22938 results for "ega"

in 41.52 milliseconds.

• RNAseq of medulloblastoma data (MB_COMICS cohort)

  Medulloblastoma (MB) is the most common malignant brain tumor in children. It is a neuroectodermal tumor located in the cerebellum. International consensus recognizes four distinct subgroups of MBs including Wingless (WNT), Sonic Hedgehog (SHH), Group 3 (G3), and Group 4 (G4) with distinct molecular characteristics, prognoses, and mortality rates in patients. Here, we have compiled and evaluated a large international MB cohort for which we generated transcriptomic data (RNAseq) for 208 primary MB patient samples.

  Study EGAS50000000410

• Immune control of functional memory CD8 T cells in normal-appearing vitiligo skin

  This study aimed to characterize immune cell states in nonlesional (NL) and perilesional (PL) skin of patients with vitiligo using single-cell RNA sequencing. Shared CD8⁺ T cell clusters were detected in both regions, with PL-derived cells enriched for immune activation pathways and NL skin showed stronger infiltration of regulatory T cells. These findings reveal functional T cell heterogeneity in vitiligo and highlight regulatory mechanisms that may limit depigmentation in NL skin.

  Study EGAS50000001317

• Genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers

  This data includes targeting sequencing of the immunopeptidome from 94 samples, usually individual laser microdissected cancer glands, from 11 cases of colorectal cancer. The data were used to test for evidence of immunoediting (antigen depletion) in colorectal cancers. The full data description is provided in the original manuscript https://pmc.ncbi.nlm.nih.gov/articles/PMC10888923/. The 11 colorectal cancers had been previously multiomic profiled with data described in the parts of this disposition.

  Study EGAS50000001154

• The origin of post-transplant clonal hematopoiesis can be traced to prenatal development.

  Clonal hematopoiesis (CH), a prevalent and premalignant state in the elderly, can occur in young individuals under selective pressures such as hematopoietic cell transplantation (HCT). However, the origin of CH and mutational processes underlying CH driver mutations in young individuals remain unclear. Here, we used genome-wide somatic mutation profiles to retrospectively trace the origin of DNMT3A-mutant CH in three individuals, 14-41 years after childhood HCT.

  Study EGAS50000000919

• Hashed data from three immortalized fibroblastic reticular cells (iFRCs)

  Co-culture experiments of primary lymphoid and DLBCL-derived immortalized FRCs (iFRC) followed by scRNA-seq. iFRCs as well as lymphocytes from DLBCL samples (n=3) were harvested after 24h of incubation and different experimental conditions were multiplexed using in-house cell multiplexing oligonucleotides (CMOs; full list of barcodes provided in Table S9). Cells were incubated with CMOs at a final concentration of 1.8 μM for 20 minutes on ice, followed by four washes with PBS (centrifugation at 400 × g for 3 minutes at 4 °C). Single-cell RNA sequencing (scRNA-seq) and multiplexing libraries were prepared using the 10x Genomics Single Cell 3′ Gene Expression v4 assay, according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 platform using paired-end 100 bp reads on an S4 flow cell.

  Dataset EGAD50000001779

• Deciphering the aggressive nature of morphoeic basal cell carcinoma

  Morphoeic basal cell carcinoma (mBCC) has a high risk of local recurrence compared to the more indolent nodular subtype reflected by a different set of driver mutations including FLNB and HECTD4. Surrounding mBCC stroma is abnormal, containing mutations such as EPHA3. Hedgehog pathway over-expression is seen in both the tumour and stroma of morphoeic tissue with the latter potentially being partly responsible for its aggressive nature and risk of recurrence.

