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• Pre_clinical_evolution_of_haematological_malignancies

  Deep targeted sequencing of 291 peripheral blood samples taken 1-20 years prior diagnosis of a haematological malignancy alongside age- and sex-matched controls. Key objective is to distinguish indolent age-related clonal haematopoiesis from pre-cancer and to derive predictive models for early risk-stratification.

  Study EGAS00001002964

• Exome_sequencing_of_patients_with_Ewings_sarcoma_

  Cancer is driven by mutations in the genome. We will uncover the mutations that give rise to Ewing’s sarcoma, a bone tumour that largely affects children. We will use second generation Illumina massively parallel sequencing, and bespoke software, to characterise the genomes and transcriptomes of Ewings’ sarcoma tumours.

  Study EGAS00001000266

• Isotype_resolved_sequencing_of_B_cell_receptor__in_health_and_disease

  Sequencing of B-cell receptor repertoires in healthy individuals and patients with chronic lymphocytic leukemia. 1) 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 please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002634

• RNA sequencing of multiple myeloma identifies genes dysregulated by structural variants.

  Multiple myeloma is a disease of structural changes brought about by copy number abnormalities and translocations. Many of these changes result in super-enhancers being placed next to key oncogenes. Here, we have investigated which genes are commonly dysregulated by these changes.

  Study EGAS00001003411

• Personalized Medicine Based on Genomic Data

  Understanding how an individual's genetics are associated with their susceptibility to complex diseases and phenotypes is fundamental to advancing precision medicine. This study involved a series of integrative analyses of biospecimens and corresponding clinical data. This study aims to comprehensively investigate genotype-phenotype associations.

  Study JGAS000874

• 2014 Lung squamous cell carcinoma WES analysis result

  This data is belong to 2014 Lung squamous patients' exome data which is aligned to human reference(human_g1k_v37.fasta). There are 104 paired tumor/normal samples from SMC. All samples has passed QC and re-calibration steps while aligning to reference.

  Dataset EGAD00001003960

• 2014 sequenced WGS-Lung Cancer sample 30 pair

  This data is belong to WGS-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 30 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003978

• 2018 AML-ETO WGS analysis result

  This data is belong to 2018 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 12 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003912

• 2014 sequenced AML-WGS analysis result

  This data is belong to 2014 AML-WGS patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 10 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003925

• 2016 AML prospective_v1 analysis result

  This data is belong to 2016 AML prospective_v1 patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 5 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003928

• Pheno-seq profiles of single clonal tumor spheroids derived from a patient with colorectal cancer

  Pheno-seq is a new approach that integrates high-throughput imaging and transcriptomic profiling of clonal spheroids/organoids to dissect functional tumor cell heterogeneity in 3D cell culture systems. The method is based on the iCELL8 technology (TakaraBio) that uses barcoded nanowells and a micro-solenoid valve dispenser. The CRC_spheroid dataset contains demultiplexed RNA-sequencing profiles (FASTQ file format, NextSeq 500) of 95 clonal tumor spheroids derived from a patient with colorectal cancer.

  Dataset EGAD00001004131

• Pediatric HGG WES and RNA-Seq

  Paediatric high-grade glioma (pHGG) is the leading cause of paediatric brain tumour death. Here we performed RNA and whole exome sequencing on pHGG samples to analyse transcriptomic and genetic alterations associated with this devastating disease, and to understand the relationship between them.

  Study EGAS00001005687

• Mexican Biobank Project

  In this study, we present the data from the Mexican Biobank Project: 50 WGS from individuals with Native American ancestry, and 6000 genotypes from samples from this project. This project highlights the necessity of better diversity representation in genomic databases is a scientific imperative.

  Study EGAS00001005797

• PROJET DREPANOCYTOSE ET PALUDISME

  The goal is to study and specify the response to treatment against Plasmodium falciparum malaria in subjects with sickle cell disease in order to propose to the National Malaria Control Program of Côte d'Ivoire effective prevention and treatment strategies for this population at risk.

  Study EGAS00001006008

• Synthetic genotypes and phenotypes of 500.000 individuals

  The goal of our study is to establish a pipeline for creating synthetic genotype and phenotype data on a Biobank scale. Such data can be used for developing new methodologies of analysis of common and rare diseases without risking de-identifying the underlying samples.

