Search Results - EGA European Genome-phenome Archive

BASIS miRNA data

399 tumors profiled using Agilent miRNA microarrays (Product Number G4872A, design ID 046064). The arrays are based on miRBase release 19.0 and 2006 human miRNAs are represented. 150 ng total RNA was used as input.

Dataset EGAD00010000917

miRNA expression in response to LPS stimulus in macrophages

Our lab is currently using macrophages as a model system for understanding how genetic variation modulates the response to external environmental stimulus. We want to extend this beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq

Dataset EGAD00001002196

TTV018 RORC IBD-associated genotype effects on RORgT expression and function in ex vivo T cells (2019-02-15)

RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-02-15.

Dataset EGAD00001004777

UMCU Molpheno Closed

This dataset contains Whole Genome Sequencing and, if available, RNA-sequencing and/or ATAC-sequencing data obtained from PBMCs derived from blood samples of two patients with intellectual disability and/or multiple congenital anomalies and eight parents included in the University Medical Center Utrecht (The Netherlands). Data access is closed.

Dataset EGAD00001004864

Next Generation Sequencing Characterization of Tregs in Human Peripheral Blood during Autoimmunity

Tregs were sorted as CD4+CD25+CD127- cells from peripheral blood of 14 healthy individuals, 8 patients with mild/severe rheumatoid arthritis, 1 patient with systemic lupus erythematosus/rheumatoid arthritis, 2 patients with ulcerative colitis and 2 patients with Chrohn's disease. RNA was extracted and polyA libraries were prepared using the Illumina Truseq sample preparation kit v.2. Single-end 75bp sequencing was performed on NextSeq500.

Dataset EGAD00001005446

Single circulating tumor cells in hepatocellular carcinoma

We determined intra- and inter-vascular transcriptional heterogeneity within the circulatory system using single-cell RNA-sequencing of 113 CTCs isolated from four key vascular sites along their dissemination route in ten HCC patients. The dataset consists of 146 paired-end fastq files from 113 sigle CTCs, HuH-7 cell line, Hep3B cellline, white blood cell, tumor and normal bulk tissue.

Dataset EGAD00001007642

Neuroblastoma patient WGS data

Paired tumor and normal WGS of primary neuroblastomas. This is an update of the „Berlin Neuroblastoma Dataset” (EGAS00001004022). This data was used for the analysis of circular RNA expression and regulation in neuroblastoma.

Dataset EGAD00001008123

LSC RNA-Sequencing

To infer the proteomic Mito signature in the LSC subcompartiment, myeloid blasts for 10 patients from the discovery cohort were FACS-sorted into CD34-GPR56+NKG2DLigands- (CD34-), alias 61dc5fb798e2520001702c03 CD34+GPR56+NKG2DLigands- (CD34+), alias 61dc5fb798e2520001702c03 Detailed gating strategy will be described in Donato, Correia, Andresen and Trumpp et al., (manuscript in preparation)

Dataset EGAD00001008488

RNAseq Iron-Treated iPSC-derived Microglia

Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.

Dataset EGAD00001008660

Sequencing data for oesophageal and related samples - Scott et al (WGS, RNA)

Data supporting: "Evidence that polyploidy in esophageal adenocarcinoma originates from mitotic slippage caused by defective chromosome attachments" Scott et al. WGS and RNAseq sequencing data Organoid, tumour and normal samples BAM files

Dataset EGAD00001006738

Sequencing data for oesophageal and related samples - Izadi et al (WGS, RNA)

Data supporting: "Genomic analysis of response to neoadjuvant chemotherapy in esophageal adenocarcinoma" Izadi et al. WGS for tumour and normal samples. RNAseq for tumour samples.

Dataset EGAD00001007493

Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19

These data correspond to samples used in the following papers: 1. GWAS and meta-analysis identifies 49 genetic variants underlying critical Covid-19 2. Genetic determinants of monocyte splicing are enriched for disease susceptibility loci including for COVID-19. 3. Identification of Genetic Determinants of Transcriptional Response to Metformin in Primary Human Monocytes. They are the raw RNA sequencing files as used in all downstream analysis.

Dataset EGAD00001010176

Sequencing data for oesophageal and related samples - Nowicki-Osuch, Zhuang et al (bulk RNA)

Data supporting: “Deep molecular phenotyping reveals the identity of Barrett’s esophagus and its malignant transition.” Nowicki-Osuch, Zhuang et al. RNAseq (BAM files) 12 Barrett's samples 12 normal oesophageal samples 11 normal gastric cardia samples

Dataset EGAD00001006882

Cell types of the human retina and its organoids at single-cell resolution. Cowan et al

Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers, and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas.

Dataset EGAD00001006350

Pan Cancer Investigation of Human Leukocyte Antigen Loss of Heterozygosity

Cancer cells can escape immune recognition through human leukocyte antigen (HLA) loss of heterozygosity (LOH) which results in deletion of HLA alleles, causing a reduction in presentation of tumor neoantigens. Despite its influence on immunotherapy response, few methods exist to detect HLA LOH, and accuracy of the approaches is poorly defined. Here, we present DASH (Deletion of Allele-Specific HLAs), a machine learning-based algorithm developed to detect HLA LOH from paired tumor-normal sequencing data. Using DASH to characterize HLA LOH in 610 patients across 15 cancer types, we found that 18% of patients had loss of heterozygosity in at least one HLA allele, suggesting the HLA LOH is a widespread, and potentially key immune resistance strategy in multiple cancers.