  Study EGAS00001001915

• Spatial profiling of hepatocellular carcinoma identifies distinct tumor and immune micro-ecosystems related to patient outcomes

  Hepatocellular carcinoma (HCC) shows substantial intra-tumor heterogeneity that remains poorly understood. Using spatial transcriptomics, we identified 13 recurrent tumor and stromal micro-ecosystems (MES) and mapped their spatial organization and biological functions. One immune-enriched MES containing Kupffer cell–like macrophages was strongly associated with improved disease-free survival and response to atezolizumab–bevacizumab. Our findings demonstrate the value of spatial profiling for revealing rare but clinically meaningful cellular communities.

  Study EGAS50000001474

• Bone morphogenetic protein-9 controls pulmonary vascular growth and remodeling

  Human PMECs from 10 donor lungs were isolated, cultured (passages 3 to 4), synchronized by serum starvation (0.3% FCS), and stimulated with 10 ng/mL BMP-9 for 4 h. Single-cell profiling was performed using the 10X Genomics Chromium RNA 3' V3.1 kit. Five experimental groups were analyzed using cell hashing and sequenced on an Illumina NextSeq500. Data were processed with Cell Ranger and Seurat for differential gene expression and functional enrichment analysis.

  Study EGAS50000001026

• Sarcopenia related to Head and Neck squamous cell carcinomas: transcriptome modifications of muscle cells induced by distant malignant cells

  The biological mechanisms of sarcopenia are still very poorly understood, particularly in the case of Head and Neck Squamous Cell Carcinomas (HNSCC). However, there is good reason to believe that diffusible factors originating from tumor cells exert a distant deleterious effect on muscle cells. To test this hypothesis we implemented a dual approach based both on experiments carried out in vitro and on the study of muscle fragments from patients.

  Study EGAS50000000669

• PTEN homozygous deletion is a negative prognostic factor in Tumor Treating Fields-treated glioblastoma, IDH wildtype patients

  This study investigates genomic determinants of outcome in glioblastoma, IDH-wildtype patients treated with Tumor Treating Fields (TTFields) in addition to standard radiochemotherapy. Tumor tissue from primary glioblastoma at initial diagnosis was profiled using the Illumina TruSight Oncology 500 (TSO500) targeted sequencing panel to characterise somatic alterations. The overarching goal is to provide exploration of genomic determinants of survival and treatment response in TTFields-treated glioblastoma, IDH-wildtype.

  Study EGAS50000001469

• Broad utility of ultrasensitive analysis of ctDNA dynamics across solid tumors treated with immunotherapy

  Plasma ctDNA sequencing data from samples collected from a pan-cancer cohort of patients with advanced-stage disease treated with IO therapies. This study highlights the broader applicability of ultrasensitive ctDNA as a biomarker across cancer types and immunotherapy modalities. Here, we applied a whole-genome, tumor-informed approach to study ctDNA in 202 advanced-stage cancer patients treated at VHIO. This study captures the plasma sequencing data from the project.

  Study EGAS50000001271

• ecDNA copy number heterogeneity

  Neuroblastoma exhibits significant inter- and intra-tumour genetic heterogeneity and varying clinical outcomes. Here, we used DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. We reveal extensive intercellular ecDNA copy number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells.

  Study EGAS50000000509

• RNaseq of mantle cell lymphoma patient samples

  This study presents bulk RNA sequencing data from 78 clinical mantle cell lymphoma (MCL) samples. Following rigorous quality control and batch effect correction to account for sample type and redundancy, 62 samples from 59 patients were included in the final analysis. The transcriptomic profiles capture the molecular diversity across both solid and liquid tumor contexts and support investigations into the phenotypic plasticity and metabolic states of drug-tolerant persister (DTP) cells.

