Search Results - EGA European Genome-Phenome Archive

H3Africa ACEGID H3Africa Array Genotype

SNP Genotyping for Lassa Fever cases and population controls from Nigeria and Sierra Leone using Illumina H3Africa array version 1

Dataset EGAD00010002510

Whole genome sequencing profiling of patient-derived organoids (PDO)

Whole genome sequencing profiling of 41 PDAC patient-derived organoids (PDO) - WGS unmapped reads, sequenced using NovaSeq 6000, 15x coverage 160 million reads per sample.

Dataset EGAD50000000280

N2M2 methylation array data

Methylation profiling of 228 samples, using the approach described in "Molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed glioblastoma without MGMT promoter hypermethylation (N2M2/NOA-20 phase I/IIa umbrella trial)"

Dataset EGAD00010002747

WES_dataset1

Fourteen MEITLs and one EATL previously had been sequenced using the SureSelectXT Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA).

Dataset EGAD50000001620

LBC1921 gvcfs

297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the gvcfs.

Dataset EGAD00001006416

Whole Exome Sequencing of gliomas

15 whole exome sequencing datasets from five patients. Data is provided as bam files. Libraries were generated using the SeqCap EZ Exome v3.0 kit and sequenced on an Illumina sequencer

Dataset EGAD00001003763

666PG SNVs

SNV calls generated using SomaticSniper in VCF format from the CPCGene 666PG study

Dataset EGAD00001006148

Whole genome sequencing in myasthenia gravis

This dataset contains whole genome sequencing data on 25 individuals with myasthenia gravis. The data was generated using Illumina sequencing technology and is presented as BAM files for each sample.

Dataset EGAD00001005262

666PG indels

Indel calls generated using Pindel in VCF format from the CPCGene 666PG study

Dataset EGAD00001006147

Macrophage response in term and preterm infants

The data set comprises 48 samples from term and preterm infants. Expression profiles were generated using different stimuli (O2 3%, 21%, 65%; LPS stimulation).

Dataset EGAD00001006885

Saliva microbiota in Finnish children

The saliva microbiota of 972 Finnish children, aged 9-14 years was characterized using the 16S rRNA (V3-V4) gene sequencing with Illumina Hiseq platform.

Dataset EGAD00001004145

666PG Somatic CNA calls

Filtered somatic CNA calls detected using Battenberg from the CPCGGene 666PG study

Dataset EGAD00001007699

WCDT Hi-C assays performed mCRPC biopsies - Part 2

13 paired FASTQ files from a Hi-C assay performed on mCRPC tumors. Sequencing was performed using 150nt paired reads generated by a Novaseq 6000 instrument.

Dataset EGAD00001009417

Microbial infections in Alzheimer’s patients

In the present study, we have examined fungal and bacterial infection in brain tissue from 10 AD patients and 16 control subjects by next-generation sequencing NGS using MiSeq sequencing platform (Illumina).

Dataset EGAD00001003886

HIV positive individuals (first batch)

Contains 30x coverage whole genome sequence data from 40 HIV+ South Africans. Samples sequenced using Illumina HiSeq. BAM files have been uploaded. Sequenced at Edinburgh Genomics.

Dataset EGAD00001007589

Copy number profiling using PlasmaSeq

In order to establish copy number profiles from the various samples we prepared libraries and subjected them to whole-genome sequencing at a shallow sequencing depth (0.1x)

Dataset EGAD00001000761

Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing

The dataset comprises of muscle samples from three patients with mitochondrial disease: Patient 1, age9; Patient 2, age16; and Patient 3, age 58.

Dataset EGAD00001006079

PBMCs of HCC Patients treated with anti-PD1 ICB

10 samples (one baseline, 9 on-treatment). Fastq files containing 5'GEx data, prepared using 10x Genomics pipeline, sequenced on Illumina HiSeq4000.

Dataset EGAD00001006645

Copy Number Variation using Affymetrix Optima Array

Diagnostic yield of affymetrix optima microarray in patients with non-syndromic autism spectrum disorders in India.

