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• SYN500k_genotypes

  Synthetic dataset containing genome-wide genotypes of 500.000 individuals was generated using a hybrid approach combining coalescent approach and resampling based methods


  Dataset EGAD00010002453

• MB_450k_methylation

  450k methylation arrays of primary and relapse tumor of a single case of sonic hedgehog medulloblastoma with Li-Fraumeni syndrome

  Dataset EGAD00010002370

• Biallelic HMBS Inactivation Defines a Homogenous Clinico-Molecular Subtype of Hepatocellular Carcinoma

  Dataset EGAD00001009745

• Whole Exome Sequencing of INTERVAL

  Whole exome sequencing of a subset of participants from the INTERVAL study.

  Dataset EGAD00001002221

• A non-canonical lymphoblast in refractory childhood T-cell leukaemia

  This dataset contains 75 WGS samples of T-ALL (including matched remission samples where available).

  Dataset EGAD00001015727

• TREM2+ Cells in Human Basal Cell Carcinomas

  To explore the tumor immune microenvironment heterogeneity in sporadic human basal cell carcinoma tumors, we profiled two individual patient tumors by scRNA-Seq. We identified a population of TREM2+ macrophages, which have been implicated in promoting an immunosuppressive tumor microenvironment. We identify that TREM2+ can promote tumor epithelial proliferation in an immunosuppressive independent manner.

  Study phs003242

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Whole Exome Sequencing of Six Signet Ring/Plasmacytoid Variant Bladder Tumors

  In this study, six plasmacytoid bladder cancers were analyzed by whole exome sequencing. The results show loss of the CDH1 gene in every sample and correlate with E-cadherin loss of expression by immunohistochemistry. A separate validation cohort of plasmacytoid samples showed loss of E-cadherin expression by CDH1 mutation or promoter hypermethylation.

  Study phs001064

• Glucose Binds and Activates NSUN2 to Promote Translation and Epidermal Differentiation

  This study was undertaken to determine the role of NSUN2 in epidermal homeostasis. Primary neonatal foreskin keratinocytes were obtained from discarded surgical samples at a California hospital. Samples were anonymous and not selected. NSUN2 was found to promote epidermal differentiation and alter translation using the methods of RNA-seq, CLIP-seq and Ribo-seq.

  Study phs003767

• Single-cell genotype-to-phenotype (scG2P) data of single nuclei from cell line mixing experiment and six donors

  We developed Single-cell genotype-to-phenotype (scG2P) to profile mutations in driver gene hotspots and capture mRNA targets of interest, validating this assay in a cell line mixing experiment of KYSE-270, KYSE-410, and HCT-116, and applied the assay to esophageal biopsy samples from six donors.

  Study EGAS50000001429

• Single-cell RNA sequencing of metastatic colorectal cancer organoids treated with cetuximab

  Single-cell RNA sequencing was performed on metastatic colorectal cancer (mCRC) organoids derived from a cetuximab-sensitive patient-derived xenograft (PDX) model. The objective of this analysis was to investigate, at single-cell resolution, the transcriptional changes previously identified in bulk RNA-seq analyses of PDX models exposed to anti-EGFR therapeutic pressure.

  Study EGAS50000001460

• PDX gene expression

  Investigation of the anti-tumor activity of the potent, highly selective, orally bioavailable CHK1 inhibitor (CHK1i), SRA737, in both acquired PARPi-resistant BRCA1/2 mutant and CCNE1amp high-grade serous ovarian cancer (HGSOC) models. We analyzed gene expression in five patient derived xenografts (PDX) that responded to CHK1i and three PDX that had a poor response to CHK1i.

  Study EGAS50000000084

• Immunoreactive_p53_areas_in_human_skin_2

  Previous work has suggested that in mice there may be a difference in mutational burden between areas expressing stabilised p53 protein and others. We wish to see if this observation holds true in human sun-exposed epidermis. We will take 0.25mm punch biopsies from peeled human skin epidermis which will be submitted to the low input pipeline prior to sequencing.

