information is likely to be of value to understand how T cell activating drugs exert their action.

Dataset EGAD00001000325

Ewings Sarcoma RNA-seq drug sensitivity

Illumina RNA-Seq will be performed on four Ewing's sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol.

Dataset EGAD00001000337

Balanced Ependymoma

We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

Dataset EGAD00001000350

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

CD74-NRG1 study - RNASeq dataset

RNAseq data, Publication Fernandez-Cuesta et al., 2014, CD74-NRG1 fusions in lung adenocarcinoma

Dataset EGAD00001000716

BLUEPRINT: WGBS-seq of multiple myeloma and plasma cells

Whole-genome Bisulfite sequencing of two multiple myeloma samples and one pooled sample of plasma cells.

Dataset EGAD00001000672

Genome-wide analysis of H3K27me3 occupancy and DNA methlytion in pediatric high-grade glioma

Genome-wide analysis of H3K27me3 occupancy and DNA methylation in K27M-mutant and H3.3-WT primary pediatric high-grade gliomas (pHGGs) as well as pediatric pHGG cell lines. The study aims to elucidate the connection between K27M-induced H3K27me3 reduction and changes in DNA methylation as well as gene expression.

Dataset EGAD00001000677

Angiosarcoma follow-up 2 validation study

A bespoke targeted pulldown experiment will be performed on patients with Angiosarcoma. the resulting products will be sequenced to determine the prevalence of previously found mutations in these patients.

Dataset EGAD00001000679

DIPG_ICR_WGS

Whole genome sequencing of 20 tumour and normal pairs of diffuse intrinsic pontine glioma (DIPG)

Dataset EGAD00001000705

Chordoma Sequencing Project Whole Genome

This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

Dataset EGAD00001000721

Osteosarcoma whole genome rearrangement screen

Genomic libraries (500 bps) will be generated from total genomic DNA derived from Osteosarcoma cancer patients and subjected to short paired end sequencing on the llumina platform. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

Dataset EGAD00001000368

Balanced Brain Tumour Whole Genome Sequencing

We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

Dataset EGAD00001000369

Sporadic Parathyroid Carcinoma

This dataset is compromised of 5 sequencing experiments from a single patient with sporadic and recurring parathyroid carcinoma. The samples include whole genome sequence of the primary tumor, the first recurrent tumor and peripheral blood. Whole transcriptome sequence of the first and second recurrent tumors are also included.

Dataset EGAD00001000370

Uveal melanoma whole genome sequencing, SNP arrays and RNA-seq

We conducted whole genome sequencing and DNA SNP array of 12 uveal melanoma genomes and their matched DNA from blood. We also conducted RNA-seq of the 12 tumour samples.

Dataset EGAD00001000372

A study of the molecular pathogenesis of Splenic Marginal Zone and Diffuse Large B-Cell Lymphoma

We will perform exome sequencing on selected cases of splenic marginal zone lymphoma (SMZL) and diffuse large B-cell lymphoma (DLBCL) in order to characterise their genetic makeup and identify biomarkers for prognosis and prediction of treatment response.

Dataset EGAD00001000410

Ewings Sarcoma Rearrangement Screen

Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours.

Dataset EGAD00001000389

Chondrosarcoma Validation Study

Agilent whole exome hybridisation capture was performed on genomic DNA derived from Chondrosarcoma cancer and matched normal DNA from the same patients. Next Generation sequencing performed on the resulting exome libraries and mapped to build 37 of the human reference genome to facilitate the identification of novel cancer genes. Now we aim to re find and validate the findings of those exome libraries using bespoke pulldown methods and sequencing the products.

