23014 results for "ega"

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• Amplicon_based_sequencing_of_drug_resistant_lung_cancer_cell_lines

  A EGFR mutant NSCLC cell line which is sensitive to AZD9291 inhibition was mutagenised with the chemical mutagen ENU and then drug selected using a AZD9291. Single cell derived colonies were then manually picked and expanded in drug. Resistance was confirmed in a 14 day assay and DNA was collected. These then underwent targeted amplicon-based sequencing to confirm candidate resistance effectors hypothesised from currently available literature.

  Study EGAS00001001675

• The evolution of adult T-cell acute lymphoblastic leukemia

  We profile the whole-genome of 19 primary T-ALLs from adult patients and the corresponding relapse malignancies. Concretely, samples were taken at the time of diagnosis (primary), at time of remission (used as control) and at recurrence of the malignancy after treatment (relapse). The libraries were sequenced on HiSeq 4000 or NovaSeq 6000 (Illumina) with a paired-end read length of 2x151bp.

  Study EGAS00001004750

• Exome_Sequencing_of_Poor_Prognosis_Acute_Myeloid_Leukaemia

  We plan to sequence the exomes of 4 AML cases (tumour and germline) in an effort to discover new mutations in this disease that could improve our understanding of leukaemogenesis and guide the development of new targeted therapies. The Sanger Institute will sequence the exomes of 4 Acute Myeloid Leukaemia cases including tumour and germline DNA so that somatically-acquired, AML-specific mutations can be accurately designated.

  Study EGAS00001000146

• HipSci___Whole_Exome_sequencing___HSP

  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 whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with hereditary spastic paraplegia

  Study EGAS00001001979

• Non_Tumour_Renal_Cell_Line_Sequencing

  Genomic libraries (500 bps) will be generated from total genomic DNA derived from commomon epithelial cancer samples and subjected to total of eight lanes of 37 bp, paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000205

• HipSci HumanExome BeadChip analysis - Primary immune deficiency

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Primary immune deficiency.

  Study EGAS00001002012

• Test_of_PCR_library_method_on_whole_genmoe_samples

  We will sequence 2 whole genome pairs which have had the libraries prepared with a PCR step. The resulting sequence will be compared to teh same samples which have had sequence obtain using a no_PCR library method. the sequence obtained in this experiment may or may not be used in conjunction with the other sequence obtain for these samples in the search for novel cancer mutations.

  Study EGAS00001000214

• Genome_Diversity_in_Africa_Project___GemCode_libraries_

  High depth whole genome sequencing from GemCode (10x Genomics) DNA libraries containing long range linkage information for one Baganda trio and one Baganda child (parent already sequenced at high depth). 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 EGAS00001001828

• Illumina HiSeqX whole genome sequence data on 58 samples including 54 with known HTT triplet repeat expansions (2 premutation and 52 full expansions)

  Whole genome sequence (WGS) data was generated on 58 samples with validated repeat lengths for the CAG repeat associated with Huntington disease, These samples were sequenced using 2x150bp reads on an Illumina HiSeqX sequencer and the repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data.

  Study EGAS00001002593

• Analysis of transcriptomic profiles from affected and recovered muscle biopsies from children with reversible infantile respiratory chain deficiency.

  All patients carry mitochondrial mutation m.14674T>C but not must also carry mutations in related genes such as TRMU and EARS2. Analysis compares muslce biopsies of affected patients to controls, a patient after recovery to themselves during the the disease phase, and compared patients with additional EARS2 mutations to patients without pathogenic EARS2 mutations.

  Study EGAS00001004647

• Whole transcriptome and exome sequencing of childhood ALL

  Gene fusion is a major class of genomic abnormalities in childhood acute lymphoblastic leukemia (ALL) and sentinel chromosomal rearrangements involving EP300 and CREBBP may cause global epigenetic deregulation during leukemogenesis with potentials for therapeutic targeting. This dataset includes whole transcriptome sequencing of 231 children with acute lymphoblastic leukemia from a Singapore-Malaysia frontline clinical treatment protocol.

