23272 results for "ega"

in 38.89 milliseconds.

• Fragmentomics analyses of urinary cfDNA for urologic cancers

  This dataset contains sequencing data of human urinary cell-free DNA. Whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) was performed after DNA extraction from the urine samples. All samples were pair-end sequencing on Illumina system and were aligned to human genome GRCh37 (hg19). WGS and WGBS reads were aligned by SOAP2 and Methyl-Pipe, respectively. The dataset includes samples from healthy subjects, haematuria (non-cancer), and patients of bladder, kidney, or prostate cancer. Pair-end FASTQ files were provided for all the samples mentioned above.

  Dataset EGAD50000002068

• Shallow Whole-Genome Sequencing of Plasma ctDNA in Relapsed/Refractory Germ Cell Tumors

  This dataset comprises shallow whole-genome sequencing data (~3× coverage) of circulating tumor DNA extracted from baseline and on-treatment plasma samples of patients with relapsed or refractory germ cell tumors treated with salvage high-dose chemotherapy. Libraries were generated from 20 ng of cfDNA using the KAPA Hyper Prep protocol with unique dual indexing and sequenced on an Illumina NovaSeq 6000 platform to enable genome-wide copy number and biomarker analyses associated with treatment response and clinical outcome.

  Dataset EGAD50000002183

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set3)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of 10 B-other ALL patients (ALLT-369,ALLT-378, ALLK-109, ALLK-110, ALLK-115, ALLT-391, ALLK-101, ALLK-113, ALLK-123, ALLT-393). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEBNext® Ultra™ II DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using Illumina NovaSeq 6000.

  Dataset EGAD50000002158

• Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution

  Raw sequencing data for the manuscript "Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution". It includes PacBio long-read scRNA-seq, illumina short-read scRNA-seq and Twist-based targeted scRNA-seq datasets for two adrenal samples.

  Study EGAS50000001537

• RNA sequencing of BCP-LBL and EM B-ALL patients samples

  In order to perform comprehensive transcriptomics and gene fusion analyses of a cohort of BCP-LBL and extramedullary (EM) manifestations of B-ALL patients, we performed RNA sequencing of 16 tissue samples from BCP-LBL and EM B-ALL patients. Because the material was available as FFPE, and had a relative low quality, we used a capture-based approach, where NGS libraries obtained from total RNA were captured in 4-plex, using a whole exome capture panel.

  Dataset EGAD50000002047

• PHRT study of longitudinal sampling in ovarian cancer

  High-grade serous ovarian cancer presents significant challenges due to its poor prognosis and high heterogeneity, both of which complicate treatment responses. This project aims to understand intra-patient tumor evolution by investigating different sampling sites (primary and metastatic) at the time of diagnosis and during disease recurrence.

  Study EGAS50000001424

• A single-cell atlas of the early COPD lung

  Single cell atlas of the human airways from 10 patients suffering of early stage Chronic Obstructive Pulmonary Disease and 12 healthy age matched volunteers. This dataset was sequenced by 10X Genomics 3’ RNA-seq profiling. It is composed of more than 400 000 cells coming from 119 samples total. Sampling was performed by brushings and biopsies from the nose to the 6 th division of the airways.

  Dataset EGAD50000001001

• Transcriptomics for 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. This dataset contains transcriptomics data processed with the STAR pipeline. Two sequencing kits were employed: Roche KAPA for high-quality RNA samples and Takara SMART-Seq Stranded for samples with limited RNA quantities.

  Dataset EGAD50000002236

• snRNA-seq data of 11 regionally sampled GBM tissue for 4 patients

  This dataset contains snRNA-seq data of 11 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed in an unbiased manner without any sorting procedure. Nuclei were dissociated from frozen tissue using Chromium Nuclei Isolation Kit. Nuclei barcoding, cDNA preparation, and library construction were performed following the Evercode WT or WT mini User Manual, by combinatorial barcoding to assign a unique barcode to each cell.

  Dataset EGAD50000000778

• A clinically and genomically annotated Early onset colorectal cancer and late onset colorectal cancer

  This study aimed to identify genomic characteristics of early-onset colorectal cancer (EOCRC) compared to late-onset cases. Whole-genome sequencing (WGS) was performed on EOCRC and late-onset colorectal cancer (LOCRC) tissues and blood samples to analyze their genomic profiles.

