23144 results for "ega"

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• WES analysis of patients with USP8 wild-type corticotroph adenomas

  The overall goal of the Identification of recurrent mutations in Cushing’s disease project is to study the impact of whole-exome sequencing (WES) on the clinical care of cancer patients and oncology provider practices. The aims of Project are to implement and establish the feasibility of WES in patients with USP8 wild-type corticotroph adenomas; to develop a framework for the understanding of the molecular mechanism of the pathogenesis of corticotroph adenoma.

  Dataset EGAD00001004136

• Anaplastic Thyroid Cancer somatic variants (MuTect)

  Sequence was aligned to the GRCH38 reference genome. Aligned sequence was analyzed with GATK/MuTect, to generate somatic variant calls across the SureSelect All Exon V5+UTR target region. Somatic variant calls are in VCF format. In total there are 166 tumour samples, 94 of which have a matched normal. Somatic variants for tumours without a matched normal, were called against a panel of normals. Details for the mutect call can be found in the vcf header.

  Dataset EGAD00001004129

• Raw sequencing data for donor and patient fecal samples

  Microbiome analysis was performed on the patient samples collected pre-FMT and on days after FMT, and on samples collected from the FMT donor. Genomic bacterial DNA was extracted from fecal samples using the QIAamp DNA Stool kit (Qiagen, Hilden, Germany), with the addition of a bead-beating lysis step. Genomic 16S ribosomal-RNA V4 variable regions were amplified and sequenced on the Illumina MiSeq platform.

  Dataset EGAD00001004371

• DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - phenotypic and family descriptions

  DDD DATAFREEZE 2017-12-15: 13,462 trios and probands only - phenotypic and family descriptions

  Dataset EGAD00001004388

• EORTC study on the evolution of driver mutations and MGMT promotor methylation in glioblastomas treated with standard of care: Correlation with survival and impact on trial design

  Precision medicine trials in glioblastoma should be conducted at tumor recurrence. However, second surgery for recurrent GBMs is not routinely performed and therefore molecular data is predominantly derived from primary samples. This study aims to establish the frequency of driver changes at tumor recurrence.

  Dataset EGAD00001004593

• BLUEPRINT September 2016, ChIPmentation Lymphoma_Follicular from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Lymphoma_Follicular from lymph node, on Genome GRCh38. 7 run(s), 6 experiment(s), 6 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002931

• 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)

  Dataset EGAD00001000343

• BLUEPRINT September 2016, ChIPmentation Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38

  ChIPmentation data for 1 sample(s) Acute Lymphocytic Leukemia from bone marrow, on Genome GRCh38. 2 run(s), 2 experiment(s), 2 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002930

• GoNL release 5 raw SNV calls

  These files contain a total of 20.4M SNVs and the complete information output by the GATK UnifiedGenotyper v1.4 on all 767 GoNL samples. These calls are not trio-aware and all genotypes were reported regardless of their quality. Both filtered and passing calls are reported in these files. Filtered calls include (1) calls failing our VQSR threshold and (2) calls in the GoNL inaccessible genome.

  Dataset EGAD00001000743

• BLUEPRINT release January 2015, RNA-Seq for Leukemia

  RNA-Seq data for 1 Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_rnaseq_analysis_crg_20140811

  Dataset EGAD00001001178

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

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

  Dataset EGAD00001000677

• BLUEPRINT release January 2015, ChIP-Seq for monocyte

  ChIP-Seq data for 2 monocyte sample(s). 7 run(s), 7 experiment(s), 7 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_chipseq_analysis_ebi_20140811

  Dataset EGAD00001001197

• BLUEPRINT release January 2015, Bisulfite-Seq for CD34-negative, CD41-positive, CD42-positive megakaryocyte cell

  Bisulfite-Seq data for 1 CD34-negative, CD41-positive, CD42-positive megakaryocyte cell sample(s). 14 run(s), 1 experiment(s), 1 alignment(s). Part of BLUEPRINT release January 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001001150