  Study EGAS50000001086

• Circulating Tumor DNA Analysis Profiles of Repotrectinib in NTRK fusion–positive advanced solid tumors: a phase 1/2 trial

  The dataset contains circulating tumor DNA (ctDNA) profiles from frozen plasma samples of 593 patients from the TRIDENT-1 clinical trial. Plasma was processed with centrifugation and automated liquid handling systems, and cell-free DNA was extracted using the Qiagen QIAsymphony platform. ctDNA libraries were constructed with the Guardant360 2.11 assay, which used targeted, hybridization-based capture and barcoding of cfDNA fragments for digital analysis, followed by high-throughput sequencing on the Illumina NextSeq 550 instrument. Sequencing data were processed and interpreted using the Bioinformatics Pipeline (BIP v3.5.2 or later) for variant calling and quantification and managed within LabVantage LIMS (v3.7 or later) to support sample tracking and workflow integration. Aligned read files are provided in bam and bai formats.

  Dataset EGAD50000002249

• IMMUcan Lung NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001558

• Single cell RNA and ATAC sequencing data from GBM patients

  Glioblastoma cells infiltrate and incorporate into the normal brain parenchyma. We conduct unbiased multimodal single-cell and spatial sequencing to capture GBM cells and the surrounding tumor microenvironment using a regional sampling strategy. For each patient, we profile the peritumoral region, tumor edge, and tumor core, providing a comprehensive characterization of the transcriptional and epigenetic landscape of GBM spatial heterogeneity, with a specific focus on infiltrative cells.

  Study EGAS50000000547

• Bulk RNA-seq paired fastq files from i3Ns harbouring a SNCA A53T mutation, with or without RSL3 treatment

  FASTQ files from bulk RNA sequencing of a iPSC-derived rapid neuronal model (i3Ns) harbouring the SNCA A53T mutation in a WTC11 background as a model of synucleinopathy, with or without treatment of 300nM RSL3 for 6 hours. Libraries were prepared using the Watchmaker rRNA and globin depletion kit and sequenced on a NovaSeq X with an average depth of ~27 million paired-end reads with a fragment length of 100 base pairs, per sample. 19 samples are included in this dataset, each with two paired fastq files (R1 and R2). The dataset includes control neurons (WT: dcas9 parental line and C4 CRISPR control) and A53T clones (B7, H8 and L8) across two neuronal inductions (ind1 vs ind2), with or without treatment of RSL3 (UT vs. RSL3).

  Dataset EGAD50000002209

• Whole Genome Sequencing from patients with multiple myeloma treated with BCL2 inhibitor based treatment

  Samples was collected at the Mayo Clinic. MM tumor samples were enriched using the StemCell EasySep Human CD138 positive selection kit II (StemCell, Cambridge, MA). DNA from CD138+ MM cell (tumor) or peripheral blood samples (germline control) at Mayo Clinic (Rochester or Arizona) underwent WGS. For samples collected at Mayo Clinic Rochester, library preparation was completed using the NEB Ultra II (New England Biolabs, Ipswich, MA) and the Nextera Flex systems (Illumina, San Diego, CA) and sequenced at the Mayo Clinic Genome Analysis Core with an approximate depth of 30X for tumor samples and 60X for the germline control. For samples collected at Mayo Clinic Arizona, Novogene was used for WGS following random shearing of the DNA, end-repairs, A-tailed and ligated with Illumina adapters. Sequencing was performed on the Illumina Novaseq 6000 sequencer Reference Genome: GRCh38.

  Dataset EGAD50000002132

• RNA sequencing of untreated head and neck cancer patient-derived xenografts (PDXs) and matched patient tumor tissue.

  RNA sequencing was performed on untreated patient tumor tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC). The aim of this analysis was to characterize the transcriptional landscape of the tumors in the in vivo setting. 117 total samples were sequenced with paired reads on 10 lanes from different flowcells. They were loaded as 2400 separate files to maintain the data as it was received from BGI - each sample is therefore composed of 5 separate EGAN with 4 files each, adding a 0.1 - .. - 0.5 to each BioSample ID to generate sample aliases. All R1 (and R2, separately) files referring to a BioSample ID should be concatenated to obtain fastq files corresponding to single patients or PDXs.