  Study EGAS00001001858

• Normal brain controls for ICGC PedBrain DNA methylation sequencing

  DNA methylation profiling of 8 control samples from adult (4) and fetal brain (4) used, for example, for the following studies: Mack, Witt, et al. Epigenomic alterations define lethal CIMP-positive ependymomas of infancy. Nature 506(7489):445-450, 2014 (see EGAS00001000443) Hovestadt, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. 510(7506):537-541, 2014 (see EGAS00001000561)

  Study EGAS00001000909

• Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms

  Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous neoplasms. We used a multi-omics approach to uncover the molecular factors underlying this heterogeneity and derive a potential disease classification. Transcriptomic analysis of 84 primary PNEN specimens, drawn from two cohorts (n = 36 and 48), identified four subgroups with distinct molecular profiles. Whole-exome sequencing revealed subgroup-enriched mutational differences.

  Study EGAS00001005024

• HipSci___Whole_Exome_sequencing___Battens

  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 whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease

  Study EGAS00001001975

• Mapping_genetic_variants_underlying_gene_regulation_in_inflammed_intestinal_cell_types_to_identify_novel_IBD_drug_targets

  Biopsies from the terminal ileum and rectum of individuals with Crohn's disease are digested on ice to single cells and processed for single-cell RNA-sequencing (10X Genomics and Illumina) 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 EGAS00001003770

• HipSci___Whole_Exome_sequencing___Macular_dystrophy

  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 whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Macular dystrophy

  Study EGAS00001001982

• HipSci___Whole_Exome_sequencing___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 whole exome sequencing using Agilent whole exome pulldown method on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with blood and platelet disorders

  Study EGAS00001001983

• HipSci HumanExome BeadChip analysis - Hereditary Spastic Paraplegia

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hereditary Spastic Paraplegia.

  Study EGAS00001002006

• HipSci HumanExome BeadChip analysis - Congenital Hyperinsulinia

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Congenital Hyperinsulinia.

  Study EGAS00001002010

• HipSci HumanExome BeadChip analysis - Hypertrophic Cardiomyopathy

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hypertrophic Cardiomyopathy.

  Study EGAS00001002011

• HipSci HumanExome BeadChip analysis - Battens disease

  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 performed Genotyping analysis using the Infinium HumanExome BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease.

  Study EGAS00001002016

• HipSci HumanHT 12 Expression BeadChip analysis - Alport syndrome

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Alport syndrome.

  Study EGAS00001002024

• HipSci HumanHT 12 Expression BeadChip analysis - Hypertrophic Cardiomyopathy

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Hypertrophic Cardiomyopathy.

  Study EGAS00001002026

• HipSci HumanHT 12 Expression BeadChip analysis - Macular Dystrophy

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Macular Dystrophy.

  Study EGAS00001002029

• HipSci HumanHT 12 Expression BeadChip analysis - Battens disease

  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 performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Battens disease.

  Study EGAS00001002031

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

  Pilocytic Astrocytoma (PA) is the most common pediatric brain tumor. While genome and transcriptome landscapes are well-studied, data of the complete methylome, tumor cell composition and immune infiltration are scarce. We generated whole genome bisulfite sequence data (WGBS) of nine PAs to find evidence for a link of focal methylation differences and differential gene expression to immune infiltration.

  Study EGAS00001004019

• Transcriptomic and epigentic analysis of human peripheral blood NK cell subsets revealing role of Bcl11b in differentiation

  Transcriptomic analysis of seven human peripheral blood NK cell subsets and three T cell subsets purified from healthy cytomeglovirus seropositive donors. Epigenetic analysis including identification of open chromatin and active enhancer elements confirms key regulatory factors defining an NK cell differentiation axis. Chromatin-immunoprecipitation sequencing reveals contribution of key transcription factors associated with NK cell differentiation including Bcl11b.