• BLUEPRINT release August 2016, Bisulfite-Seq for monocyte - RPMI_T=24hrs, on genome GRCh38

  Bisulfite-Seq data for 1 monocyte - RPMI_T=24hrs sample(s). 14 run(s), 1 experiment(s), 2 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002335

• BLUEPRINT release August 2016, Bisulfite-Seq for band form neutrophil, on genome GRCh38

  Bisulfite-Seq data for 3 band form neutrophil sample(s). 34 run(s), 3 experiment(s), 6 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_bisulphite_analysis_CNAG_20160816

  Dataset EGAD00001002378

• BLUEPRINT release August 2016, ChIP-Seq for Lymphoma_Follicular, on genome GRCh38

  ChIP-Seq data for 3 Lymphoma_Follicular sample(s). 11 run(s), 11 experiment(s), 11 analysis(s) on human genome GRCh38. Part of BLUEPRINT release August 2016. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20160816/homo_sapiens/README_chipseq_analysis_ebi_20160816

  Dataset EGAD00001002389

• BLUEPRINT release August 2015, Bisulfite-Seq for hematopoietic multipotent progenitor cell, on genome GRCh38

  Bisulfite-Seq data for 1 hematopoietic multipotent progenitor cell sample(s). 5 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001493

• BLUEPRINT release August 2015, RNA-Seq for Leukemia, on genome GRCh38

  RNA-Seq data for 1 Leukemia sample(s). 1 run(s), 1 experiment(s), 1 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_rnaseq_analysis_crg_20150820

  Dataset EGAD00001001551

• Genome and transcriptome sequence data from a melanoma skin cancer - squamous cell carcinoma patient

  Genome and transcriptome sequence data from a melanoma skin cancer - squamous cell carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002018

• 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.

  Dataset EGAD00001002186

• Chondrosarcoma Validation Study

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

  Dataset EGAD00001000392

• BLUEPRINT release August 2015, Bisulfite-Seq for inflammatory macrophage, on genome GRCh38

  Bisulfite-Seq data for 6 inflammatory macrophage sample(s). 83 run(s), 6 experiment(s), 6 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_bisulphite_analysis_CNAG_20150820

  Dataset EGAD00001001491

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

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

  Dataset EGAD00001001968

• BLUEPRINT September 2016, ChIPmentation Burkitt Lymphoma from lymph node, on Genome GRCh38

  ChIPmentation data for 3 sample(s) Burkitt Lymphoma from lymph node, on Genome GRCh38. 10 run(s), 8 experiment(s), 8 alignment(s). Part of BLUEPRINT (September 2016).

  Dataset EGAD00001002939

• BLUEPRINT September 2016, Bisulfite-Seq Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38

  Bisulfite-Seq data for 1 sample(s) Acute Lymphocytic Leukemia for precursor B cell from bone marrow, on Genome GRCh38. 3 run(s), 1 experiment(s), 0 alignment(s). Part of BLUEPRINT (September 2016).Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20140811/homo_sapiens/README_bisulphite_analysis_CNAG_20140811

  Dataset EGAD00001002969

• Genome and transcriptome sequence data from a metastatic neuroendocrine carcinoma of unknown primary patient

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

  Dataset EGAD00001002975

• Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of anus patient

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

  Dataset EGAD00001002994

• Genome and transcriptome sequence data from a metastatic adenocarcinoma presumably of ovarian origin patient

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

  Dataset EGAD00001003008

• Genome and transcriptome sequence data from a squamous cell carcinoma of the lung patient

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

  Dataset EGAD00001003011

• Genome and transcriptome sequence data from a metastatic ductal carcinoma of the breast patient

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

  Dataset EGAD00001003016

• Genome and transcriptome sequence data from a metastatic large cell neuroendocrine tumour of the lung patient

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

  Dataset EGAD00001003017

• Next generation sequencing data of circulating tumor DNA and matched tumor tissues

  For each subject, genomic DNA from whole blood, circulating cell free DNA and tumor tissues (whenever possible) were performed targeting next generation sequencing on Illumina Miseq or Hiseq 4000 platforms. The sequencing results of whole blood were used to distinguish germline and somatic mutations. Specimens were collected from patients with different kinds of solid tumors, but most are lung cancer patients.