  Dataset EGAD50000002278

• Flexible and rapid validation of structural variants using adaptive sampling

  The goal of the study is to confirm and further characterize structural variants and complex genomic rearrangements using adaptive sampling with Oxford Nanopore Sequencing. Individuals with known structural variants were included in the study and the known rearrangement regions were targeted in the sequencing experiments. In addition to long-read coverage over the targeted regions (around 25X coverage), the rest of the genome is covered by short off-target reads (around 5X coverage).

  Study EGAS50000001279

• Rare Germline Variants in CDKN2A-Negative Children and Adolescents with Cutaneous Melanoma

  Cutaneous melanoma is a complex disease influenced by both environmental and genetic factors. Inherited susceptibility plays a significant role, involving a combination of high-, intermediate-, and low-penetrance genes. Melanoma in children and adolescents has been speculated to have a stronger genetic component due to the early onset. This study investigates germline variants in early-onset melanoma through exome sequencing of 154 patients in Australia diagnosed with cutaneous melanoma before the age of 20.

  Study EGAS50000001311

• Transcriptome analysis of a novel human iPSC-derived 3D cortical tissue model - WT, APP KI, Abeta-treated, Abeta/Aducanumab-treated

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model. Samples include distinct conditions (each as biological duplicates): - wild-type cells from cultures after 1 month (WT_1mo, cell lines: A18, KOLF) and 3 months (WT_3mo, cell lines: SA2, KOLF, A18) of culturing - knock-in cells from cultures carrying three familial AD mutations in the APP gene (Swedish, Iberian, Arctic; introduced by CRISPR/Cas9-mediated knock-in) after 3 months of culturing (KI_3mo, cell lines: SA2, A18) - subset of WT 1 month-old samples were exposed to 500nM synthetic Abeta42 for 2 consecutive feeds, and a subset of these subsequently treated with 1µg/ml Aducanumab antibody for 14 days

  Dataset EGAD50000002031

• EstMB cohort participants sequenced with MGISEQ-2000 platform

  Participants collected a fresh stool sample immediately after defecation using a sterile Pasteur pipette and placed it in a 15 mL conical polypropylene tube. They were instructed to collect the sample as close as possible to their study center visit. Samples were transported and stored at −80 °C until DNA extraction. Microbial DNA was extracted from 200 mg of stool using a QIAamp DNA Stool Mini Kit (Qiagen), following manufacturer's instructions, after all samples were collected. DNA was quantified using a Qubit 2.0 Fluorometer with a dsDNA Assay Kit (Thermo Fisher Scientific). Library preparation and circularization of equimolarly pooled libraries were done with MGIEasy FS DNA Library Prep Set (MGI Tech Co, Ltd, Shenzhen, China) according to the standard protocol. The sequencing was performed with MGISEQ-2000 High-throughput Sequencing Set (FCL PE150) according to the manufacturer’s instructions (MGI Tech, Shenzhen, China)

  Dataset EGAD50000002213

• Whole-exome sequencing (WES) analysis of untreated head and neck cancer patient-derived xenografts (PDXs) matched patient tumor tissue and normal mucosa tissue.

  WES analysis was performed on untreated patient tumor/normal mucosa tissue and matched patient-derived xenograft (PDX) models of primary head and neck squamous cell carcinoma (HNSCC) to investigate the preservation of tumor-specific genomic alterations in the in vivo context. 183 total samples were sequenced with paired reads on 8-10 lanes from different flowcells. They were loaded as 3538 separate files to maintain the data as it was received from BGI - each sample is therefore composed of 5 separate EGAN with 2-4 files each, adding a 0.1 - .. - 0.5 to each BioSample ID to generate sample aliases. All R1 (and R2, separately) files referring to a BioSample ID should be concatenated to obtain fastq files corresponding to single patients or PDXs.