  Study EGAS50000000544

• 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.

  Study EGAS50000001595

• Enzymatic methylation sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains comprises enzymatic methylation sequencing (EM-Seq) data generated from 208 rectal mucus samples from patients suspected to have colorectal cancer and healthy controls. Targeted CpG sites were enriched using a panel of genes implicated in colorectal cancer, and libraries were prepared with NEBNext EM-Seq prior to Illumina sequencing. Sequencing was performed on the Illumina NovaSeq6000 platform, producing paired-end FASTQ files. These data support analyses of DNA methylation patterns in CRC detection and progression

  Dataset EGAD50000001871

• Single nucleus mRNA sequencing of immune cells from diverse CNS regions in human health and diseases

  CNS nuclei were isolated from frozen specimen, stained with anti-NeuN and anti-Olig2, FACS purified (DAPI+NeuN-Olig2-), and analyzed with single nucleus RNA-seq. One batch of samples was also labelled with CMO and allows distinguishing indivudal samples within the analysis. A combined seurat object was generated to include all the analyses and samples were integrated using Harmony integration.

  Dataset EGAD50000001835

• Transcriptome analysis of human iPSC-derived microglia in a novel human 3D cortical tissue model

  scRNA-seq analysis of human iPSC-derived microglia in a novel, human in vitro 3D cortical tissue model. Samples include three distinct conditions (each as biological duplicates): wild-type microglia extracted from cultures after 1 month (WT_1mo) and 3 months (WT_3mo) of culturing, as well as knock-in microglia extracted 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).

  Dataset EGAD50000000677

• scRNA-seq of a 3D human cortical tissue model from human iPSCs exploring 2D versus 3D co-culturing

  Single-cell RNA-seq analysis of human iPSC-derived microglia/astrocytes/neurons in a novel, human in vitro 3D cortical tissue model, as well as 2D co-cultures for comparison. Samples include distinct conditions as described in the Study section. The dataset was generated using the BD Rhapsody technology and sequenced paired-end with Illumina NovaSeq2000. Information on the multiplexing of samples is reported in the Analyses section.

  Dataset EGAD50000002021

• Targeted Next-Generation Sequencing Data of IDH1 Exon 4 in Intrahepatic Cholangiocarcinoma Samples

  This dataset contains targeted next-generation sequencing data from 76 FFPE tumor tissues focusing on IDH1 exon 4 and codon 132. Genomic DNA was isolated using the QIAamp DNA FFPE Tissue Kit and sequenced on the Illumina MiSeq platform with 200x minimum coverage. The results are provided as encrypted somatic variant call files (VCF) generated through the Nextera XT library preparation protocol. This collection represents the specific somatic mutation profiles of the intrahepatic cholangiocarcinoma cohort for controlled access.

  Dataset EGAD50000002345

• 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.

  Study EGAS50000001622

• CEITEC DAC

  A CEITEC Data Access Committee (DAC) is a body of one or more named individuals who are responsible for data release to external requesters. The members of DAC are selected members of research groups and their respective leaders. Multiple datasets may be affiliated to a single DAC. DAC continues communication with requester to understand the purpose of use, i.e. research setting the dataset is envisioned for by requester, to identify if data sharing is possible directly under current conditions for the dataset, or actions such as re-consenting is needed and desirable to accommodate the proposed research setting/data use.

  Dac EGAC50000000049

• Error-corrected targeted sequencing of rectal mucus from patients suspected to have colorectal cancer

  This dataset contains error-corrected next-generation sequencing (ecNGS) data generated from 161 rectal mucus samples. These samples belong to colorectal cancer, adenoma, and control participants. Genomic DNA was extracted and processed using a hybrid-capture panel targeting 50 colorectal cancer–associated genes, incorporating unique molecular identifiers (UMIs) for duplex consensus error correction. Libraries were sequenced on an Illumina NovaSeq 6000 (paired-end 150 bp) producing paired-end FASTQ files. These data support analyses of DNA mutations in CRC detection and progression.

  Dataset EGAD50000002032

• Data Access Committee for the DNA sequencing data included in the study "Multifocal cohort analysis unveils cell types associated with regional lymph node seeding in prostate cancer".

