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• NIDDK IBD Genetics Consortium Repository Exome Chip

  The Illumina Infinium HumanExome+ BeadChip contains putative functional exonic variants selected from individual exome and whole-genome sequences from diverse populations. It includes nonsynonymous variants, splice variants and stop-altering variants. It also includes tags for previous GWAS-identified loci, ancestry informative markers, markers designed for identity by descent analyses, synonymous variants, fingerprint SNPs common to major genotyping platforms, mitochondrial SNPs, chromosome Y SNPs, and HLA tag SNPs. For more information as well as a detailed description of the variant calling and QC procedures, see Li et al. (2016). Li, D., et al. (2016) A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition. Gastroenterology, 151, 1-9. PMID: 27492617.

  Study phs001723

• Whole-Exome Sequencing and Targeted DNA Sequencing of Matched Ocular Melanocytosis and Uveal Melanoma

  Ocular melanocytosis is the most important predisposing condition for the eye cancer uveal melanoma (UM). Here we used whole-exome and deep targeted sequencing to identify for the first time a clonal Gq pathway mutation in ocular melanocytosis, which gave rise to UM. Additionally, we elucidated the order in which canonical genetic aberrations were acquired during tumor evolution. These findings provide a mechanistic explanation for the well-known clinical association of ocular melanocytosis with UM, and they provide new insights into UM tumor evolution. Reprinted from: Durante MA, Field MG, Sanchez MI, Covington KR, Decatur CL, Dubovy SR, Harbour JW. Genomic evolution of uveal melanoma arising in ocular melanocytosis, with permission from Cold Spring Harbor Molecular Case Studies.

  Study phs001835

• Cergentis FFPE-TLC

  In this study, formalin-fixed paraffin-embedded targeted locus capture (FFPE-TLC) sequencing is used as a novel technology for targeted detection of tumor-specific genomic structural variants (SVs) in the primary tumor of 29 colorectal cancer patients with metastatic disease. The tumor region was macrodissected and sequenced for 29 patients, and the "normal" region of the same slide was macrodissected and sequenced for 8 of these patients. SVs were found in the common fragile site (CFS)-associated genes MACROD2, PRKN, FHIT and WWOX as well as SVs caused by three LINE transposable elements. Tumor-specificity of selected SVs was independently verified by droplet digital PCR of tumor tissue DNA and their applicability as plasma circulating tumor DNA biomarkers was demonstrated.

  Study EGAS50000000427

• Investigation of a method for generating cells for regenerative medicine using comprehensive nucleic acid analysis of iPS cell-derived cardiomyocytes.

  Regenerative medicine for heart failure is expected to restore cardiac function by using human iPS cells (hiPSCs). In our laboratory, it was shown that transplantation of cardiomyocytes (CMs) derived from hiPSCs into a pig model of myocardial infarction improves the disease condition. However, the instability of differentiation efficiency and tumorigenicity after transplantation are still issues to be resolved. We attempt to identify and analyze the genes and DNA methylation associated with the induction of differentiation of hiPSCs into CMs with the aim of achieving stable induction of CMs differentiation. Furthermore, we aim to analyze genes involved in tumorigenesis in CMs, and to develop a predictive marker for tumorigenesis to ensure the safety of cells before transplantation.

  Study JGAS000665

• Bioinformatic Methods and Bridging of Assay Results for Reliable Tumor Mutational Burden Assessment in Non-Small Cell Lung Cancer