  Study EGAS00001005025

• Brain transcriptome of hereditary cerebral haemorrhage with amyloidosis–Dutch type (HCHWA-D)

  HCHWA-D is an early onset hereditary form of Cerebral Amyloid Angiopathy (CAA) caused by a point mutation resulting in an amino acid change (NP_000475.1:p.Glu693Gln) in the Amyloid Precursor Protein (APP). Post-mortem brain tissue (9 patients and 9 age-related controls; frontal and occipital cortex) was used for next generation sequencing of RNA (RNA-Seq with ribosomal RNA depletion).

  Study EGAS00001002730

• INSIGHT: VHL Case Report

  The overall goal of this study is to uncover contributors to inherited cancer through analysis of individuals and families with, or at risk of, a hereditary cancer syndrome. In addition, we hope to elucidate novel mechanisms of tumourigenesis in hereditary cancer patients. This specific report highlights a rare case of VHL mosaicism and shows the value of tissue testing in VHL variant negative cases.

  Study EGAS00001005895

• Whole-exome sequencing of Fanconi anemia-like inherited bone marrow failure syndrome

  We identified three fibroblast cultures derived from aplastic anemia patients in the Japanese Cancer Research Resources Bank (JCRB) Cell Bank that showed high levels of sister chromatid exchanges (SCEs) in PHA-stimulated lymphoblasts. To elucidate the genetic basis of the high SCE, we carried out whole exome sequencing of these samples. Subsequently, germline variants were analysed for these patients.

  Study EGAS00001003809

• Exome sequencing of Fibromyalgia patients

  Fibromyalgia is a complex disorder characterized by increased sensitivity to pain and extreme tiredness. It affects mostly women, and its causes are unknown. In this study we have performed exome sequencing of 87 fibromyalgia cases, including some sibling pairs, to perform rare variant association analysis and identify fibromyalgia risk factors. A few of the included samples have been also included in a previous GWAS study.

  Study EGAS00001003826

• Leeds Melanoma Cohort (LMC) gene expression study

  Array-based profiling (whole genome DASL HT12.4, Illumina Inc) in over 700 FFPE tumour blocks from the population-based Leeds Melanoma cohort recruited in the North of England, with a long follow up. Data used in tumour immune micro-environment investigation (Nsengimana et al 2018, J Clin Invest doi: 10.1172/JCI95351).

  Study EGAS00001002922

• Whole-exome sequencing of intravascular large B-Cell lymphoma

  Intravascular large B-cell lymphoma (IVLBCL) is a unique form of diffuse large B-cell lymphoma (DLBCL) characterized by extranodal cell growth especially in small vessels without systemic lymphadenopathy. The limitation in obtaining sufficient tumor materials hampers understanding the molecular pathogenesis of IVLBCL. We performed whole-exome sequencing of IVLBCL using plasma-derived cell-free DNA (cfDNA) and patient-derived xenograft (PDX) samples.

  Study EGAS00001003970

• Oesophageal_Adenocarcinoma_Organoids_Iso_Seq

  RNA 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 PacBio RNA data will be combined with other sequencing data in order to generate accurate reference cancer genomes and study how structural variants affect gene expression

  Study EGAS00001004051

• Expression-Based Subtypes Define Pathologic Response to Neoadjuvant Immune-Checkpoint Inhibitors in Muscle-Invasive Bladder Cancer

  Checkpoint immunotherapy (CPI) has increased survival for some patients with advanced stage bladder cancer (BCa). However, most patients do not respond. Here, we characterized the tumor and immune microenvironment in pre- and post-treatment tumors from the PURE01 neoadjuvant pembrolizumab immunotherapy trial, using a consolidative approach that combined transcriptional and genetic profiling with digital spatial profiling.