  A data transfer agreement (DTA), based on the example DTA provided by UZ Gent, is to be filled out by the requester and Multifocal RNA-seq and tNGS data from primary and metastatic tissues of locally advanced and de novo metastatic cohorts - Data Access Committee. https://www.uzgent.be/nl/over-uz-gent/organisatie/data-access-comite/wat-zijn-de-opdrachten-van-het-data-access-comite Coordinator: Muriel Fouquet E-mail: dataaccesscommittee@uzgent.be

  Dac EGAC50000000930

• Whole genome sequencing of matched patient sample sets of normal and tumor DNA

  Sixteen matched, male and female patient sample sets, each comprising normal DNA, tumor DNA, and RNA, were processed for storage comparison studies. Upon receipt, 10 μl quality control aliquots were prepared from each sample. DNA samples were characterized using Qubit dsDNA High Sensitivity assay for quantification, Genomic DNA TapeStation for integrity assessment (DIN scores), and NanoDrop for purity evaluation. RNA samples were analyzed using Qubit RNA High Sensitivity assay, RNA TapeStation (RIN scores), and NanoDrop. Each sample was divided equally by volume for parallel processing.

  Dataset EGAD50000002441

• IBD_Whole_Genome_Sequencing

  Whole genome sequences at 15X depth of patients with Inflammatory Bowel Disease. 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 EGAS00001002754

• The role of MALT1 in driving IBN resistance in MCL

  The bulk RNA-seq dataset was generated for the cell lines below and used for two major purposes: 1. DEG analysis and GSEA analysis comparing IBN-R and IBN-S cells 2. DEG analysis and GSEA analysis comparing MCL cells with/without MI-2 treatment.

  Study EGAS00001006832

• Repeated_clinical_malaria_episodes_are_associated_with_modification_of_the_immune_system_in_children_

  Repeated clinical malaria episodes are associated with modification of the immune system in children.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 EGAS00001003167

• Microinjection_of_hIPSC_derived_intestinal_organoids_with_Salmonella_Typhimurium

  To generate an RNA-Seq dataset for organoids apically stimulated with Salmonella Typhimurium.These data are 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 EGAS00001001253

• RRBS data from TRACERx non-small cell lung cancer (NSCLC) tumours and matched normal adjacent tissue.

  TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective cohort study designed to investigate intratumor heterogeneity (ITH) in relation to clinical outcome, and to determine the clonal nature of driver events and evolutionary processes in early stage non-small cell lung cancer (NSCLC).

  Study EGAS00001008071

• Resolving_the_Genetic_Architecture_of_Aseptic_Loosening_After_Total_Hip_Replacement

  This is a genome-wide association scan of aseptic loosening after total hip replacement in a Norwegian population. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001883

• Molecular characterisation of paediatric PDX cells before and after 3D RASTRUM bioprintin

  This dataset is a part of the publication and contains source data for comparative analysis of the molecular (TSO500, RNAseq) characteristics between patient-derived xenograft (PDX) cells from high-risk paediatric neuroblastoma and sarcoma models before and after 3D bioprinting using RASTRUM Bioprinter.

  Study EGAS00001008220

• HipSci_RNASEQ_PID

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Platelet and bleeding disorders patients

  Study EGAS00001001990

• ESGI___Molecular_diagnosis_for_mitochondrial_disorders_

  The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients.

  Study EGAS00001000164

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00001000585

• An exome sequencing pilot study of HIV elite-long term non progressors and rapid progressors

  A pilot study examining genetic determinants associated with elite long term non progression and rapid progression using exome sequencing of individuals at the extremes of the distribution of HIV control and progression. Data can only be used for HIV related research.

  Study EGAS00001000057

• Exomes of High-risk Prostate cancer

  DNA extracted from tumoral tissue of 39 patients was used for exome sequencing. As a comparison, DNA extracted from blood was used as a non-tumoral control. DNA was captured using the EZ SeqCap v3 exome kit from Roche and sequenced using an Illumina HiSeq instrument.

  Study EGAS00001001015

• Radiotherapy_induced_Sarcoma_exome

  Whole exome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations

  Study EGAS00001000194

• Human_primary_melanoma_project

  Mutational burden and profiles to be studied in approx. 500 human primary melanomas with matched normal samples, part of the Leeds melanoma cohort. New custom design targeted capture panel covering melanoma-specific copy number alterations, promoter mutations, gene fusions, coding genes, HLA regions and IFNg/JAK/STAT pathway genes.