Study EGAS00001006439

"Single nucleotide variant detection in multiple foci of three prostate cancer tumors"

Dataset EGAD00001000035

"Copy number variant detection in multiple foci of three prostate cancer tumors"

Dataset EGAD00001000036

WGS data of serially passaged TIC-enriched spheres of colorectal cancer

Dataset EGAD00001006265

Single cell sequencing of ovarian cancer

Single cell sequencing of 12 ovarian cancer biopsies from 7 patients.

Dataset EGAD00001006898

Whole_genome_sequencing_of_rhabdomyosarcoma_tumouroids

The aim of this study is to investigate the genomic landscape of human cancer.

Study EGAS00001008270

Whole_Genome_sequencing_of_rhabdomyosarcoma_tumour_tissue

The aim of this study is to investigate the genomic landscape of human cancer.

Study EGAS00001008274

Investigation of a method for generating cells for regenerative medicine using comprehensive nucleic acid analysis of iPS cell-derived cardiomyocytes.

Regenerative medicine for heart failure is expected to restore cardiac function by using human iPS cells (hiPSCs). In our laboratory, it was shown that transplantation of cardiomyocytes (CMs) derived from hiPSCs into a pig model of myocardial infarction improves the disease condition. However, the instability of differentiation efficiency and tumorigenicity after transplantation are still issues to be resolved. We attempt to identify and analyze the genes and DNA methylation associated with the induction of differentiation of hiPSCs into CMs with the aim of achieving stable induction of CMs differentiation. Furthermore, we aim to analyze genes involved in tumorigenesis in CMs, and to develop a predictive marker for tumorigenesis to ensure the safety of cells before transplantation.

Study JGAS000665

Genetics and therapeutic responses to TIL therapy of pancreatic cancer PDX models

Pancreatic cancer is the 7th leading cause of cancer-related deaths worldwide. Checkpoint immunotherapy has not yet showed encouraging results in pancreatic cancer possibly owing to a poor immunogenicity and/or an immune suppressive microenvironment. The aim of this study was to develop patient-derived xenografts (PDX) models and to assess if autologous tumor-infiltrating lymphocytes (TILs) would have anti-tumoral activity in pancreatic cancer. Tumor biopsies from 29 patients were subcutaneously transplanted into NOG mice. Tumor growths were confirmed in 11 out of 29 transplantations. The PDX tumors histologically resembled their original biopsies, but since stromal cells in the PDX model tumors were from mouse, their gene expression differed from the original biopsies. Immune checkpoint ligands other than PD-L1 were expressed in pancreatic cancers but PD-L1 was rarely expressed. One of the three tumors that did express PD-L1 was an adenosquamous cancer and another had a mismatch repair deficiency. TILs were expanded from six tumors and were injected into NOG or human interleukin-2 transgenic-NOG (hIL2-NOG) mice carrying PDX tumors. Regression of tumors could be verified in hIL2-NOG mice in 3 of the 6 PDX models treated with autologous TILs, including the adenosquamous PDX model. In conclusion, PDX models of pancreatic cancer can be used to learn more about tumor characteristics and biomarkers, and to evaluate responses to ACT and combination therapies. The major benefit of the model is that modifications of T cells can be tested in an autologous humanized mouse model to gain preclinical data to support the initiation of a clinical trial.

Study EGAS00001005596

Frequent post-treatment monitoring of colorectal cancer using individualized ctDNA validated by multi-regional molecular profiling

Purpose: Circulating tumor DNA (ctDNA) analysis has been proposed as an approach for prediction of post-treatment patient outcomes. However, whether a single platform will provide optimal information in all patients or alternatively a patient-specific monitoring approach based on assessment of mutations in the primary tumor from that patient remains an urgent question. Experimental Design: We conducted multiregional sequencing of 42 specimens of 14 colorectal tumors (Stage III and more) from 12 patients, including two double cancer cases, to identify the full spectrum of mutational heterogeneity and identify aberrations that could be used to develop personalized ctDNA assays. Results: ?Founder? mutations that occur in all regions of the sample were identified in 12/14 (85.7%) tumors. Subsequent phylogenetic analysis of each tumor showed that 12/14 tumors (85.7%) carried at least one ?truncal? mutation. Most founder and truncal mutations exhibited higher variant allele frequency (VAF) than ?non-founder? and ?branch? mutations. In addition, both founder and truncal mutations were more likely to be detected as ctDNA than non-founder and branch mutations. Synchronized ctDNA dynamics of multiple mutations suggested those mutations from the same clonal origin. For 10/12 patients (83.3%) with nearly 1,000 days of post-operative observation, the validity of frequent personalized ctDNA monitoring was confirmed in terms of early relapse prediction, treatment efficacy, and non-relapse corroboration. Conclusions: Personalized ctDNA monitoring based on aberrations with a high VAF in the primary tumor site should be explored in larger prospective clinical trials to determine the full clinical validity.