  Dataset EGAD00001003176

• Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma

  This dataset includes genomic information of 19 adult cerebellar glioblastomas (C-GBMs). Whole-exome sequencing data are available for 9 C-GBMs and their 8 corresponding matched blood samples, and glioma-specific targeted-DNA sequencing (GliomaSCAN) data from additional 10 C-GBMs are also available. Among them, Whole-transcriptome sequencing data were conducted for 6 C-GBM tumors.

  Dataset EGAD00001003417

• Genome and transcriptome sequence data from a metastatic neuroendocrine tumor arising from small bowel patient

  Genome and transcriptome sequence data from a metastatic neuroendocrine tumor arising from small bowel patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001003686

• Genome and transcriptome sequence data from a spindle cell carcinoma of the left parotid patient

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

  Dataset EGAD00001003734

• RNA sequencing of multiple tumor biopsies and patient-derived spheroids from five colorectal cancer patients (BAM files)

  Whole transcriptome, strand-specific RNA-seq libraries were prepared from total RNA purified using RNeasy mini kit (Qiagen) using Ribo-Zero technology (Epicentre, an Illumina company) for depletion of rRNA followed by library preparation using ScriptSeq ScriptSeq RNA-Seq Library preparation Kit from Illumina. The paired raw sequence reads were processed using TopHat2 and mapped to the humane reference genome HG19.

  Dataset EGAD00001003820

• CD49f single-cell methylomes

  74 CD49f single-cell methylomes are from cord blood of donor1, and 84 from cord blood of donor2. Samples from donor1 have one sequencing lane, and samples from donor2 have five sequencing lanes. This dataset was generated using Post-Bisulfite Adapter Ligation (PBAL), a bisulfite based whole genome protocol. In total this dataset consists of 494 runs.

  Dataset EGAD00001003913

• Fetal body map

  From 2nd trimester human foetuses we derived liver and intestinal stem cells. These were clonally expanded until enough material was available for whole genome sequencing. For each foetus, reference tissue (skin or bulk liver) was also sequenced to determine all germline variants. These were subtracted from the clones to determine all somatic mutations that had been acquired during embryonic and fetal development.

  Dataset EGAD00001003997

• Low-coverage Whole Genome Sequencing, Colorectal adenomas, NKI-AvL TGO series Stool-Proteomics

  For this tissue dataset, we applied low-pass whole genome sequencing to 98 non-advanced and advanced adenomas. As small number of lesions was sequenced multiple times, this dataset consists of 103 fastq files. These adenomas were classified as lesions with low-risk or high-risk of progression, according to the presence of specific DNA copy number changes (Carvalho et al, CancerPrevRes, 2018).

  Dataset EGAD00001004075

• WGS of cell line MMML-seq / MALY-DE tumor_4167452

  This dataset contains the aligned whole genome sequencing data of cell line 380. This cell was established from the peripheral blood of a 15-year-old boy with acute lymphoblastic leukemia at relapse, showing an immature phenotype and carrying an IGH-MYC (t(8;14)) as well as an IGH-BCL2 (t(14;18)) chromosomal translocation. The sequencing was performed on an Illumina X-ten sequencer.

  Dataset EGAD00001004090

• The spatio-temporal evolution of lymph node spread in early breast cancer

  Set of multi-region sequenced breast cancer primary samples, lymph nodes and ctDNA. We collected samples from 11 breast cancer patients with lymph node involvement but no sign of distant metastasis. We performed a mix of whole-exome sequencing, targeted capture sequencing, and whole-genome sequencing of primary tumour samples and lymph nodes, as well as targeted capture sequencing of circulating tumour DNA.

