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• ENU_NCI_H508_cetuximab_fixed_concentration_project

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC

  Study EGAS00001001744

• ENU_NCI_H508_Cetuximab_SecondRound

  Cetuximab is a targeted monoclonal antibody against the epidermal growth factor receptor (EGFR) which is used therapeutically for the treatment of KRAS wild-type colorectal cancer (CRC). The Cetuximab sensitive KRAS wild-type CRC cell line NCI-H508 has been treated with a fixed concentration of ENU for 24 hours and then selected with Cetuximab until drug resistant clones were ready to be picked and grown up as sub-clones of the parental cell line. These will have genes causally implicated in cancer sequenced to identify common point mutations in multiple independently derived drug resistant clones as a forward genetic screen for mechanisms of resistance to Cetuximab in CRC

  Study EGAS00001001745

• The Haplotype Reference Consortium

  The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts. By combining together multiple cohorts, the reference panels produced by the project will be as large as possible in terms of both number of haplotypes, and numbers of variants. This will increase the accuracy of the genotype imputation, especially at low-frequency variants, and the number of imputable variants, thus increasing the power of GWAS.

  Study EGAS00001001710

• SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x]

  CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding, which was associated with a loss of recognition and functional responses by CD8+ T cells isolated from HLA-matched COVID-19 patients. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through sporadically emerging escape mutations in MHC- I restricted viral epitopes.

  Study EGAS00001005060

• Pre-existing immunity drives the response to neoadjuvant chemotherapy in esophageal adenocarcinoma

  Esophageal adenocarcinoma (EAC) is a highly aggressive tumor. Patients with locally advanced disease undergo neoadjuvant chemotherapy (nCT) before surgery, however fewer than 30% of treated patients achieve a pathological complete response associated with increased 5-year overall survival. We set out to elucidate the mechanisms the response to nCT by multi-dimensional profiling of pre-treatment tumor biopsies and blood samples from EAC patients. In particular we performed whole exome sequencing (WES) and RNAseq on n=26 baseline EAC tumor; two additional EAC samples underwent only WES. WES on matched peripheral blood mononuclear cells (PBMCs) were used as germline control.

  Study EGAS00001007245

• RNA sequencing data of 257 samples from the CORALLEEN trial

  Early-stage Luminal B breast cancer is frequent and is a major cause of breast cancer death due to its poor prognosis. Our proposal aims to study the biology behind the sensitivity and resistance of Luminal B breast cancer to chemotherapy (CHT) or a non-CHT regimen composed of hormone therapy in combination with ribociclib, a CDK4/6 inhibitor. To accomplish this, we first completed the SOLTI-1402 CORALLEEN phase II trial, a study where 106 patients with early-stage Luminal B breast cancer were randomized to standard neoadjuvant CHT for 6 months, or neoadjuvant letrozole and ribociclib for 6 months. After treatment, patients underwent surgery. The primary results of the study, which showed that the response rate to letrozole+ribociclib was similar to CHT, was reported (Prat et al; Lancet Oncol). Tumor biopsies were available at baseline, week 3 and surgery. A total of 257 samples were analyzed using the Illumina TruSeq Stranded Total RNA w/Ribo Zero Gold with MiSeq in TGL (Sequencer NovaSeq S4/PE/100x)

  Dataset EGAD00001010121

• Understanding Self- Organising Capacity of Stem Cells during Implantation and Early Post-implantation Development in vitro and in vivo: Implications for Human Development (2020-04-20)

  The aim of this project is to differentiate human embryonic stem cells to an extra-embryonic fate, specifically the hypoblast. This is of uttermost importance given the current lack of human hypoblast stem cells. We hypothesized that the pluripotent characteristics of the starting human embryonic stem cell population may dictate the competency for extra-embryonic cell fate specification. Based on this hypothesis and using human embryonic stem cells maintained in different naïve-like culture regimes, we have now developed conditions that allow the differentiation of human embryonic stem cells to a stable GATA6+ SOX2- population. This suggests that these cells may be putative human hypoblast stem cells. To validate this finding here we propose to perform RNA sequencing experiments of the differentiated human embryonic stem cells. By comparing their RNA expression profile to the single cell sequencing data of the human embryo that we are currently generating, we will be able to determine the identity of our GATA6+ SOX2- cells, and establish whether they represent the in vivo human hypoblast. This dataset contains all the data available for this study on 2020-04-20.

  Dataset EGAD00001006056

• TRACERx100 metastatic samples

  Whole exome sequencing of 10 metastatic biopsies from four TRACERx100 patients (see EGA dataset EGAS00001002247), collected either after relapse or death. The data from these samples are initially published with Abbosh, C. et al. Phylogenetic ctDNA analysis depicts early stage lung cancer evolution. Nature, http://dx.doi.org/10.1038/nature22364 (2017). Abstract: Earlier detection of relapse following primary surgery for non-small cell lung cancer and the characterization of emerging subclones seeding metastatic sites might offer new therapeutic approaches to limit tumor recurrence. The potential to non-invasively track tumor evolutionary dynamics in ctDNA of early-stage lung cancer is not established. Here we conduct a patient-specific approach to ctDNA profiling in the first 100 lung TRACERx (TRAcking Cancer Evolution through therapy (Rx)) study participants, including one patient co-recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release in early-stage non-small cell lung cancer and perform tumor volume limit of detection analyses. Through blinded profiling of post-operative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients destined to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastases, providing a new approach for ctDNA driven therapeutic studies.