Study JGAS000243

Analysis of mutational and proteomic heterogeneity of gastric cancer to monitor post-treatment tumor burden using circulating tumor DNA

It remains unclear whether complete spectrum of tumor heterogeneity is reflected in circulating tumor DNA (ctDNA). Here, we performed multi-regional target sequencing of primary tumors from 10 patients who underwent surgical resection for gastric cancer. A total of 126 non-synonymous mutations were identified from 30 samples from 10 tumors. Of these, 16 (12.7%) were likely mutations that occurred early in tumor development (i.e., present in all three regions) and were designated founder mutations. Among those validated with highly sensitive digital PCR (dPCR), 93% of non-founder mutations were found in all three regions. Variant allele frequencies (VAFs) of founder mutations were significantly higher than those of non-founder mutations. Phylogenetic analysis demonstrated that five of eight tumors (62.5%, excluding two hypermutator) had at least one identifiable truncal/founder mutation. These findings led us to prioritize founder mutations for ctDNA detection with individually-designed primer/probe sets for dPCR. Marked proteomic diversity was present across the tumor regions both within and between patients independent of mutational status. In preoperative plasma, the average ctDNA VAF of founder mutations was significantly higher than that of non-founder mutations (p = 0.039). Our present data demonstrated that high VAF mutations in the tumor likely represent founder or truncal mutations. However, mutation patterns alone appear insufficient to predict protein heterogeneity. These results suggest that, in practice, mutations having high VAF identified without multi-regional sequencing may be useful for ctDNA monitoring but are inadequate to fully predict proteomic heterogeneity of the tumor.

Study JGAS000231

Treatment stratification and biomarker validation using patient-derived head and neck cancer organoids

Background Organoids are three-dimensional structures that can be grown from patient-derived material including carcinomas. These in vitro models can be cryopreserved to generate “living” biobanks that reflect patient heterogeneity. Head and neck cancer (HNC) is a collective term used for tumors arising in the head and neck area, including squamous cell carcinomas (HNSCC) and adenocarcinoma of the salivary gland. Methods to culture patient-derived HNC organoids have previously been described. Methods Organoids were derived from resection or biopsy material of patients included between 2016 and 2022. Organoids were characterised with immunohistochemistry and whole exome sequencing (WES) and exposed to chemo-, radio- and targeted-therapies. CRISPR/Cas9-based gene editing was applied to validate proposed biomarkers. Results We have extended our previously published organoid biobank to a total of 110 organoid models, some of which were characterised by histology and WES. Organoids recapitulated both single nucleotide variants and copy number alterations as found in patient HNSCC samples. Organoid and patient response to radiotherapy (RT; primary (n=6) and adjuvant (n=15)) could be compared in 21 HNC cases. In the adjuvant RT group, organoids derived from patients that relapsed were more resistant to RT in vitro, showing potential for guiding treatment options in this subset of patients. Conclusion Taken together, these results indicate illustrate the potential of organoids as a diagnostic tool in personalised medicine for HNC and indicate the potential of this technology for biomarker discovery and validation within the context of relevant patient heterogeneity.

Study EGAS00001007076

Hereditary Cancer Predisposition Syndromes and Uveal Melanoma

Uveal melanoma (UM) is a subtype of melanoma characterized by the strong contribution of genetic rather than environmental factors in the pathogenesis of the disease, making it an ideal model disease to study the genetic basis of cancer. The long-term goal of our laboratory is to determine the genes and mechanisms responsible for hereditary cancer predisposition associated with UM. BAP1 has been identified as a candidate gene with definitive association with predisposition to UM. However, pathogenic variants in BAP1 are detected in only a small subset of UM patients even those with strong personal and family history of cancer suggesting the existence of other candidate genes. The goal of this project is to identify novel candidate genes contributing to hereditary predisposition to UM in patients with no detectable germline pathogenic variant in BAP1.