  Tumor mutational burden (TMB) has emerged as a predictive biomarker of response to immune checkpoint inhibitors. Standardization of TMB measurement is essential for implementing diagnostic tools to guide treatment. Here we evaluate bioinformatic TMB analysis by whole exome sequencing (WES) in formalin-fixed, paraffin-embedded samples. In CheckMate 026, TMB was retrospectively assessed in 312 patients with non-small cell lung cancer (58% of the intent-to-treat population) who received first-line nivolumab treatment or chemotherapy. We examined the sensitivity of TMB assessment to bioinformatic filtering methods and assessed concordance between TMB data derived by WES and the FoundationOne CDx™ assay. TMB scores comprising synonymous, indel, frameshift, and nonsense mutations (all mutations) were 3.1-fold higher than data including missense mutations only, but values were highly correlated (Spearman’s r = 0.99). Scores from CheckMate 026 samples including missense mutations only were similar to those generated from data in The Cancer Genome Atlas, but those including all mutations were generally higher. Using databases for germline subtraction (instead of matched controls) showed a trend for race-dependent increases in TMB scores. Parameter variation can therefore impact TMB calculations, highlighting the need for standardization. Encouragingly, WES and FoundationOne CDx outputs were highly correlated (Spearman’s r = 0.90) and differences could be accounted for by empirical calibration, suggesting that reliable TMB assessment across assays, platforms and centers is achievable.

  Dataset EGAD00001005035

• Pediatric Non-Down Syndrome Acute Megakaryoblastic Leukemia is Characterized by Distinct Genomic Subsets with Varying Outcomes

  Acute Megakaryoblastic Leukemia (AMKL) is a subtype of acute myeloid leukemia (AML) in which cells morphologically resemble abnormal megakaryoblasts.  While extremely rare in adults, AMKL accounts for 4-15% of newly diagnosed childhood AML1-3.  A significant proportion of pediatric AMKL cases occur in children with Down syndrome (DS).  These patients have excellent outcomes and are characterized at the genomic level by a founding GATA1 mutation4-6.  In contrast, AMKL in patients without DS (non-DS-AMKL) is frequently associated with poor outcomes.  Previous efforts have identified chimeric oncogenes in a significant number of cases, including RBM15-MKL1, CBFA2T3-GLIS2, KMT2A gene rearrangements and NUP98-KDM5A7-9.  The etiology of 30-40% of cases, however, remains unknown.  To better understand the genomic landscape of non-DS-AMKL, we performed RNA and exome sequencing on specimens from 99 patients (75 pediatric and 24 adult).  We demonstrate that pediatric non-DS-AMKL is a heterogeneous malignancy that can be divided into seven subgroups with varying outcomes.  These subgroups are characterized by chimeric oncogenes with cooperating mutations in epigenetic and kinase signaling genes.  Overall, these data shed light on the etiology of AMKL and provide useful information for treatment tailoring. 

  Study EGAS00001002183

• The CCA Genome Core is responsible for archiving the sequencing data generated by the Cancer Centre Amsterdam (CCA).

  Dac EGAC00001000181

• Psoriasis PBMCs

  This DAC is for the purpose of controlling access to Psoriasis PBMC scRNA-seq data of the study Spermidine/spermine N1-acetyltransferase controls tissue-specific regulatory T cell function in chronic inflammation

  Dac EGAC50000000470

• COMET TCRseq raw data

  This is the raw TCRseq data for the manuscript T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases.

  Dataset EGAD00001010269

• PAX4 loss of function increases diabetes risk by altering human pancreatic endocrine cell development

  The coding variant (p.Arg192His) in the transcription factor PAX4 is associated with an altered risk for type 2 diabetes (T2D) in East Asian populations. In mice, Pax4 is essential for beta cell formation but its role on human beta cell development and/or function is unknown. Participants carrying the PAX4 p.His192 allele exhibited decreased pancreatic beta cell function compared to homozygotes for the p.192Arg allele in a cross-sectional study in which we carried out an intravenous glucose tolerance test and an oral glucose tolerance test. In a pedigree of a patient with young onset diabetes, several members carry a newly identified p.Tyr186X allele. In the human beta cell model, EndoC-βH1, PAX4 knockdown led to impaired insulin secretion, reduced total insulin content, and altered hormone gene expression. Deletion of PAX4 in human induced pluripotent stem cell (hiPSC)-derived islet-like cells resulted in derepression of alpha cell gene expression. In vitro differentiation of hiPSCs carrying PAX4 p.His192 and p.X186 risk alleles exhibited increased polyhormonal endocrine cell formation and reduced insulin content that can be reversed with gene correction. Together, we demonstrate the role of PAX4 in human endocrine cell development, beta cell function, and its contribution to T2D-risk.