  Study EGAS00001004463

• DCLRE1B/Apollo germline mutations associated with renal cell carcinoma

  Highlights of Bories et al. article submitted to BBA - Molecular Basis of Disease: We identified 2 germline mutations in the DCLRE1B gene encoding the Apollo protein by Whole Exome Sequencing (WES) in two families with inherited clear-cell Renal Cell Carcinoma. Our study suggests a putative link between DNA repair, telomere protection and renal oncogenesis.

  Study EGAS50000000216

• snATAC-seq fragment files from 10x Multiome profiling of human fetal liver hematopoiesis

  This dataset provides snATAC-seq fragment files from a single-nucleus multiome study of 53 human fetal liver samples (5–18 post-conception weeks). Live CD45+CD235- cells were sorted from dissociated tissue, and isolated nuclei were processed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. Raw sequencing data were processed and aligned to GRCh38-2020-A-2.0.0 using Cell Ranger ARC v2.0.2.

  Dataset EGAD50000002572

• The role of the mammalian SWI/SNF chromatin remodeling complex in neuroendocrine prostate cancer

  We sought to determine the effects of SMARCA4 and SMARCA2 depletion in prostate cancer cell lines. We performed siRNA-mediated knock-down of SMARCA4 and SMARCA2 in an androgen-sensitive (LNCaP) cell line and in a castration-resistant prostate cancer (CRPC)-adenocarcinoma cell line (22Rv1) and compared global transcriptional alterations using RNA-seq.

  Study EGAS00001004177

• Oesophageal_Adenocarcinoma_Organoid_Hi_C

  Hi-C Sequencing of 6 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 Hi-C data will be combined with other sequencing data in order to generate accurate reference cancer genomes.

  Study EGAS00001003122

• HipSci_Illumina 450K Methylation analysis_Healthy volunteers

  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 Methylation analysis using the Infinium HumanMethylation450 BeadChip on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000865

• Triple_Negative_Breast_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Triple negative 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. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.

  Study EGAS00001000426

• Whole exome DNA sequence profiling of spatial biopsies of high grade serous epithelial ovarian cancer

  The study aims at dissecting the heterogeneity across multiple biopsies of high grade serous epithelial ovarian cancer (HGS-EOC) through a comprehensive characterization of variants and structural changes at the whole exome level. To this aim, the study uses samples from multiple bioptic sites taken from eight HGS-EOC patients.

  Study EGAS00001003048

• Gene expression in brain (Schizophrenia) study

  The study included post-mortem brain tissue samples from 68 schizophrenia patients and 44 age and sex matched control subjects. Whole transcriptome poly-A selected paired-end RNA sequencing was performed on tissue from prefrontal cortex and orbitofrontal cortex. RNA expression differences were detected between case and control individuals, focusing both on single genes and pathways.

  Study EGAS00001004199

• Single-cell RNA-sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We undertook single-cell RNA sequencing to establish gene expression and lymphocyte receptor sequences of CSF and peripheral blood leukocytes derived from patients with a variety of inflammatory, infectious and non-inflammatory neurological disorders. The aim of the study was the investigation of functional changes of the cells involved in neuroinflammatory responses.

  Study EGAS00001007954

• WGS of gastric cancer in the Japanese population (81 gastric cancers of NCC)

  As a contribution to The International Cancer Genome Consortium Accelerating Research in Genomic Oncology (ICGC ARGO), whole-genome sequencing of 81 cases from Japanese gastric cancer with various histological subtypes has been conducted. This study aims to reveal the landscape of structural variants (SV) in gastric cancer and analyze mutational and rearrangement signatures simultaneously

  Study EGAS00001006051

• Childhood Cancer Model Atlas

  we establish a single-site collection of 243 cell lines, including 207 paediatric cancer cell lines representing 14 distinct extracranial and brain childhood tumour types. We subjected 164 paediatric cancer cell lines to multi-omic analyses across three dimensions (DNA-sequencing, RNA-sequencing, DNA methylation) to classify them based on clinically relevant molecular subtypes.

  Study EGAS00001006320

• Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions

  The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD through an in-depth profiling of the sputum metagenome, metabolome, host transcriptome and proteome from 99 COPD patients and 36 healthy individuals in China.

  Study EGAS00001006398