  Dataset EGAD50000002325

• Effect of inflammation on human hematopoietic stem cells in a xenograft model

  Transcriptional heterogeneity in cord blood HSCs was investigated by 10X single-cell Multiome (RNA+ATAC). To investigate the effect of inflammatory stress on human HSC, 10X single-cell Multiome profiling of cells from xenografted mice recovered from repeated inflammatory challenge was performed. To investigate transmission of inflammatory stress-related molecular programs from HSC to their progeny, 10X single-cell RNA sequencing was performed on committed progenitor and myeloid cells from the same mice.

  Study EGAS50000001624

• Policy Documentation

  Policy Documentation The following policy documentation is required to be prepared and submitted to the EGA, together with your data files and associated metadata. Data Access Agreement (DAA) The Data Access Agreement is a contract made between Data User and Data Access Committee. The agreement should be drafted by the DAC and includes, but is not limited to, details of data use, publication embargoes and storage. Completion of a DAA by the applicant/s should form part of the application process to the DAC. NOTICE The data access agreement template below is provided for guidance only and should be adapted as you see fit to suit your own purpose. In the interest of promoting data sharing, we suggest that if an agreement cannot be met around clause 19 in this example that both parties should agree to remain silent, and that the clause should be removed from the agreement. Example DAA template Alternate (harmonised) DAA template

  Documentation access/data-access-committee/policy-documentation

• Mutational_Signatures_of_relapse_in_rectal_cancer_FFPE_samples_in_the_CR07_clinical_trial

  The CRO7 clinical trial recruited patients with clinically operable rectal adenocarcinoma. Patients were randomized to either pre-operative short course surgery followed by chemo-radiotherapy only in those patients at high risk of local relapse. Patients in both arms the received standard %-FU based adjuvant chemotherapy as per local policy. We intend to use FFPE derived DNA from the primary tumours to identify patterns of mutations or copy number alterations that are predictive of local or distant relapse.

  Study EGAS00001000651

• Comprehensive miRNA Sequence Analysis Reveals Survival Differences in Diffuse Large B-cell Lymphoma Patients

  Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease, with 30-40% of patients failing to achieve complete responses to standard therapy. miRNAs are RNA molecules that attenuate expression of their mRNA targets. To characterize the DLBCL miRNome, we sequenced miRNAs from 92 DLBCL and 15 benign centroblast fresh frozen samples and from 140 DLBCL formalin-fixed, paraffin-embedded tissue (FFPET) samples for validation.

  Study EGAS00001001025

• Egypt_Genome_Project___low_coverage_whole_genome_sequencing

  All humans outside Africa are descendants of the same single exit, usually dated at 50-70 thousand years ago. However, the route taken out of Africa is still debated. The two main candidates are a northern route via Egypt and the Levant, or a southern route via Ethiopia and the Arabian Peninsula. We are generating genetic data to evaluate these two possibilities. In this study we propose to generate low-coverage sequencing data for 100 Egyptian samples.

  Study EGAS00001000480

• Leiden_melanomafamilies

  Around 10% of patients who present in melanoma clinics have a first degree relative with a previous diagnosis of melanoma. While around 3% have three or more relatives who have been diagnosed with the disease. In this project we will whole genome sequence patients from large Dutch familial melanoma pedigrees to identify mutations in genes that drive melanomagenesis. The identification of these genes will facilitate the management of familial melanoma patients and their families.

  Study EGAS00001000627

• Exome_sequencing_of_a_cohort_of_Rett_syndromelike_patients

  The aim of the project is the definition of the molecular defect in a cohort of Rett-like patients negative for mutations in known disease genes. To this aim, a number of unrelated trios (patients plus parents) will be analysed by exome sequencing. 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/

  Study EGAS00001002059

• The_genomic_architecture_of_mesothelioma_

  The genome-wide landscape of somatically acquired mutations in mesothelioma has not been deeply characterised to date, but advances in DNA sequencing technology now allow this to be addressed comprehensively. Harnessing massively parallel DNA sequencing platforms, we will identify somatically acquired point mutations in all coding regions of the genome from patients with mesothelioma. In addition, using paired-end sequencing, we will map copy number changes and genomic rearrangements from the same patients.