Study phs001943

Evolutionary Origins of Recurrent Pancreatic Cancer

Surgery is the only curative option for patients with Stage I/II pancreatic cancer, nonetheless most patients will recur after surgery and die of their disease. To identify novel opportunities for management of recurrent pancreatic cancer we performed whole exome or targeted sequencing of 10 resected primary cancers and their matched intrapancreatic recurrences or distant metastases. We identified that recurrent disease develops from a monophyletic or polyphyletic origin, and this distinction has potential clinical relevance. In all patients, treatment induced genetic bottlenecks led to a modified genetic landscape and subclonal heterogeneity for driver gene alterations in part due to intermetastatic seeding. In one patient what was believed to be recurrent disease was an independent (second) primary tumor. These findings strongly advocate for routine post-treatment sampling in the management of recurrent pancreatic cancer.

Study EGAS00001004097

WGS of liver cancer in the Japanese population

Hepatocellular carcinoma (HCC) is the third leading cancer-related cause of death and the seventh most common form of cancer worldwide, with an estimate of more than 700,000 new cases each year. The most established risk factors of HCC are chronic HBV and HCV infection. HBV infection is responsible for over 50% of the worldwide attributable risk of HCC, especially in East Asia and Africa, while in Japan and several Western countries HCV infection is the most common risk factor for HCC. To gain insights into the molecular alterations of virus-associated HCC, we performed whole genome sequencing (WGS) of 321 HCC tumors from 159 patients. This work was performed as a part of the ICGC (International Cancer Genome Consortium) project.

Study EGAS00001000678

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBM), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identify the functional consequence of these mutations in GBM to be recruitment of the multimeric GABP transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native ETS motifs critically cooperate with these mutations to activate TERT, likely by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.

Study EGAS00001001242

PanCuRx Translational Research Initiative

The goal of the PanCuRx TRI is to seek solutions to the high fatality rate of pancreatic adenocarcinoma (PDAC), the most common type of pancreatic cancer, by generating new knowledge about the genetics and biology of the disease, mechanisms of how tumours grow and tailored treatment options. PDAC is the fourth leading cause of cancer death in Canada and is expected to become the second-leading cause of cancer death within the next decade. The current five-year survival rate of eight per cent is the lowest of all epithelial cancers. There are major clinical challenges to treating the disease, including the fact that PDAC spreads to other parts of the body early so surgical removal of the tumour benefits few patients, that PDAC has proven relatively resistant to systemic therapies such as chemotherapy and that there has been limited benefit from the use of newer molecular targeted agents. The PanCuRx team has created the world’s first resource of tumour-purified PDAC whole genomes; more than 500 PDAC samples, with combined clinical annotation, have been successfully sequenced and analyzed at the Ontario Institute for Cancer research in Toronto. The resulting clinical genomic resource created from this data has led to multiple new findings that have established a framework to better understand PDAC biology and lays the foundation for new genomic approaches to better understanding the disease. The team also launched a clinical trial called COMPASS (Comprehensive Molecular Characterization of Advanced Ductal Pancreas Adenocarcinoma for Better Treatment Selection: A Prospective Study), which is recruiting patients with advanced PDAC (both locally advanced and metastatic) at The Princess Margaret Cancer Centre (PM) in Toronto. The study uses the molecular results from individual patient tumours to guide selection of better second line treatment on a case-by-case basis. The primary objective of the initial study was to assess the feasibility of collecting tumour materials from patients with advanced PDAC and delivering results within 56 days of biopsy. Having achieved this objective, the trial has expanded to other cancer centres across Canada. Pancreatic cancer is one of the most deadly forms of cancer and outcomes have not improved in four decades. The PanCuRx initiative is providing a better understanding of the disease and actively applying new knowledge to cancer patients through clinical trials. This knowledge will help to improve quality of life and prolong survival for pancreatic cancer patients worldwide.