  Dataset EGAD50000000516

• How are we funded?

  How are we funded? The EGA is provided infrastructure, administrative support, advisory input, and other relevant and necessary aspects by: CRG The EGA at the CRG is funded and supported by “La Caixa Foundation”, The Generalitat de Catalunya (Catalan Government), the Spanish Ministerio de Asuntos Económicos y Transformación Digital (Spanish Government) and the Instituto de Salud Carlos III. The Generalitat de Catalunya contributes with funding to the CRG and to the Barcelona Supercomputing Centre (BSC). The Barcelona Supercomputing Center is decisively contributing to EGA by providing the required compute, storage and networking resources, as well as key personnel for shared operations of EGA infrastructure. EMBL-EBI As part of the European Molecular Biology Laboratory (EMBL), the EGA at EMBL’s European Bioinformatics Institute receives funding from the governments of EMBL’s member states. The UK government, via UK Research and Innovation, also continues to support EMBL-EBI technical infrastructure, with EMBL supporting operational costs. A major source of funding for the EGA both at CRG and EMBL-EBI are competitive projects.The EGA resource continues to be funded through strategic engagement in collaborative partnerships and projects. Please see our projects page for more information. Other funders include the European Commission, the US National Institutes of Health, the Wellcome Trust, UK Research Councils, and our Industry Programme partners. Last updated on October, 2024.

  Documentation about/projects-and-funders/funders

• A National Translational Science Network of Precision-Based Immunotherapy for Primary Liver Cancer (PLC)

  The primary objective of the NCI-CLARITY study is to establish a biospecimen repository for genomic, genetic and epigenetic analysis to study the biology of primary liver cancer (PLC) development and progression. Secondary objectives include predicting overall and progression-free survival following immunotherapy. In the retrospective phase, anonymous archival tissue from PLC patients was obtained from five participating sites. Whole exome and transcriptome sequencing was generated and used to predict overall survival in response to immunotherapy.

  Study phs003074

• TIRE-seq: an Integrated Sample Extraction and Transcriptomics Workflow for High Throughput Perturbation Studies

  TIRE-seq is a novel RNA sequencing method that integrates mRNA purification directly into library preparation, eliminating separate RNA extraction. The technique demonstrated utility across three biological applications, including capturing transcriptional changes in human T cells, identifying genes driving murine dendritic cell differentiation, and analyzing the dose-response effects of temozolomide on patient-derived neurospheres. With its simplified approach and high sequencing efficiency, TIRE-seq offers a cost-effective solution for large-scale gene expression studies.

  Study EGAS50000000867

• ATAC-seq iPSC cells or smNPC cells for allelic imbalance

  In order to confirm the predicted impact of the PD-associated allele of rs144814361 on BAG3 promoter, we proceeded with genome editing of the TH-REP1 cell line by using prime editing to insert the “T” allele at the position chr10:119651405 in the BAG3 promoter. 3 replicates for each condition: 1) iPSC Wild Type 2) SNP-BAG3 variant in iPSC 3) SNP-BAG3 variant in smNPC. Allelic imbalance is further assessed using read counting at this specific position.

  Study EGAS50000001579

• Functional genomics approaches to understand osteoarthritis (2019-08-01)

  The aim of this work is to apply an integrated systems approach to understand the biological underpinnings of large joint (hip and knee) osteoarthritis which culminates in the need for total joint replacement (TJR). We will obtain diseased and non-diseased cartilage as well as other disease-relevant tissue following TJR, coupled with a blood sample. We will generate genotype data and will characterise the pairs of diseased and non-diseased tissue samples in terms of methylation, transcription (RNASeq) and expression (quantitative proteomics). We will apply integrative approaches to combine information across the omics levels to characterise genes, pathways, and networks that underlie osteoarthritis progression. 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 2019-08-01.