Dataset EGAD00001000392

UK10K_RARE_COLOBOMA REL-2013-04-20

Dataset EGAD00001000415

Pilocytic Astrocytoma ICGC PedBrain whole genome sequencing

Dataset EGAD00001000616

Characterization of individual foci of multicentric/multifocal breast cancer using targeted next generation sequencing

Multifocality or multicentricity in breast cancer may be defined as the presence of two or more tumor foci within a single quadrant of the breast or within different quadrants of the same breast, respectively. This original classification of the breast cancer as multicentric or multifocal was based on the assumption that cancers arising in the same quadrant were more likely to arise from the same ductal structures than those occurring in separate areas of the breast. The problem with these definitions is that the ?quadrants? of the breast are arbitrary external designations, as no internal boundaries do exist. This project will therefore focus both on synchronous multifocal and multicentric tumors. The incidence of multifocal and multicentric breast cancers was reported to be between 13 and 75% depending on the definition used, the extent of the pathologic sampling of the breast and whether in situ disease is considered evidence of multicentricity (1). Although this incidence is variable, those figures show that it is a frequent phenomenon. Multiple (multifocal/multicentric) breast carcinomas, especially when occurring in the same breast, represent a real challenge for both pathologists and clinicians in terms of identifying the cellular origin and the best therapeutic management of the cancer. Multifocality or multicentricity has been associated with a number of more aggressive features including an increased rate of regional lymph node metastases and adverse patient outcome when compared with unifocal tumors (2-3), and a possible increased risk of local recurrence following breast conserving surgery (4). For the moment, the literature is divided on whether there is a corresponding impact on survival outcomes. Today, the current convention to stage and to treat multifocal and multicentric tumors is the classical tumor-node-metastasis (TNM) staging guidelines with which tumor size is assessed by the largest tumor focus without taking other foci of disease into consideration. If some papers, as the recent one from Lynch and colleagues, support the current staging convention (3), others, however, as Boyages et al. suggested that aggregate size and not the size of the largest lesion should be considered in order to refine the prognostic assessment of those tumors (5). On the top of that, the question whether multifocal/multicentric carcinomas are due to the spread of a single carcinoma throughout the breast or is due to multiple carcinomas arising simultaneously has been a matter of debate. Some studies suggested that multifocal breast cancer may result from either intramammary spread from a single primary tumor or multiple synchronous primary tumors; whereas others suggest that multiple breast carcinomas always arise from the same clone (6-8). Recently, Pietri and colleagues analyzed the biological characterization of a series of 113 multifocal/multicentric breast cancers (8) which were diagnosed over a 5-year period. The expression of estrogen (ER) and progesterone (PgR) receptors, Ki-67 proliferative index, expression of HER2 and tumor grading were prospectively determined in each tumor focus, and mismatches among foci were recorded. Mismatches in ER status were present in 5 (4.4%) cases and PgR in 18 (15.9%) cases. Mismatches in tumor grading were present in 21 cases (18.6%), proliferative index (Ki-67) in 17 (15%) cases and HER2 status in 11 (9.7%) cases. Interestingly, this heterogeneity among foci has led to 14 (12.4%) patients receiving different adjuvant treatments compared with what would have been indicated if we had only taken into account the biologic status of the primary tumor. This study therefore showed that differences in biological characteristics of multifocal/multicentric lesions play a crucial role in the adjuvant treatment decision making process. In this study, we will concentrate on a larger series of patients with multifocal invasive ductal breast cancer lesions. We aim at: 1. Evaluating the incidence of multifocality according to the different breast cancer molecular subtypes (ER-/HER2-, HER2+, ER+/HER2-). 2. Evaluating the incidence of multifocality in patients with hereditary breast cancer disease (presence of germline BRCA1 or BRCA2 mutations). Moreover, we would like to investigate if multifocal lesions with BRCA1 or BRCA2 mutations exhibit a characteristic combination of substitution mutation signatures and a distinctive profile of deletions as demonstrated recently by Nik-Zainal and colleagues (9). 3. Correlating multifocality with clinical information in order to define its influence on patients? survival (DFS and OS). 4. Carrying high coverage targeted gene sequencing of driver cancer genes and genes whose mutation is of therapeutic importance in order to compare clinically-relevant genetic differences between several multifocal breast cancer lesions. 5. Evaluating the impact of the distance between the different lesions on the clinical outcome but also on the genetic differences. 6. Comparing gene expression patterns between several multifocal breast cancer lesions and correlate them with the results of the targeted genes screen. 7. Characterizing the genomic and transcriptomic status of cancer related genes in metastatic lesions (local recurrence, positive lymph node or distant metastatic sites) from the same multifocal invasive ductal breast cancer patients in order to evaluate the consequence of genomic and transcriptomic heterogeneity of multifocal lesions on metastatic lesions. Multiple (multifocal/multicentric) breast carcinomas, especially when occurring in the same breast, represent a real challenge for both pathologists and clinicians in terms of identifying the cellular origin and the best therapeutic choice. This project has the potential to identify genetic/transcriptomic differences existing between several lesions constituting multifocal breast cancers, which in the routine clinical practice are usually considered to be homogeneous among them. We foresee validating significant results in a larger series of patients and this, in turn, could have a remarkable impact on the treatment and clinical management of multifocal breast cancers. Indeed, we hope to provide some evidence whether or not each focus matters in multifocal and multicentric breast cancer to define the adequate therapeutic approach, especially in the context of targeted therapies. The work to be done at Sanger will be target gene screen pooling of 1400 samples.