  Study EGAS00001002409

• Succession Of Transiently Active Tumour-Initiating Cell Clones inHuman Pancreatic Cancer

  To elucidate whether newly acquired genetic alterations during serial transplantation of patient derived primary pancreatic cancer cultures contribute to the observed clonal dynamics in vivo, all coding genes of two patient derived primary cultures and derived genetically marked serial xenografts (1°/2°/3°) were sequenced.

  Study EGAS00001000882

• Spatiotemporal genomic architecture informs precision oncology in glioblsatoma

  We characterized genomic and expression profiles across 127 multi-sector or longitudinal specimens from 52 glioma patients. We showed that, while samples from nearby geographical location shared similar genomic alterations (clonal or subclonal) and expression signatures, multifocal tumors were seeded from individual clones.

  Study EGAS00001001880

• Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions

  Long-read whole genome sequencing, long-read long-range PCR sequencing, targetted long fragment long-read sequencing data of the CLCNKA/CLCNKB locus in 27 Bartter syndrome patients. Multiple different deletion alleles are identified and a new common transposition haplotype predisposing for CLCNKB deletions is described.

  Study EGAS00001007339

• Comparison of HCC cell lines and primary HCCs

  There are concerns about whether cancer cell lines could faithfully represent the matched primary cancer cells. Comparison of the HCC cell lines and primary HCCs demonstrated that, during long-term in vitro culture, cell lines retain the genetic landscape of the matched primary HCCs.

  Study EGAS00001001678

• An efficient and comprehensive strategy for genetic diagnostics of polycystic kidney disease

  We established and validated sequence capture based NGS testing approach for all genes known for cystic and polycystic kidney disease including PKD1. This setup overcomes the complication of unspecific capture of pseudogenes by applying a mapping algorithm efficiently and specifically aligning reads to the PKD1 locus.

  Study EGAS00001001003

• Employing_single_cell_sequencing_for_detection_of_mutational_signatures_reflecting_on_going_mutagenesis_

  12 single cells will be sequenced from a previously single-cell derived clone of a JSC-1 cell line. Additional 12 single cells are likely to be sequenced from a previously single-cell derived clone of a SW756 line. Both belong to CGP’s panel of approximately 1000 human cancer cell lines.

  Study EGAS00001002679

• Immunodeficiency_

  We are doing single-cell RNAseq from B cells from monozygotic twins discordant for common variable immunodeficiency 1) 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002667

• Fibroblast heterogeneity and immunosuppressive environment in Human breast cancer

  Carcinoma-associated fibroblasts (CAF) are key players in the tumor microenvironment. Here, by combining 6 well-known stromal markers, we identify four CAF subsets (CAF-S1 to CAF-S4) in human breast cancer (BC) that exhibit distinct activation patterns and accumulate differently in BC subtypes.

  Study EGAS00001002508

• WGS-Lung Cancer sample 30 pair

  This study includes 30 paired samples of Korean Lung Cancer paitients. 30 Lung Cancer samples are paired with each normal(Saliva derived for control) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001001474

• Whole genome sequencing and whole exome sequencing of DIPG tumors and matched normal tissue

  Diffuse Intrinsic Pontine Glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children with no effective treatment. To understand what drives DIPGs we integrated whole-genome-sequencing with methylation, expression and copy-number profiling.

  Study EGAS00001000575

• Single cell Transcriptomic Analysis of Cellular Heterogeneity in Human Colorectal Tumors

  1,591 single cells from 11 colorectal cancer patients were profiled using Fluidigm based single cell RNA-seq protocol to characterized cellular heterogeneity of colorectal cancer. 630 single cells from 7 cell lines were profiled similarly to benchmark de novo cell type identification algorithms.

  Study EGAS00001001945

• Clinical and genetic analysis of a rare syndrome associated with neoteny

  We describe a novel syndrome in six patients with extreme developmental delay and the defining characteristic of neoteny. In an effort to discover any genetic causes of this syndrome whole genome sequence (WGS) analysis of the patients and their families was performed on Complete Genomics’ nanoarray platform.