  Dataset EGAD00001005215

• Whole_Exome_Sequencing_for_Characterization_of_Disease_Causing_Mutations_in_two_Pakistani_Families_Suffering_from_Autosomal_Recessive_Ocular_Disorders_

  We propose to use whole exome Agilent solutionprobes and paired end Illumina sequencing to sequence 4 individualsfrom two families suffering from novel autosomal recessive disease[microphthalmia, MOP (OMIM %251600) and non-syndromic persistenthyperplastic primary vitreous, PHPV (OMIM %611311)]. Selectedcandidate variants will subsequently be genotyped in the remainingfamily members in Pakistan with the aim of identifying the rarehomozygous recessive mutations responsible for the disease phenotype. 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 EGAS00001000026

• Gene Expression and Epigenetic Analyses of Human Myocytes From Different Muscles

  The study contains expression and DNA methylation data of in vitro cultured myoblasts derived from biopsies of control, FSHD1 and FSHD2 patients from the tibialis anterior, quadricep, bicep and deltoid. Expression data is from bulk RNA-seq using the SmartSeq2 protocol for days 0 and 5 of in vitro differentiation of primary myocytes from the bicep and deltoid of FSHD1 patients. DNA methylation data was produced using the TruSeq Methyl Capture EPIC kit (Illumina) for days 0, 3 and 12 of in vitro differentiation of primary myocytes from the tibialis anterior and quadricep of healthy individuals and FSHD2 patients.

  Study phs002554

• High-Throughput RNA Isoform Sequencing using Programmable cDNA Concatenation

  MAS-ISO-seq is a novel technique for programmably concatenating cDNAs into single molecules for optimal long-read sequencing. In practice, this boosts throughput >15 fold to nearly 40 million cDNA reads per run on the PacBio Sequel IIe sequencer. We have validated this method via application to synthetic RNA isoforms and single-cell sequencing of tumor-infiltrating T cells. Results demonstrated a >30 fold boosted discovery of differentially spliced genes and robust cell clustering, as well as canonical PTPRC splicing patterns across T cell subpopulations and the concerted expression of the associated hnRNPLL splicing factor.

  Study phs003200

• Maternal Plasma Folate and DNA Methylation in Epigenome-Wide Meta-Analysis of Newborns

  Folic acid is routinely recommended for women trying to conceive to ensure proper fetal development. Mechanisms whereby periconceptional folate influences normal development and disease are poorly understood: epigenetics may be involved. This data represents meta-analysis results from a large epigenomics study to examine the association between maternal plasma folate during pregnancy and epigenome-wide DNA methylation using Illumina's HumanMethyl450 (450K) Beadchip in 1,996 newborns from two European cohorts. Results for all CpGs analyzed (419,905) are provided. These data may be downloaded through the dbGaP Authorized Access portal under phg000701.v1.

  Study phs001059

• NHLBI TOPMed: Diabetes Heart Study (DHS) African American Coronary Artery Calcification (AA CAC)

  The Diabetes Heart Study (DHS) is a family-based study enriched for type 2 diabetes (T2D). The cohort included 1443 European American and African American participants from 564 families with multiple cases of type 2 diabetes (Bowden et al., 2010. Review of Diabetic Studies 7:188-201. PMID: 21409311). The cohort was recruited between 1998 and 2006. Participants were extensively phenotyped for measures of subclinical CVD and other known CVD risk factors. Primary outcomes were quantified burden of vascular calcified plaque in the coronary artery, carotid artery, and abdominal aorta all determined from non-contrast computed tomography scans.

  Study phs001412

• NSD2 E1099K Drives Relapse in Pediatric Acute Lymphoblastic Leukemia by Disrupting 3D Chromatin Organization

  NSD2 p.E1099K (EK) is a mutation shown to be enriched in patients that relapse with pediatric Acute Lymphoblastic Leukemia (ALL). This work aims to uncover 3D chromatin architecture-related mechanisms responsible for drug resistance or therapy failure in these patients. We investigated this by performing Hi-C, ATAC-Seq, and RNA-Seq on three B-ALL cell lines heterozygous for EK either expressing a NSD2 targeting small RNA (sRNA) or a non-targeting small hairpin RNAs (shRNA). We also performed RNA-Seq on three matched diagnosis/relapse B-ALL samples with the relapse enriched EK mutation.