  Study EGAS00001000353

• Susceptibility_genes_for_the_development_of_SLE_during_treatment_of_IBD

  A potential and very serious side effect of treating IBD with antiTNFa therapies (the currentgold standard) is the development of systemic lupus erythematosis (SLE). This side effect israre and unpredictable. Out of several thousand cases having received treatment, theUniversity of Calgary have accumulated 12 individuals with full phenotyping and novelserological antibody discovery panel data. We propose to exome sequence these samples inan effort to identify rare highly-penetrant variants that could be underlying this severephenotype.

  Study EGAS00001000387

• Validation_of_Exome_sequencing_of_S7RE_iPSC_lines

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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/

  Study EGAS00001000423

• Deep_sequencing_of_S7EPC_genome

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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/

  Study EGAS00001000437

• Exome_sequence_of_probands_in_Barrett_s_oesophagus_families

  Barrett?s oesophagus is common in the UK affecting 2 % of the population. Family history has beenrecorded among the 4000 Barrett's cases collected so far and have 241 families. Among them wehave assessed 6 multiplex families with proven Barrett?s and defined as having 1 pro band and atleast 3 affected first degree members. We propose to exome sequence the probands of these sixfamilies to assess the presence of pathogenic rare coding variants.

  Study EGAS00001000531

• WGS and WES of 78 pairs Chinese gastric cancer

  Gastric Cancer (GC) is a highly heterogeneous disease. To identify potential clinically actionable therapeutic targets that may inform individualized treatment strategies, we performed whole-exome sequencing on 78 GCs of differing histologies and anatomic locations, as well as whole-genome sequencing on two GC cases, each with 3 primary tumours and 2 matching lymph node metastases. The data showed two distinct GC subtypes with either high-clonality (HiC) or low-clonality (LoC).

  Study EGAS00001001056

• Sequencing of heritable Bleeding and Platelet Disorders

  The BRIDGE-BPD study aims to discover new causal genes for Bleeding and Platelet Disorders (BPD) by high throughput sequencing using cluster analyses based on improved and standardized deep phenotyping of cases. BPD is one of the 13 Rare Disease projects under the NIHR BioResource Rare Diseases BRIDGE consortium, which is a collaboration aiming to discover the genetic sequence variants underlying unresolved inherited disorders and to improve identification of already identified high penetrance variants.

  Study EGAS00001001172

• Whole_Genome_Sequencing_of_JK_Family

  In collaboration with Dr David Savage, we have identified a patient with a very unusualphenotype, lacking almost all visceral fat, but showing a massive accumulation of white fattissue behind her neck and significantly elevated liver fat.Whole exome sequencing of the proband and her unaffected parents and brother has beenrun previously, however no causative variant has been found and the sequencing coveragewas generally poor. We propose to conduct whole genome sequencing of all 4 familymembers at a depth of 30X.

  Study EGAS00001001323

• Validation_of_SNVs_found_by_Exome_seq_in_S2_SF1___SF5_and__SF9_hiPSCs

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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/

  Study EGAS00001000464

• miRNA_expression_in_response_to_LPS_stimulus_in_macrophages

  Our lab is currently using macrophages as a model system for understanding how geneticvariation modulates the response to external environmental stimulus. We want to extend thisbeyond regular polyadenylated RNA to small RNAs such as miRNAs. This project wouldcover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed aspart of a rotation project in the lab. We will require a small number of miRNA libraries and asingle lane of MiSeq

  Study EGAS00001000691

• Exploration_of__mutational_processes_in_human_cancer_cell_lines__Exome

  Approximately 25 cell lines representative of 11 mutation signatures have been selected and will be grown from a single cell, referred to as parental clone, for a period of 3 months to allow accumulation of mutations. Following that period, we will obtain 2 subclones from each of the parental clone for sequencing analysis. In total we will be sequencing 2 parental clones and 4 subclones per cell line for approximately 25 cell lines.