  Study EGAS00001002419

• Whole_Genome_Sequencing_of_INTERVAL

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase II. 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 EGAS00001002461

• Tetralogy of Fallot Exome Trios

  Exome sequencing of 30 parent-offspring trios to >50X mean depth, where the offspring has sporadic TOF, to identify potential causal de novo mutations. We will use the exome plus design for pulldown that incorporates ~6.8Mb of additional regulatory sequences in addition to the ~50Mb GENCODE exome.

  Study EGAS00001000071

• H3K27ac and RNA-seq data of neuroblastoma PDXs and/or primary tumors

  This study includes H3K27ac ChIP-seq and RNA-seq data of 6 neuroblastoma PDXs. It also contains RNA-seq data of 3 pairs of neuroblastoma tumors obtained at diagnosis and relapse. The MAP-GR-B25-NB-1 PDX was derived from the relapse of pair 1.

  Study EGAS00001002505

• _Isotype_resolved_sequencing_of_B_cell_receptor__in_sorted_memory_populations

  Optimisation of ex vivo Memory B cell Expansion/Differentiation for Interrogation of Rare Peripheral Memory B Cell Subset Responses 1) 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002633

• Family-based GWAS for CRSwNP

  AbstractOur goal was to identify genetic markers and genes associated with susceptibility to chronic rhinosinusitis with nasal polyps using a family-based genome-wide association study.MethodsPatients with CRSwNP and controls were recruited. SNP association values were generated using DFAM (implemented in PLINK) and Efficient Mixed Model Association eXpedited (EMMAX).

  Study EGAS00001002665

• Whole_Genome_Sequencing_of_INTERVAL

  15x Whole Genome Sequencing of 15,000 individuals from the INTERVAL study cohort, phase III. 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 EGAS00001002787

• 2018_ETO_WGS

  This study includes 12 paired samples of Korean AML-ETO paitients.12 AML-ETO tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002804

• Predictor_ChemoNEAR_TNBC

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict.

  Study EGAS00001002806

• V2_panel_bait_design_test

  This study comprises of three different datasets. 1) 57 samples from the 1243 canapps cell line study,2) 91 FFPE normal samples and 3) 87 samples from the SCORT WS2 dataset. The aim is to sequence these 235 samples in order to test the new V2 Colorectal bait design.

  Study EGAS00001001780

• Breast_Cancer_Somatic_Genetics_Study_

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve 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.

  Study EGAS00001000195

• Genomic analysis of Japanese gastric cancer (345 gastric cancers of NCC)

  As a contribution to the International Cancer Genome Consortium, whole exome sequencing of 345 Japanese gastric cancer (345 gastric cancers of NCC) with various histological subtypes have been conducted. This study aims to identify unique and common driver genes and molecular subtypes in Japanese gastric cancer.

  Study EGAS00001002884

• Radiotherapy_induced_sarcoma

  Whole genome library making will be performed on genomic DNA derived from radiotherapy induced sarcoma samples and matched normal DNA from the same patients. Next Generation sequencing will be performed on the resulting libraries and mapped to build 37 of the human reference genome to facilitate the identification of mutations

  Study EGAS00001000138

• ENGAGE___Amendment__500_genes_exon_sequencing_

  The ENGAGE project is a FP7 funded EU project aiming to combine genetic and phenotype information from European population based cohorts. In this sub-project we aim to do whole exome sequencing of individuals selected from Health 2000 and FINRISK cohorts. Individuals have been selected based on their metabolic trait phenotypes

  Study EGAS00001000137

• Profiling of Peritoneal Metastases from Gastric Adenocarcinoma Identified Molecular Subtypes

  Peritoneal carcinomatosis (PC) occurs frequently in gastric adenocarcinoma (GAC) patients and confers poor prognosis. Multiplex profiling of primary GACs has been insightful but the underpinnings of PC’s development/progression remain largely unknown. Here we characterized exome/transcriptome/immune landscapes of PC cells from 43 patients.

  Study EGAS00001003180

• Paired whole exome sequence of subcutaneous panniculitis-like T-cell lymphoma.

  Subcutaneous panniculitis-like T-cell lymphoma (SPTCL) is a rare subtype of peripheral T-cell lymphoma affecting younger cases and associated with hemophagocytic lymphohistiocytosis. To clarify molecular pathogenesis of SPTCL, we analyzed paired tumor and germline DNAs from 13 patients by whole exome sequencing.