  Study phs003195

• Combined Targeting of CDK4/6 and HER2 Signaling in Orthotopic Patient-Derived Xenografts of HER2-Positive Breast Cancer Brain Metastases

  Patients with metastatic HER2-positive (HER2+) breast cancer will frequently develop brain metastases (BCBMs). Here, we report that p16INK4A, a tumor suppressor, is deficient in the majority of HER2+ BCBMs. Furthermore, p16INK4A deficiency, as measured by protein immunohistochemistry, can be a predictive marker associated with response to combined treatment with tucatinib and abemaciclib in our orthotopic patient-derived xenografts (PDXs) models of HER2+ BCBMs. Our findings provide the rationale for a biomarker-driven clinical trial of combined treatment with CDK4/6- and HER2-targeted agents for patients with HER2+ BCBM.  

  Study phs002482

• RNA-seq data of bone marrow CD34-positive cells from 57 patients with myelodysplastic syndromes (MDS) and 5 healthy individuals (62 participants in total)

  Genetic mutations in hematopoietic neoplasms, seen in disease-specific and non-specific ways, are key drivers in pathogenesis. Typically, these mutations alone don't cause neoplasms; rather, multiple mutations or breakdowns in regulatory mechanisms occur, progressing the disease through stages. Genetic mutation patterns vary even within subtypes, suggesting shared gene expression abnormalities from different mutations may drive neoplasm development. Identifying these "common factors" is vital for effective molecular-targeted therapy development. Our study aims to elucidate neoplasm pathogenesis by analyzing patient genetic abnormalities, pinpointing "common factors" in each subtype for novel targeted therapy development.

  Study JGAS000724

• Bleomycin Induced Pneumonitis cohort of the Exceptional Responders Program of the Garvan Institute of Medical Research

  Bleomycin is a cytotoxic antibiotic and forms a key component of the curative-intent chemotherapy regimens for germ cell tumours (GCT) and lymphoma. However, the drug can be associated with a range of lung toxicity, including idiosyncratic inflammation termed bleomycin induced pneumonitis (BIP), which can lead to irreversible interstitial fibrosis and death. This study aims to identify germline genomic changes associated with BIP in patients receiving bleomycin as treatment for GCT or lymphoma, who develop clinically significant BIP despite low predicted risk based on absence of traditional risk factors.

  Study EGAS50000001545

• COMPARE study: participants typed during UK Biobank version 2 array development phase

  The COMPARE study enrolled 29,066 British blood between donors between February 2016 and March 2017, the study aim is to find the optimum technology for haemoglobin screening (ISRCTN 90871183). All participants were at the time of recruitment active blood donors. The 4,796 participants in this dataset have consented to join the NIHR BioResource. Genotyping data was produced using the Thermo Fisher Scientific Axiom Genotyping platform. The UK Biobank version 2 array design was used, content on this array has been added to allow for accurate DNA based identification of human blood group antigens.

  Study EGAS00001003748

• Exploring_the_heterogeneity_of_sarcoma_using_single_cell_sequencing_

  Multi region samples are collected from patients, with consent, immediately after resection of the tumour. Samples are digested and sorted using FACS as single cells into lysis buffer. Cells are then stored until further processing for G&T-seq. After sequencing, we will explore intra-tumour heterogeneity using computational approaches to integrate RNA and DNA data onto the tumour phylogeny 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 EGAS00001002866

• scRNAseq and scATACseq of placebo controlled-trial on MMR non-specific effects

  The project includes sequencing data of isolated PBMCs extracted from donors that received the MMR vaccine and donors that received placebo, both containg samples before and after the vaccine. In total, 6 MMR-vaccinated and 6 Placebo donors for both timepoints were included in the scRNAseq data. In total, 12 MMR-vaccinated and 12 Placebo donors for both timepoints were included in the scATACseq data. The main goal of the project is studying the non-specific effects of the vaccine and its possible use as an inducer of trained immunity in vivo.