Dataset EGAD00001000624

Chordoma Sequencing Project RNAseq

This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

Dataset EGAD00001000653

RNAseq of patients with Ewings sarcoma

Cancer is driven my mutations in the genome. We will uncover the mutations that give rise to Ewing's sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewing's sarcoma tumours.

Dataset EGAD00001000444

Whole genome sequences of hepatocellular carcinoma (NCCRI)

Fastq files of 213 samples of hepatocellular carcinoma (NCCRI)

Dataset EGAD00001000446

The Transcriptome of PLX4032 resistance

We have collected material from a patient who had BrafV600E mutant melanoma that was treated with PLX4032. We have germline DNA from the patient and DNA and RNA from distinct lesions before and after treatment with PLX4032. We have transcriptome sequenced these samples to obtain a snap shot of the mechanisms of resistance that are operative.

Dataset EGAD00001000599

Angiosarcoma RNA sequencing

Extension of angiosarcoma whole genome sequencing study

Dataset EGAD00001000738

Somatic mutations in angiosarcoma

Here we present the genomes of three secondary angiosarcomas

Dataset EGAD00001000735

Exome sequencing reads of paediatric glioblastoma

Whole exome sequencing of paediatric glioblastoma with mutations reported in the manuscript: Mutations in ACVR1, FGFR1 and TP53 associate with tumor location in histone H3 K27M pediatric midline high-grade astrocytoma

Dataset EGAD00001000792

Integrated genomic characterization of adrenocortical carcinoma

Adrenocortical carcinomas (ACC) are aggressive cancers originating in the cortex of the adrenal glands. Despite the overall poor prognosis, ACC outcome is heterogeneous. CTNNB1 and TP53 mutations are frequent in these tumors, but the complete spectrum of genetic changes remains undefined. Exome sequencing and SNP array analysis of 45 ACC revealed recurrent alterations in known drivers (CTNNB1, TP53, CDKN2A, RB1, MEN1) and genes not previously reported to be altered in ACC (ZNRF3, DAXX, TERT and MED12), which were validated in an independent cohort of 77 ACC. The cell-surface transmembrane E3 ubiquitin ligase ZNRF36 was the gene the most frequently altered (21%), and appears as a potential novel tumor suppressor gene related to the ß-catenin pathway.Our integrated genomic analyses led to the identification of two distinct molecular subgroups with opposite outcome. The C1A group of poor outcome ACC was characterized by numerous mutations and DNA methylation alterations, whereas the C1B group with good prognosis displayed a specific deregulation of two miRNA clusters. Thus, aggressive and indolent ACC correspond to two distinct molecular entities, driven by different oncogenic alterations.

Dataset EGAD00001000764

The UCSF Glioblastoma Genome Project #1

Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients.

Dataset EGAD00001000777

POT1 splice site mutant analysis

We are interested in the contribution mutations in the Shelterin complex protein POT1 may have to the development of melanoma. We have identified a patient who carries a splice site mutation in POT1 and as part of our analysis of this gene we aim to sequence the transcriptome of this patient to see how this mutation influences splicing. RNA has been obtained from lymphocytes collected from the patient.

Dataset EGAD00001000786

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

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