  Study EGAS00001005549

• Role of cohesin/CTCF in human monocyte differentiation

  Here we study genome architecture in a postmitotic differentiation setting, the differentiation of human blood monocytes (MO). We profiled and compared epigenetic, transcriptome and 3D conformation landscapes during MO differentiation (either into dendritic cells or macrophages) across the genome, with and without siRNA-mediated depletion of RD21 or CTCF, and detected numerous architectural changes, ranging from higher level compartments

  Study EGAS00001005508

• Transcriptional changes in GBM through therapy

  Primary glioblastoma (GBM) tumours recur following therapy, owing to treatment resistance mechanisms in unresectable cells. We have sequenced RNA from paired primary and locally recurrent GBM tumours to begin characterising therapy resistant cells and thereby infer the mechanisms by which they evaded treatment. Exome sequencing data from these samples were included in the first data release from the Glioma Longitudinal AnalySiS (GLASS) consortium

  Study EGAS00001003790

• Application of Hi-C sequencing to detect structural variants in B-cell acute lymphoblastic leukemia

  Large structural variants are easily detected by Hi-C sequencing as strong, distant signals on a Hi-C contact map. Translocations are frequently evident in B-ALL and accurate identification of these translocations can guide clinical treatment options. Here were apply shallow Hi-C sequencing as an unbiased, cost-effective approach to identify translocations among B-ALL patients.

  Study EGAS00001005605

• Somatic_mutation_in_skin_epidermis__SMS_

  We aim to assess the range and depth of mutations in genes linked with cancer in skin epidermis surrounding lesions which are undergoing surgical removal. Patient history will be collected to provide a detailed outline of tumour type (including histology), skin type, and sunlight exposure. We will perform ultra-deep targeted sequencing using genes implicated in cancer to try and understand the background of mutations surrounding these lesions

  Study EGAS00001002165

• IVF Whole genome prediction

  Preimplantation Genetic Testing (PGT) of in vitro fertilized (IVF) embryos has been proposed as a method to reduce transmission of common disease, although comprehensive genetic assessment remains unavailable. Here we use a combination of molecular and statistical techniques to reliably and accurately infer inherited genome sequence in 110 embryos. We combine polygenic risk scores (PRS) and rare variation to model susceptibility across 12 common conditions.

  Study EGAS00001005619

• Indonesian sea-nomads genomic history

  This study observes the origin of the last living sea nomad group in Indonesia using genome-wide SNP data, and tracks their dispersal in the archipelago. This study involves new samples on not only the sea nomad group, but also surrounding populations where the sea nomad settled. We revealed the scenario of their origin and unique admixture patterns during their dispersal and re-settlement.

  Study EGAS00001002246

• Cylindromas_sun_protected_and_exposed

  The project aims to look at mutational signatures in a rare inherited skin tumour syndrome called CYLD cutaneous syndrome. These patients develop multiple skin tumours that are seen at sun exposed and sun protected sites. We plan to carry out WGS on carefully curated tumours from such patients. We then plan to analyse this data for mutational signatures, comparing this between sun exposed and sun protected sites.

  Study EGAS00001002521

• Drug-induced epigenomic plasticity reprograms circadian rhythm regulation to drive prostate cancer towards androgen-independence (RNA-seq)

  Understanding how prostate cancer cells adapt to AR-targeted interventions is critical for identifying novel drug targets to improve the clinical management of treatment-resistant disease. Our study revealed an enzalutamide-induced epigenetic plasticity towards pro-survival signaling, and uncovered circadian regulator ARNTL as an acquired vulnerability after AR inhibition, presenting a novel clinical lead for therapeutic development.

  Study EGAS00001006016

• Clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial

  ABACUS is a single arm phase 2 study that investigated 2 cycles of atezolizumab (1200mg Q3) prior to cystectomy in 95 patients with muscle invasive transitional cell cancer (T2-4N0M0). Pathological complete response (pCR) occurring in ≥20% of patients was the primary endpoint. Biomarker analysis on sequential tissue was a co-primary endpoint.

  Study EGAS00001004445

• ANGIOPREDICT - an FP7-funded project enabling personalised medicine for patients with metastatic colorectal cancer.

  In ANGIOPREDICT, academic cancer biologists and industry-based biotechnology researchers will work together with clinicians to identify biomarkers to predict whether individual metastatic colorectal cancer patients will respond positively to Avastin® combination therapy. Diagnostic tests using these biomarkers will also be developed to provide clinicians with the means to predict patient treatment responses in the future.

  Study EGAS00001005423