  Study EGAS00001006787

• ICARUS-BREAST01-RNAseq

  Efficacy, safety and biomarker analysis of ICARUS-BREAST01: a phase 2 Study of Patritumab Deruxtecan in patients with HR+/HER2- advanced breast cancer. RNA-squencing is available for 44 samples comprising 22 samples collected at entry into the trial and 22 samples collected during treatment (cycle 1 day 3, cycle 1 day 19, or cycle 2 day 3) from 22 patients.

  Study EGAS50000000543

• Longread sequencing of selected 12q-amplified osteosarcomas

  Longread sequencing of selected 12q-amplified osteosarcomas for verification of SV data. This was carried out in order to verify findings from mate-pair sequencing regarding the structure of the chromosome 12q-amplicons and whether material from other chromosomes is also intertwined and amplified in a bid to further characterise these tumours beyond CDK4 and MDM2 amplification.

  Study EGAS50000000495

• DAC-2023-07-05-Ritz (DAC-007) - Diagnosis of tuberculosis infection in children with a novel skin test and the traditional tuberculin skin test: an observational study

  Diagnosis of tuberculosis infection in children with a novel skin test and the traditional tuberculin skin test: an observational study This is only the location for the raw data and any check if the dataset may be relevant please refer to the MF-DAC Zenodo community (https://zenodo.org/records/11237107).

  Study EGAS50000000780

• Targeted pancancer RNA-Seq

  This dataset contains targeted RNA-Seq generated with the Illumina RNA Pan-Cancer panel. It comprises 2200 cancers from children and adults. The cancers represent a wide range of CNS, solid and haematopoeitic tumours. Samples are from pathology specimens including FFPE, fresh frozen, bone marrow aspirate and peripheral blood.The data is used for tumour driver identification. SNVs, indels and fusion detection.

  Study EGAS50000000700

• Systematic identification of long non-coding RNAs potentially involved in gastrointestinal carncer

  Recent work has suggested various important functions and molecular mechanisms for long non-coding RNAs (lncRNAs) and they are also thought to play critical roles in cancer. However the importance of lncRNAs in cancer biology is still unclear. In this study, we aim to comprehensively identify novel lncRNAs that are critically involved in tumorigenesis and progression in gastrointestinal cancer.

  Study JGAS000011

• Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study

  This is a case-control study in which differences in the gut microbiome of patients with bipolar disorder and schizophrenia spectrum disorders were assessed. The study contains the samples in this dataset, except for G002, G025, G041, G093, G106, G107, G120 and G123. These samples were not yet available at the time the study was performed.

  Study EGAS50000000969

• RNA-seq data of proliferative vitreoretinal diseases and healthy human retinal pigment epithelium

  This Data Access Committee (DAC) evaluates access requests for RNA-seq data generated from: - Membranes from proliferative vitreoretinal diseases, including proliferative vitreoretinopathy and epiretinal membranes. - Retinal pigment epithelial cells isolated from healthy ocular globes obtained from deceased donors. Collection and analysis of these residual human materials were conducted with the approval of the ULB-Erasme Ethical Committee (P2019/066 A2022/136) and of the Eye Bank (CHU Liège), with no need for informed consent in compliance with Belgian law. All data are pseudonymised, and access is restricted to qualified researchers whose proposed use of the data is consistent with the applicable ethical approval and legal requirements, including the General Data Protection Regulation (GDPR).

  Dac EGAC50000000721

• Whole genome sequencing data of paediatric ETV6::RUNX1 acute lymphoblastic leukemia

  ETV6::RUNX1 (E::R) subgroup is the second most frequent form of B cell acute lymphoblastic leukemia (B-ALL) in childhood. This subgroup of ALL generally presents with low-risk features and responds well to chemotherapy with ensuing favorable prognosis. Some patients, however, have a slow response to induction treatment and carry increased risk for relapse.