  Study EGAS00001003282

• High_powered_complex_trait_association_mapping_through_whole_genome_sequencing_of_a_selected_subpopulation_of_the_INGI_Val_Borbera_genetic_isolate

  The VBSEQ project aims to combine available extensive genetic and phenotypic data to the latest high-throughput genome sequencing technology and ad hoc statistical analysis to identify new rare genetic variants underlying complex traits. Up to 100 Val Borbera samples will be sequenced to a 6x depth.

  Study EGAS00001000398

• 1054 Flemish Gut Flora Project (FGFP) samples (16S sequencing, dual index)

  Study exploring the taxonomic component of the human gut microbiota in relation to quality of life and depression. This dataset includes 16S rRNA gene sequencing data from 1054 individuals from the Flanders region in Belgium. Microbiota covariates used in the study are provided.

  Study EGAS00001003296

• Korean Lung Cancer - 36 pair WES data

  This study includes 36 paired samples of Korean Lung Cancer paitients.36 Lung Cnacer samples are paired with each normal(Saliva derived for control) sequencing data.The results of this WES study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002843

• High-resolution analyses of human sperm dynamic methylome reveals thousands of novel age-related epigenetic alterations

  Age-dependent modifications of the germ cells epigenome remain poorly understood. Our objective was to assess the DNA methylation profile of human spermatozoa during aging. A cohort study was designed to investigate the effects of age and fertility status on sperm DNA methylation.

  Study EGAS00001004168

• Molecular profiling of acinar cell carcinoma of the salivary glands

  Samples of acinar cell carcinoma (AciCC) of the salivary glands and paired normal salivary gland tissue were analyzed by whole transcriptome RNA-seq (n=10), whole genome sequencing (n=6), whole genome bisulfite sequencing (n=3) and ChIP-seq (H3K27ac, H3K4me3, H3K27me3, NR4A3, CTCF).

  Study EGAS00001002795

• DKFZ-HIPO Project H021/NCT MASTER

  Clinical genome and transcriptome sequencing in younger adults with advanced-stage cancer across all histologies: DKFZ-HIPO Project H021 (http://www.hipo-heidelberg.org/hipo2/index.php/menu-item-2/32-021-prospective-genetic-characterization-of-tumors-from-individual-patients-of-special-interest) / NCT MASTER (http://www.nct-heidelberg.de/forschung/nct-master.html)

  Study EGAS00001000948

• Signatures of Aristolochic Acid Mutagenesis in Bladder Cancer

  This study looks at signatures of Aristolochic Acid mutagenesis in bladder cancer, based on exome and whole genome sequencing data. Thirteen bladder tumors and their matched normal DNAs were sequenced on Illumina platforms. Among them eleven were exome sequenced and two were whole genome sequenced.

  Study EGAS00001000975

• MDS Sequencing Project_Cancer Cell

  Myelodysplastic syndromes (MDS) are uncommon entities, heterogeneous clinically and cytogenetically. The aim of the present study is to determine genetic alteration in this subset of patients. Expected results: Identification of new aberrations and genetic markers in order to detect novel genes involved in MDS 5q-response to Lenalidomide's treatment.

  Study EGAS00001001011

• Highlighted samples from the BCH CRDC

  These exomes are from some of the patients and family members detailed in our forthcoming publication, Children’s Rare Disease Cohorts: an integrative research and clinical genomics initiative. While this paper details an institutional collection of exomes, the samples here were specifically highlighted as having significant findings.

  Study EGAS00001004436

• Platelet_collagen_defect

  As part of the Bloodomics collaboration we have several categories of pedigrees with diseases/syndromes relevant to cardiovascular diseases (CVD). One such pedigree, is from families who have a platelet collagen defect. Exome sequencing has been performed as part of a discovery program to ascertain potential causative variants of the clinical phenotype.

  Study EGAS00001000105

• EORTC RP1335 SPECTA Lung cancer data

  SPECTAlung has recruited patients with thoracic malignancies, collecting FFPE material for molecular analysis. Illumina TST170 NGS panel was used for sequencing. The goal was to identify patients for whom a personalized treatment was possible and build a clinically-annotated molecular database for thoracic patients.