Study phs002783

The aim of this project is to identify, on 15 French Caucasian and 10 African-Caribbean men, through an integrative approach of DNA sequencing and transciptomic analyses, relevant genomic events that characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer.

Every year about 70,000 new cases of prostate cancer are diagnosed in France and 8,700 men died from this disease. But the incidence and the rate of mortality per 100,000 men in the French West Indies are respectively 1.5x and 2x upper than the rates observed in the metropolitan France. The aim of this project is to identify, on 15 French Caucasian and 10 African-Caribbean men, through an integrative approach of DNA sequencing and transciptomic analyses, relevant genomic events that characterize or allow targeting the various phenotypes of aggressiveness of early stages of prostate cancer.

Study EGAS00001002176

16 Year Life History and Genomic Evolution of an ER+ HER2- Breast Cancer

We reconstructed the genomic evolution through the sixteen year history of an ER+ HER2- breast cancer patient to investigate molecular mechanisms of disease relapse and treatment resistance after long term exposure to hormonal therapy. Genomic and transcriptomic profiling was performed on primary breast tumor (2002), initial recurrence (2012) and liver metastasis (2015) tumor samples. Cell free DNA analysis was performed at eleven timepoints (2015-2017).This phylogenetic reconstruction of the life history of a single patient's cancer as well as monitoring tumor progression through liquid biopsies with the detection of a resistant clone harboring a de-novo ESR1 E380Q mutation allowed for uncovering the molecular mechanisms leading to initial relapse, metastatic spread and treatment resistance.

Study EGAS00001004624

Deciphering the genomic, epigenomic and transcriptomic landscapes of pre-invasive lung cancer lesions to determine prognosis

Background: Lung carcinoma-in-situ (CIS) lesions are the pre-invasive precursor to lung squamous cell carcinoma. However, only half progress to invasive cancer in three years, while a third spontaneously regress. Whether modern molecular profiling techniques can identify those pre-invasive lesions that will subsequently progress and distinguish them from those that will regress is unknown. Methods: Progressive and regressive CIS lesions were laser-captured and their genome, epigenome and transcriptome interrogated. We analysed 83 progressive lesions, 41 regressive and 33 normal epithelial control samples. DNA methylation and gene expression profiles were further validated using publicly available lung cancer data. Results: Somatic mutation burden was higher in progressive lesions than regressive CIS lesions, across base substitutions, rearrangements, and copy number changes. Driver mutations were present in both progressive and regressive CIS lesions, but were more numerous in progressive cases. Progressive and regressive CIS lesions had distinct epigenomic and transcriptional profiles, with a strong chromosomal instability signature. Gene expression, methylation and copy number profiles can all predict accurately which CIS lesions will progress to lung cancer. Conclusion: Pre-invasive CIS lesions that will subsequently progress to invasive lung cancer can be distinguished from those that will regress using molecular profiling. Progression is associated with a strong chromosomal instability signature. These findings inform the development of novel therapeutic targets.

Dataset EGAD00001003883

A Pilot Study Using Next Generation Sequencing in Advanced Cancers: Feasibility and Challenges

In this study, we used NGS to identify somatic events in advanced stage cancer patients to demonstrate the feasibility for using this approach to improve patient treatment.

Study phs000657

Human Tumor Atlas Network (HTAN)

An NCI-funded Cancer Moonshot initiative to construct 3-dimensional atlases of the dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.

Study phs002371

Germline sequencing

Detection of SNV/indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants. Included in this EGA upload are the parents of the children in EGA uplodad EGAD00001008763.

Study EGAS00001006651

EGAD00000000054

NCI-H209 is an immortal cell line derived from a bone marrow metastasis of a patient with small cell lung cancer, taken before chemotherapy. The specimen showed histologically typical small cells with classic neuroendocrine features. NCI-BL209 is an EBV-transformed B-cell line derived from the same patient as the small cell lung cancer cell line, NCI-H209

Dataset EGAD00000000054

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

Prostate Cancer Whole Genome Validations

We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331

Dataset EGAD00001000621

Triple Negative Breast Cancer Whole Genome Validations

We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.

Dataset EGAD00001000662

Dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA

The dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA includes 602 bam files from next-generation sequencing on the Illumina HiSeq2500 or MiSeq. The samples analyzed include cancer cell lines as well as plasma and tissue specimens from healthy individuals and patients with cancer.

Dataset EGAD00001003601

Cancer Genomics of the Kidney

The aim of CAGEKID is to carry out comprehensive detection of DNA markers for conventional (clear cell) renal carcinoma. The project includes complete analysis of somatic and constitutional DNA variation, methylation patterns and expression in a large number of constitutional/tumor pairs. CAGEKID is a part of the International Cancer Genome Consortium, ICGC.