  Dataset EGAD00001003301

• Transcriptome analysis of endometrial organoids derived from patients with Mayer-Rokitansky-Küster-Hauser syndrome

  The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by agenesis of the uterus and upper part of the vagina in females with normal ovarian function. The cause of the disease is still enigmatic. Here, we developed organoid cultures from endometrium found in uterine rudiment horns of MRKH patients. Phenotypically they share great similarity between healthy control organoids and are fully hormone responsive. Transcriptome analysis using RNA-seq identified possible disease-causing pathways altered in MRKH patients during development of the female reproductive tract. Thus, the organoid cultures provide a powerful research model for further insight into disease-causing alterations.

  Study EGAS00001005908

• Walter and Eliza Hall Institute Research Data Access Committee

  Dac EGAC00001002877

• Carcinosarcoma Cohort from NHS Greater Glasgow, Clyde Biorepository, and Imperial College London

  Dac EGAC00001003299

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001003220

• Data Access Commitee for single-cell analysis of multiple myeloma and precursors

  Dac EGAC00001002920

• Longitudinal DNA methylation in the Lothian Birth Cohorts of 1921 and 1936

  Dac EGAC00001000218

• Associations between APOE and cognitive ability in Generation Scotland.

  Dac EGAC00001000332

• Peter Mac Translational Breast Cancer Genomics and Therapeutics Lab Data Access Committee

  Dac EGAC00001000837

• DAC: Whole-genome and transcriptome sequencing of tumor-stage mycosis fungoides

  Dac EGAC00001000847

• The APL DAC comprises a clinician and biologist who conducted the study.

  Dac EGAC00001000865

• DAC for Integrated Genomic, Epigenetic, and Expression Analyses of Ovarian Cancer Cell Lines

  Dac EGAC00001001101

• Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles

  Dac EGAC00001001591

• Human MPN RNA-seq and DNA methylation data requests committee

  Dac EGAC00001001688

• University of Helsinki Systems Biology and Turku University Hospital Data Access Committee

  Dac EGAC00001001978

• Data access committee for Gut microbiome of BA patients and normal controls

  Dac EGAC00001002146

• Department of Pathology and Tumor Biology, Kyoto University Data Access Committee

  Dac EGAC00001002205

• Variation and transmission of the human gut microbiota across generations - 16S data

  Dac EGAC00001002344

• Variation and transmission of the human gut microbiota across generations - shotgun data

  Dac EGAC00001002355

• "DAC for RNAseq from regions of insitu and invasive human mammary ductal disease"

  Dac EGAC00001002538

• DAC - U1085 Team Physiology and Physiopathology of the urogenital tract (INSERM / IRSET)

  Dac EGAC00001002830

• DAC - Liquid biopsy with matched tumor tissue and saliva: CRC + controls

  Dac EGAC00001002835

• EGAD00010000704

  610k genotyping imputed on Hapmap 3 and 1000G Phase 1 CEU

  Dataset EGAD00010000704

• saudi_qc_data

  Genotyped case and control sampes using HumanExome Beadchip

  Dataset EGAD00010000872

• Single-cell sequencing of adipose-derived mesenchymal stromal cells and dermal fibroblasts.

  Dac EGAC00001003062

• Mitochondrial DNA (mtDNA) analyses in patients with schizophrenia and healthy control individuals

  Study EGAS00001003269

• ATAC-Seq and CTCF ChIP-Seq on the OCIAML-2 cell line

  Study EGAS00001004741

• Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer

  Study EGAS00001004328

• Atrial appendage miRNA-seq in non-, paroxysmal and persistent atrial fibrillation

  Study EGAS00001005296

• Human gut microbiome in babies with biliary atresia and normal controls

  Study EGAS00001005350

• RNAseq from regions of insitu and invasive human mammary ductal disease

  Study EGAS00001005370

• Optimisation of CITE-seq on liquid and solid tissues

  Study EGAS00001005849

• Oesophageal adenocarcinoma whole exome and RNA-seq raw sequencing data

  Study EGAS00001005957

• Quantitative Exploratory Proteomics Analysis of Glioblastoma in Initial and Recurrent Tumors

  Study EGAS00001006395

• Sequencing Data of HGSC patient-derived cell lines and organoids

  Study EGAS00001006557

• Treated and control Patient Derived Xenografts of colorectal cancer (CRC) samples

  Study EGAS00001006973

• Advanced iPSC-CMs maturation by integrating maturation medium, nanopatterning, and electrical stimulation

  Study EGAS00001007491

• Array-based methylation analysis of SDHB-deficient pheochromocytoma and paraganglioma

  Study EGAS00001007844

• DAC for Clonal driver neoantigen loss under EGFR TKI and immune selection pressures

  Dac EGAC00001003522

• Population Genomics of Native Americans from Andes and Amazon

  Study EGAS00001004639

• Single-cell multi-omics and mtDNA genotyping of human peripheral blood cells

  Dac EGAC50000000583

• Genomewide Association Study of Inflammatory Bowel Disease - Combined Controls

  WTCCC genome-wide case-control association study for Inflammatory Bowel Disease (IBD) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000007

• WTCCC case-control study for Rheumatoid Arthritis - Combined Controls

  WTCCC genome-wide case-control association study for Rheumatoid Arthritis (RA) using six disease collections together with the 1958 British Birth Cohort and the UK National Blood Service collections as controls.

  Study EGAS00000000012