  Dataset EGAD00001004122

• Anaplastic Thyroid Cancer aligned sequence data

  Sequence data in fastq format was aligned to the GRCH38 reference genome. Aligned sequence was preprocessed with GATK for Indel Realignment and Base Quality Score Recalibration. Duplicates were marked with Picard Mark Duplicates. Aligned sequence is in bam format. Details of the alignment can be found int he bam header. In total, data generated from 174 tumour samples 102 matched blood normal controls was aligned. Tumour samples were classified as Anaplastic Thyroid, Poorly-differentiated or well-differentiated cancers.

  Dataset EGAD00001004126

• Genotype calls (vcf files)

  Genotype calls for 83 Aboriginal Australian genomes split by chromosomes. In short, genotypes were called individually with samtools. They were subsequently filtered with thresholds related to sequencing depth, location of variants, sequencing error, and strand bias. Once combined, the genotypes were filtered when not in Hardy-Weinberg equilibrium. The genomes were phased with IMPUTE using the 1000 Genomes reference panel. NB: for the Y chromosomes​, only the 44 Aboriginal Australian males are included.

  Dataset EGAD00001004155

• GoDARTS T2D-GENES Exome Sequencing Study

  The GoDARTS T2D-GENES exome sequencing study includes 1924 samples, 965 T2D cases and 959 T2D controls, from European ancestry. This cohort is part of a larger exome sequencing effort from the T2D-GENES project and contains the exome sequencing vcf from the GoDARTS samples. The other data generated from the T2D-GENES project can be found in dbGAP. Samples underwent deep exome sequencing, with SNVs and INDEls called according to GATK best practices.

  Dataset EGAD00001004311

• RNAseq of 76 samples from Uveal Melanoma tumors

  Hotspot mutations in the spliceosome gene SF3B1 are reported in 20% of uveal melanomas. SF3B1 is involved in 3'-splice site (3'ss) recognition during RNA splicing; however, the molecular mechanisms of its mutation have remained unclear. Here we show, using RNA-Seq analyses of uveal melanoma, that the SF3B1 R625/K666 mutation results in deregulated splicing at a subset of junctions, mostly by the use of alternative 3'ss.

  Dataset EGAD00001004398

• FASTQ files of the Exome-Seq data for the study "Genomic landscape of lung adenocarcinoma in East Asians"

  FASTQ files of the Exome-Seq data for both the normal and tumor samples for the study "Genomic landscape of lung adenocarcinoma in East Asians". For mutations and copy number variants called by this study, please download from https://src.gisapps.org/OncoSG_public/study/summary?id=GIS031 by clicking the download icon next to the dataset title.

  Dataset EGAD00001004422

• RNA-seq of hepatocellular carcinoma xenografts established from needle biopsies

  RNA-sequencing of human hepatocellular carcinoma biopsies (n=14), 44 HCC xenografts derived from 11 HCC biopsies and 3 lymphoma xenografts derived from 3 HCC biopsies. RNA-sequencing was performed using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (lllumina). SR126 sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry according to the manufacturer’s guidelines.

  Dataset EGAD00001004541

• PanCurX Translational Research Initiative - RNA-Seq mapped and unmapped reads

  Integration of Genomic and Transcriptional Features in Pancreatic Cancer Reveals Increased Cell Cycle Progression in Metastases - RNA-Seq mapped and unmapped reads

  Dataset EGAD00001004548

• Whole exome sequencing and target gene sequencing of ESCC cases and healthy controls from Henan high-risk region

  In total, 186 FH+ ESCC cases were sequenced using whole-exome sequencing, then 1935 ESCC cases and 1186 geographically-matched healthy controls were sequenced using 7 Mb custom designed Roche SeqCap kit which targeted about 600 genes. The libraries were constructed and then sequenced in Illumina platform.

  Dataset EGAD00001004556

• Repeated clinical malaria episodes are associated with modification of the immune system in children. (2019-01-17)

  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/. . This dataset contains all the data available for this study on 2019-01-17.

  Dataset EGAD00001004570