  Study EGAS50000001599

• Sputum bacterial microbiota in an overall healthy population in Guangdong province, China

  This repository contains raw sequencing data for sputum fungal microbiota in an overall healthy population in Guangdong province, China. The aim of the study is to provide a comprehensive insight on the multi-kingdom airway microbiome, how it may underlie the interplay between exposure and healthy outcomes, and whether it can be employed to inform airway health and diseases.

  Study EGAS00001006721

• Sputum fungal microbiota in an overall healthy population in Guangdong province, China

  This repository contains raw sequencing data for sputum fungal microbiota in an overall healthy population in Guangdong province, China. The aim of the study is to provide a comprehensive insight on the multi-kingdom airway microbiome, how it may underlie the interplay between exposure and healthy outcomes, and whether it can be employed to inform airway health and diseases.

  Study EGAS00001006720

• ICGC_Benchmarking_Exercise

  The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark.

  Study EGAS00001000433

• Investigating_the_impact_of_MBD4_on_the_mutability_of_the_germline

  We will be testing the hypothesis that MBD4 PTV germline carriers also show an increased number of C toT germline mutations in their offspring. 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 EGAS00001002861

• Whole Exome Sequencing of High grade T1 non-muscle invasive bladder cancer

  High-grade T1 (HGT1) bladder cancer (BC) is the highest risk subtype of non-muscle-invasive BC with unpredictable outcome and poorly understood risk factors. Here we performed whole exome sequencing across 61 HGT1 samples to identify genomic predictors of good outcome, recurrence or progression. This study includes somatic mutation calls and clinical data for 61 HGT1 tumors.

  Study EGAS00001004603

• Gene_Characterization_in_Carbohydrate_metabolic_alterations__neonatel_diabetes___congenital_hyperinsulinemic__in_early_childhood

  Whole Exome Sequencing of trios (proband + parents) or probands only with Neonatal Diabetes Mellitus (NDM) or Congenital Hyperinsulinism of Infancy (CHI) of unknown genetic origin. 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 EGAS00001002074

• Chronic myelomonocytic leukemia

  Chronic myelomonocytic leukemia is an aggressive hematological malignancy with dismal outcomes, with the pCMML subtype in particular having median OS of <2 years and high rates of AML transformation (Patnaik et al., 2014). Given limited therapeutic options for affected patients, we carried out this study to define the genetic and epigenetic landscape of pCMML and identify therapies that could modify disease biology.

  Study EGAS00001005107

• Multiple esclerosis and mixed microbial infections

  This Project deals with the sequencing of ITS1 region, which is highly variable both in length and in nucleotide sequence for different yeast using yeast-specific primers ITS1 and ITS2. A total of 19 samples involving different brain regions from patients with different conditions were analysed. Of these, 10 are controls-healthy patients and 9 multiple sclerosis (MS) patients.

  Study EGAS00001002957

• Next Generation Children project - WGS study of patients in NICU and PICU and their families

  With growing evidence that rare single gene disorders present in the neonatal period, there is a need for rapid, systematic, and comprehensive genomic diagnoses in ICUs to assist acute and long-term clinical decisions. This study aimed to identify genetic conditions in neonatal (NICU) and paediatric (PICU) intensive care populations. Whole genome sequencing data.

  Study EGAS00001003002

• Analysis of exonic somatic variants in light-chain amyloidosis (ALA) and ALA concomitant with multiple myeloma

  We aim to provide the very first insight into ALA+MM molecular profiles and compare the results with ALA and with MM. Our detailed study of ALA and ALA+MM represents an important step towards improved understanding of their genetic and transcriptomic background, which is a prerequisite for development of optimal treatment strategies in the future.

  Study EGAS00001004214

• whole-genome sequencing of gastric cancer

  Gastric cancer is one of the most common cancers. Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer tumorigenesis. Here, we analyzed structural variations and mutational signatures via whole-genome sequencing of 168 gastric cancer samples. Our data demonstrates diverse models of complex structural variations operative in GC, which lead to high-level amplification of oncogenes.