Dataset EGAD00001004018

Exome sequencing of a novel cervical cancer cell line

In this work, we establish and characterized a low-passage cervix cancer cell line from a Brazilian patient with squamous cell carcinoma. The dataset contains three samples from the same patient (blood, tumor tissue and the primary cell line). The technology used was exome sequencing and the file type available is fastq files.

Dataset EGAD00001004480

ICGC breast cancer sequencing project SNP6 data

Affymetrix SNP6.0 breast cancer genome sequencing data

Dataset EGAD00010000915

WES on tumor DNA and germline DNA in pediatric cancer

This dataset contains whole exome sequencing (WES) data (various enrichment methods) from tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on a Novaseq6000 or Hiseq2500 (Illumina).

Dataset EGAD00001007816

NSCCG_CRC_GWAS

Genotype data of 7,281 individuals with colorectal cancer from the National Study of Colorectal Cancer Genetics (NSCCG) study. Individuals genotyped on the Illumina OncoArray. Data provided in plink format and has not been quality controlled. Control samples used were obtained from the PRACTICAL and BCAC consortia, and are available through the respective Data Access Coordination Committees (http://practical.icr.ac.uk and http://bcac.ccge.medschl.cam.ac.uk/)

Dataset EGAD00010002184

Pre-neoadjuvant treatment biopsy RNAseq breast cancer dataset

This dataset contains RNAseq data of n=87 pre-treatment biopsies of triple negative and luminal- type breast cancer patients, all scheduled to receive neoadjuvant chemotherapy. Gene expression data is linked with treatment response and survival.

Dataset EGAD00001008433

Triple Negative BC WGS Dataset

We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

Dataset EGAD00001001335

Sequence of breast cancer bone metastases PDX before and after palbociclib treatment resistance

RNAseq sequencing of 10 breast cancer bone metastasis PDX. Samples were obtained from 5 PDX that acquired palbociclib resistance (palboR) and 5 from the parentale PDX (palboS).

Dataset EGAD00001009068

Differential methylation positions

This dataset includes an analyzed DMP file that provide the information about differential methylation positions based on Illumina Infinium MethylationEPIC BeadChip. All samples (5 lung cancer cases vs. 5 benign lung disease controls) were obtained from bronchial washings at the site of the lesion under bronchoscopy manipulation. Of the five lung cancer cases, 3 are adenocarcinoma and 2 are squamous carcinoma.

Dataset EGAD00001010147

47 urothelial cancer patients WES and 38 RNAseq

We performed a global mutational landscape analysis using tumor samples from the 47 urothelial cancer patients included in MATCH-R or MOSCATO studies, with advanced metastatic disease and WES available (RNAseq is included for 38 patient samples).

Dataset EGAD00001011063

Characterization of Cell Free Plasma Methyl-DNA From Xenografted Tumors to Guide the Selection of Diagnostic Markers for Early-Stage Cancers

Circulating cell-free methyl-DNA (mcfDNA) contains promising cancer markers but its low abundance and possibly diverse origin pose challenges toward the accurate diagnosis of early stage cancers. By whole-genome bisulfite sequencing (WGBS) of cell-free DNA (cfDNA) from about 0.5 mL plasma of mice xenografted with human tumors, we obtained and aligned the reads to the human genome, filtered out the mouse and carrier bacterial sequences, and confirmed the tumor origin of methyl-cfDNA (mctDNA) by methylation-sensitive restriction enzyme digestion prior to species-specific PCR. We estimated that human tumor-specific reads (ctDNA) or mctDNA comprised about 0.29 or 0.01%, respectively of the xenograft mouse cfDNA, and about 0.029 or 0.001% of the cfDNA of human early stage cancer patients. Similar WGBS of early stage (0-II, node- and metastasis-free) breast, lung or colorectal cancer samples identified hundreds of specific DMRs (differentially methylated regions) compared to healthy controls. Their association with tumourigenesis was supported by stage-dependent methylation, tumor suppressor or oncogene clusters, and genes also identified in the xenograft samples. Using 20 three-cancer-common and 17 colorectal cancer-specific DMRs in combination (top 0.0018% of the WGBS methylation clusters) was sufficient to distinguish the stage I colorectal cancers from breast and lung cancers and healthy controls. Our data thus confirmed the tumor origin of mctDNA by sequence specificity, and provide a selection threshold for authentic tumor mctDNA markers toward precise diagnosis of early stage cancers solely by top DMRs in combination. Biological Materials were provided by the Ontario Tumour Bank, which is funded by the Ontario Institute for Cancer Research Reference for citation: Ling Liu, Jinghua Feng, Julian Polimeni, Manli Zhang, Hai Nguyen, Urmi Das, Xu Zhang, Harminder Singh, Xiao-Jian Yao, Etienne Leygue, Sam K.P. Kung, and Xie J. Characterization of cell free plasma methyl-DNA from xenografted tumours to guide the selection of diagnostic markers for early-stage cancers. Frontiers in Oncology, 2021 Feb. 5. DOI: 10.3389/fonc.2021.615821.

Study EGAS00001006175

9338 results for "cancer rna-seq"

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