  Study EGAS00001000790

• Whole genome and RNA sequencing of paediatric glioblastoma in the ICGC PedBrain project

  Paediatric glioblastoma (pedGBM) is characterised by substantial intertumoural heterogeneity. In order to identify the genetic lesions underlying tumourigenesis, we analysed whole genomes and transcriptomes of pedGBMs and in vitro model systems by next generation sequencing. Novel fusions of the receptor tyrosine kinase MET lead us to investigate targeted therapy using MET inhibitors. This study is part of the International Cancer Genome Consortium PedBrain Tumor Project (ICGC PedBrain, http://www.pedbraintumor.org/).

  Study EGAS00001001139

• Genetic Landscape of Esophageal Squamous Cell Carcinoma Defined by Exome Sequencing on Chinese Patient Cohort and Cell Lines

  Esophageal Squamous Cell Carcinoma (ESCC) is one of the deadliest cancers worldwide. To define the genetic landscape of ESCC, whole exome sequencing was performed on 113 pairs of tumor and normal DNA samples collected from Chinese individuals with treatment-naive primary ESCC, along with 8 cell lines, including 7 from KYSE series ESCC cell lines and one immortalized esophageal squamous epithelial cell line Het-1A.

  Study EGAS00001000932

• Myelodysplastic_Syndrome_Follow_Up_Series

  Agilent whole exome hybridisation capture was performed on genomic DNA derived from MDS 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 discover the prevalence of our findings using bespoke pulldown methods and sequencing the products from a larger set of patient DNA.

  Study EGAS00001000224

• Whole-genome sequencing analysis of low-grade astrocytomas within the ICGC PedBrain Tumor Project

  In order to investigate the full range of genetic alterations contributing to the tumourigenesis of low-grade astrocytoma, we have conducted a next-generation sequencing-based analysis on a large series of matched tumor-normal pairs. This study, conducted by the International Cancer Genome Consortium PedBrain Tumor Project (ICGC PedBrain, http://www.pedbraintumor.org/), has revealed multiple new insights into the biological basis of this tumor entity.

  Study EGAS00001000381

• Recent genetic history of Denmark

  The "Where Are You From?" project explores the extent to which recent and more distant historical events left their mark on the genetic structure of the current Danish population. The project's ultimate goal is to gain insights into the historical complexity of Denmark from the genetic perspective. To this goal, a data set consisting of approximately 800 high school students from across Denmark was used to run an extensive genetic analysis.

  Study EGAS00001001868

• Subclonal_analysis_in_S7RE2_and_S7RE14_iPS_cells

  PCR products were obtained from each target loci using genomic DNA from human iPS cells. Subsequently, PCR products are pooled and subjected to Illumina library preparation. The library will be sequenced either by HiSeq or MiSeq. 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/

  Study EGAS00001000441

• Whole_genome_sequencing_of_a_Grem1_mutant_human_tumour

  The BMP antagonist Grem1 has been shown to be associated with a rare human polyposissyndrome (HMPS). We have shown that there is a 40KB duplication on chrom 15 found insome patients with HMPS. Traditional serrated adenomas (rare sporadic polyps) share somemorphological features with HMPS polyps and it has long been hypothesised that they are thesporadic version of HMPS polyps. We have obtained of one of theselesions and in this project we aim to characterise this tumour.

  Study EGAS00001000562

• Congenital Heart Disease in UK Families

  This project aims to identify highly penetrant coding variants increasing the risk of Congenital Heart Disease (CHD) performing whole exome sequencing on DNA samples from 23 affected individuals, selected from 10 families with presumed Autosomal Recessive Inheritance. This is a collaboration with Prof. Eamonn Maher and Dr. Chirag Patel from the Department of Medical and Molecular Genetics, University of Birmingham plans to sequence 23 indexed Agilent whole exome pulldown libraries on 75Bp PE HiSeq (Illumina).

  Study EGAS00001000066