  Study EGAS00001003512

• Targeted_sequencing_of_blood_DNA_from_Human_twins (2019-05-31)

  The goals of this study is to investigate the prevalence and heritability of age-related clonal haemopoeisis (ARCH) in healthy elderly individuals.We will use a bespoke bait set to pull down DNA regions of interest in whole blood samples combined with HiSeq at a deep level . By correlating findings from each individual to their respective twin we hope to elucidate whether heritable traits influence the development of ARCH. a. 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 2019-05-31.

  Dataset EGAD00001005055

• Preeclampsia InterPregGen Consortium: Whole Genome Sequencing of 100 unrelated Kazakhs (DNA samples from the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan; Gulnara Svyatova, Principal Investigator

  Whole genome sequencing of 100 unrelated Kazakhs in order to impute genotypes into PE cases and controls from Kazakhstan and to provide genetic data and infrastructure for future genetic studies in Kazakhstan and Central Asia more generally and to fill a gap in worldwide information as Central Asia is not adequately represented in available genomic data. This dataset is one component of the InterPregGen FP7 project. DNA samples for this component were collected by InterPregGen Consortium collaborators at the Scientific Center of Obstetrics, Gynecology and Perinatology, Almaty, Kazakhstan (Gulnara Svyatova, Principal Investigator)

  Dataset EGAD00001005467

• Identification of drug resistance genes in melanoma

  Our aim is to analyze the genome of human melanoma cell lines and short term culture from human melanoma samples in order to identify genes that confer drug resistance to clinically relevant targeted therapies. We will perform whole-exome sequencing, copy number variation analysis and methylome analysis in a collection of human melanoma cell lines and short term culture that will be then screened for drug sensitivity/resistance through a library of clinically relevant drugs and drug combinations. By the combined analysis of the genomic lesion and the drug sensitivity/resistance profile of different cell lines, we will look for genes whose mutation is associated to the sensitivity or resistance to a specific drug in different samples.

  Dataset EGAD00001001124

• Genetic Factors associated with Conversion from Active Surveillance to Treatment for Prostate Cancer

  This is a genome-wide association study (GWAS) of conversion from active surveillance (AS) for prostate cancer (PC) to treatment. AS is the monitoring with screening tests and/or biopsies over time of men usually with low-risk, early-stage PC to avoid harmful side effects of PC treatment. "Conversion" refers to patients who withdraw from AS (switch to active treatment) due to changes in their cancer development, anxiety about delayed treatment, or other reasons. Patients who converted because of anxiety alone were censored in the GWAS analysis. The overall goal of this study is to develop an easily measurable, germline-based panel of genetic variants to aid in selecting PC patients appropriate for AS and/or the intensity of monitoring. In total, 6,324 PC patients from 28 collaborating institutions are included in this study. Patients are those with PC who are either on AS or who have previously converted from AS to treatment. In this study, 70% of all subjects were diagnosed with very low-risk, low-risk, or low-volume intermediate-risk PC (Kryvenko and Epstein, 2016; PMID: 26709152) and have been enrolled in an AS program. DNA was extracted from blood, saliva, or formalin-fixed, paraffin-embedded (FFPE) tissue collected from the study subjects at the participating sites. Genotyping, quality control processes, and imputation were performed at the Center for Inherited Disease Research (CIDR) at Johns Hopkins University. CIDR used the Illumina Infinium Multi-Ethnic Global Array (MEGA) version 1, which included genome-wide tag SNPs and 10,000 SNPs selected with custom content. Quality control and assurance (QC/QA) checks on genotyped data involved four domains: sample-level checks, batch effects, SNP-level checks, and preliminary association tests. Samples and SNPs passing the QC/QA checks were imputed to appropriate reference panels (HRC r1.1 for patients of European ancestry) using the Michigan Imputation Server (PMID: 27571263). Unmeasured genetic variants were imputed using the Trans-Omics for Precision Medicine (TOPMed) Imputation Server, with 97,256 reference samples and 308,107,085 SNPs. Variants with imputation quality (INFO) score < 0.3 were excluded, leaving a total of 22,691,641 SNPs successfully imputed. After QC steps, a total of 5,936 samples genotyped at CIDR remained for inclusion in the GWAS.

  Study phs002056