  Study EGAS00001004485

• Integrated molecular analysis of adult T-cell leukemia/lymphoma

  This study is an integrated molecular study of adult T-cell leukemia/lymphoma which includes whole-exome (n = 81), whole-genome (n = 48), and transcriptome sequencing data (n = 57) as well as methylation (n = 109) and SNP array data (n = 426)

  Study EGAS00001001296

• RNA-sequencing of adult T-cell leukemia/lymphoma samples

  Adult T-cell leukemia/lymphoma (ATL) is a highly aggressive hematological malignancy derived from mature CD4+ T-lymphocytes. In this study, we performed RNA-sequencing (RNA-seq) analysis for ATL samples including 9 primary tumors and 1 ATL cell line to clarify gene expression profiles in this disease.

  Study EGAS00001003575

• Cancer-Associated Mutations in Endometriosis without Cancer

  Endometriosis, defined as the presence of ectopic endometrial stroma and epithelium, affects approximately 10% of reproductive-age women and can cause pelvic pain and infertility. Endometriotic lesions are considered to be benign inflammatory lesions but have cancerlike features such as local invasion and resistance to apoptosis

  Study EGAS00001003576

• Genetic dysregulation of gene expression and splicing during a ten-year period of human aging in the PIVUS study

  We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging.

  Study EGAS00001003583

• ENU_HT_29_BRAF_Triple_Therapy_Clones

  KRAS mutant CRC is currently in clinical trial with a combination of a MEK and Akt inhibitor. These patients will likely develop resistance to this combination. We aim to identify the mechanisms of resistance via ENU mutagenesis, with a view to identifying additional therapeutics which have the ability to overcome this resistance.

  Study EGAS00001001778

• Glioblastoma_CRISPR_Screen

  This is an in vitro genome-wide CRISPR/cas9 screen in human glioblastoma stem cells, screening for genes essential for survival of these cells. These cells express cas9 and have been transfected with a guide RNA library causing gene knockouts. We will analyse the sequencing data for depletion of guide RNAs.

  Study EGAS00001001519

• Signatures of mismatch repair deficiency in cancer genomes

  DNA replication errors occurring in mismatch repair (MMR) deficient cells persist as mismatch mutations and predispose to a range of tumors. Here, we sequenced the first whole-genomes from MMR-deficient tumors and observed that mutation rates were drastically increased relative to MMR-proficient endometrial tumors.

  Study EGAS00001000182

• HipSci_RNASEQ_Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we perform RNAseq on iPS lines from Usher syndrome and congenital eye defects.

  Study EGAS00001001997

• Post-zygotic germline mutations in sperm

  These data from sperm were generated to demonstrate detection of post-zygotic mutations in the male germline. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001700

• 120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  120 individuals from the TEENAGE study (Ntalla et al., 2013) have been genotyped on the Illumina HumanCoreExome-12v1-1_A array. This is a population-based study of adolescents from the Attica region in Greece

  Study EGAS00001001733

• We performed whole exome sequencing (WES) using Hiseq on 22 paired CMLs. We also performed whole exome sequencing (WES) using CG on 88 paired CMLs. All the data belongs to CML in China - ICGC project.

  We performed whole exome sequencing (WES) using Hiseq on 22 paired CMLs. We also performed whole exome sequencing (WES) using CG on 88 paired CMLs.All the data belongs to CML in China - ICGC project.

  Study EGAS00001001742

• Human_Evolution_3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Study EGAS00001000315

• Australia_and_New_Guinea_haplotype_phasing_

  Whole-genome sequencing and phasing of admixed Aboriginal Australian genomes and Papua New Guinean genomes using 10x Genomics Chromium technology. 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001853

• Copy number and mutation profiling of Stage 1 epithelial ovarian cancer biopsies

  This project aims at characterizing the genome-wide copy number profile and the variant profile of 139 genes om the five major histotytpes of early-stage (stage I) epithelial ovarian cancer (EOC), to provide insight in the the aethiology and development of the disease.

  Study EGAS00001004961

• Melanoma_brain_metastases

  This is a whole exome study of brain metastases in melanoma. We are studying the genomic evolution of primary cutaneous melanoma to brain met in patients with brain-only metastatic disease. We are also looking at the genomic heterogeneity in patients with temporally, anatomically and regionally separated brian metastases.