Study EGAS00001002543

Scalable ultra-high-throughput multiplexed single-cell chromatin and RNA profiling reveals gene regulatory dynamics during stimulation time courses and CRISPR perturbation screens

Data for 1) hiPSC-derived macrophages across a polarization time course from the naive M0-state to the M1- and M2-states, 2) Primary T-cells differentiated to helper subtypes, and 3) spontaneous differentiation of hiPSCs upon perturbation of GATA2, NR4A2 or SOX17

Dac EGAC50000000485

Waldenström Macroglobulinemia Single-Cell Data Access Committee

This Data Access Committee (DAC) is responsible for reviewing and approving access requests for controlled-access human single-cell sequencing data, including single-cell RNA sequencing and immune receptor profiling, generated from patients with Waldenström macroglobulinemia. The DAC ensures that all data access requests comply with the informed consent provided by study participants and are consistent with applicable ethical and regulatory requirements.

Dac EGAC50000000863

20190219_EGA_MelanomaOnTreatment

Illumina platform sequencing data for matched tumour-normal DNA samples from 77 melanoma patients participating in a study investigating response to immunotherapy. Selected cases also have RNA sequencing of the tumour.

Dataset EGAD00001004869

Single cell study of infant leukemias

We have performed single cell RNA-sequencing for infant and childhood B-cell acute lymphoblastic leukemias as well as infant acute myeloid leukemias at diagnosis. The sequencing was performed with 10X Chromium single cell 3’ and 5’ chemistry.

Dataset EGAD00001007853

RNA-sequencing data from vitamin C experiment

Fasq-files from 3 unaffected TET2 mutation carriers, 2 mutation carriers diagnosed with lymphoma and 3 family members without TET2 mutation. Time series data collected from 0, 6 and 12 months after daily dose of 1g vitamin C.

Dataset EGAD00001010009

DIPG MEK inhibition RNASeq

RNA sequencing of Diffuse intrinsic pontine gliomas, primary patient derived DIPG cell cultures and isogenic trametinib resistant clones

Dataset EGAD00001008212

Single-cell short-read transcriptomes from CH, MDS and AML patients with splicing factor mutations

Single-cell RNA sequencing from CH (n = 2), MDS (n = 6, MDS02 in 2 replicates) and AML (n = 1, in 2 replicates) samples with mutations in splicing factors (SF3B1 - n = 8, U2AF1 n = 1). cDNA from 10x Genomics 3' V3.

Dataset EGAD00001011283

Endometrial RNASeq of Patients with MRKH Syndrome and Healthy Controls

Raw FastQ Files of 69 samples of endometrial tissue from uterus (rudiments) of patients diagnosed with MRKH Type 1/2 or healthy controls. Each sample consists of 2 lanes paired-end RNA sequencing data.

Dataset EGAD00001006345

HPS1 patient monocyte-derived macrophage and control macrophage RNAseq with and without infection

4 HPS1 patient monocyte-derived macrophages and 4 controls were RNA sequenced at baseline and after Salmonella Typhimurium infection. We used paired end sequencing on an Illumina HiSeq 4000. Each sample was run on 3 lanes for sequencing depth, which we combined for our analysis.

Dataset EGAD00001006978

PARADIGM: Combined ctDNA and serum PSA for dynamic monitoring of metastatic prostate cancer starting first-line treatment

The prognosis of newly-diagnosed metastatic prostate cancer is highly variable. The PARADIGM prospective cohort study evaluated predictors of survival in blood collected at the start of each of the first six treatment cycles from 114 high-volume metastatic patients starting androgen deprivation therapy combined with docetaxel or an androgen receptor pathway inhibitor.

Study EGAS50000001357

Cancer_Genome_Libraries_Tests

Testing library production.Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to paired end sequencing on the llumina plateforms. 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.

Study EGAS00001000208

High intensity sequencing of plasma cfDNA and WBC gDNA

We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white-blood cell (WBC) DNA covering a large genomic region (508 genes, 2Mb, 60,000x raw-depth) in a prospective study of 124 metastatic cancer patients, with contemporaneous matched metastatic tumor tissue biopsies, and age-matched 47 non-cancer controls.

Study EGAS00001003755

14983 results for "cancer studies using rna-seq"

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