  Study EGAS00001002107

• WES of clonally related neuroblastoma and teratoma

  Mature teratomas are usually benign tumors that rarely undergo malignant transformation. We report an advanced neuroblastoma arising in a mature teratoma of the ovary. Whole-exome sequencing identified extensive copy-neutral LOH in both neuroblastoma and teratoma elements, suggesting that the neuroblastoma evolved from the teratoma.

  Study EGAS00001005116

• Genetic heterogeneity and dynamics of transcriptional subtypes in matched primary and recurrent head and neck squamous cell carcinomas

  To get a better understanding of different HNSCC subtypes, whole-exome (matched tumor-normal paits) and whole transcriptome sequencing to to elucidate underlying molecular processes. Here, we present the matched whole-exome sequencing data from 28 patients (normal tissue, tumor tissue, relapse).

  Study EGAS00001005005

• Bottleneck_Sequencing_Of_Human_Tissue__Wgs_

  Bottleneck sequencing of human tissue including neurons, cord blood, sperm 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 EGAS00001004066

• Keratinocyte_CRISPR_screens

  Immortalised HaCaT keratinocytes were transduced with Cas9 and the CRISPR-KO v1.1 genome-wide gRNA library. The gRNA library was prepared from genomic DNA isolated 14 days post library transduction. gRNA representation will be compared to the original CRISPR-KO v1.1 library to reveal genes essential for HaCaT survival and growth.

  Study EGAS00001002714

• Whole genome and whole exome sequencing of epilaptic patients

  In this project, we aim to identify genetic changes that predispose to epilepsy and those that predict the response to various anti-epileptic drugs. We sequenced whole genomes and whole exomes of epileptic individuals with different range of response to anti-epileptic drugs, and their relatives.

  Study EGAS00001002825

• Ensemble learning for classifying single-cell data and projection across reference atlases

  Single-cell data are being generated at an accelerating pace.How best to project data across single-cell atlases is an open problem. We developed a boosted learner that overcomes the greatest challenge with status quo classifiers: low sensitivity, especially when dealing with rare cell types.

  Study EGAS00001004283

• WES of melanoma tumors treated with combined immune checkpoint blockade

  This study of pre-treatment melanoma tumor samples from patients subsequently treated with combined anti-CTLA-4 and anti-PD-1 checkpoint blockade sought to identify genomic biomarkers of response to therapy. A total of 26 tumor and matched normal samples underwent whole exome sequencing.

  Study EGAS00001003857

• 2015_AML_ETO

  This study includes 10 paired samples of 2015 Korean AML-ETO paitients.10 AML-ETO tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002897

• 2015_AML_ETO_WGS_additional

  This study includes 2 paired samples of 2015 Korean AML-ETO paitients. 2 AML-ETO tumor samples are paired with each normal(Saliva or BM derived) sequencing data.The results of this WGS study were analyzed by Mutect and GATK for ranking germline variants and cancer variants to make mutational profile matrix.

  Study EGAS00001002898

• Single-cell sequencing of gammadelta and CD8+ alphabeta TCR sequences from blood and gut in coeliac disease

  Single-cell sequencing of gammadelta and CD8+ alphabeta TCR sequences from blood and gut in coeliac disease, before and during gluten challenge (Samples from baseline, day 6 and day 14 blood, and from baseline + day 14 gut). (Paired end, amplicon sequencing).

  Study EGAS00001004484

• Oesophageal_Adenocarcinoma_Organoid_ATAC

  ATAC Sequencing of 5 patient derived organoid cell models. Each model was derived from a piece of patient tumour taken following surgical rescetion of the tumour. All model derivations took place with the CGaP facility in Sanger. This ATAC data will be combined with other sequencing data in order to generate

  Study EGAS00001003890

• Unravelling the contribution of HIF pathway and its therapeutic potential in human AML leukemia-initiating cells

  This study hypothesized that hypoxia contributes to AML-LSCs function and represents a potential therapeutic target to sensitize AML-LSCs to chemotherapy. We provide a comprehensive single-cell expression atlas of AML patient-matched diagnostic-relapsed samples from risk-stratified human AML patients.

  Study EGAS00001005980