  Study EGAS00001006552

• Whole-Transcriptomic Profiling of Sorted Human Renal Cell Carcinoma Immune Populations

  It is poorly understood how the tumor immune micro-environment influences disease progression in renal cell carcinoma (RCC). Here we performed whole-transcriptomic profiling of immune cell populations which were derived from RCC patients representing distinct flow-sorted immune lineages.

  Study EGAS00001006593

• WES on tumor DNA and germline DNA in pediatric cancer

  This dataset contains whole exome sequencing (WES) data from tumor DNA samples of various pediatric cancer entities. Files are provided in fastq format. Samples were sequenced on a Novaseq6000 or Hiseq2500 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Study EGAS00001005429

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

  This dataset contains all available targeted exon sequencing bam files from our study, "Activating AKT1 and PIK3CA mutations in metastatic castration-resistant prostate cancer". Patient identifiers are denoted by the first segment of the sample aliases (e.g. "P1"), and additional information is appended to reflect which serial sample is referenced (1st, 2nd, 3rd, etc.), and whether the sample represents cell-free DNA ("cfdna") or paired white-blood cell control ("WBC"). All samples were sequenced using Illumina technology.

  Dataset EGAD00001006122

• Epigenetic, transcriptome and TF analysis of human NK cell and T cells

  RNA-seq 10 subsets; 5 donors. ATAC-seq 9 subsets, 4 donors; Histone modification profiling 10 subsets, 2 donors all using human NK cell and T cell subsets. TF ChIP-seq Bcl11b, Bach2, Runx2, Gata3, PLZF. Illuminia sequencing platform, ATAC-seq is Paired-end, RNA-seq/ChIP-seq is Single-end

  Dataset EGAD00001008449

• Clonal selection after gene therapy in sickle cell disease

  While gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD), the occurrence of myeloid malignancies in clinical trials has prompted concern. To interrogate potential mechanisms underlying increased cancer risk, we used hematopoietic stem cell (HSC) clonal tracking by whole genome sequencing (WGS) to map the somatic mutation and clonal landscape of 2,592 gene modified as well as unmodified single stem and progenitor cells from six SCD patients undergoing gene therapy (7-26 years old, average 12.7× depth). Pre-GT phylogenetic trees in SCD were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified. However, an increased frequency of driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) were seen in both genetically modified and unmodified cells suggested positive selection of mutant clones during gene therapy. This work sheds light on the mutation landscape and HSC clonal dynamics in gene therapy for SCD and highlights enhanced fitness of some HSCs harboring pre-existing driver mutations following gene therapy. Future studies should define the long-term fate of mutant clones including any contribution to expansions associated with myeloid neoplasms.

  Dataset EGAD00001010913

• Exome Sequencing of a family with thrombocytopenia, red cell macrocytosis, and lymphoblastic leukemia predisposition

  A family with a history of bleeding, variable thrombocytopenia, red cell macrocytosis and two cases of pre B-cell acute lymphoblastic leukemia was studied in a single visit. The family was assessed for bleeding history using a bleeding questionnaire. Additionally, complete blood counts were measured and whole blood was collected from five affected individuals and three unaffected individuals for DNA extraction and whole exome sequencing. The goal of this study is to determine the genetic cause of thrombocytopenia, red cell macrocytosis, and predisposition to leukemia in a family. It is hoped that the information obtained from this study will help researchers understand the genetic and molecular basis of platelet and red cell production, as well as leukemia predisposition.

  Study phs000873

• Pharmacogenomics of Metformin Dose Response in T2DM Patients

  Type 2 Diabetes Mellitus (T2DM) is a chronic and sometimes debilitating disease that affects millions of adults in the USA. Metformin is commonly prescribed for T2DM; yet some T2DM patients do not tolerate it or respond well. This pharmacogenomics study will examine response, as both change in T2DM patients' weight and hemoglobin A1c (HbA1c) levels, to different doses of metformin, by extracting this data from the electronic health record (EHR), for T2DM subjects taking metformin found by prescription orders in the EHR, and identified as cases with the EHR phenotype algorithm published by Kho et. al. in 2012 (PMID: 22101970 as part of the eMERGE (electronic Medical Records and Genomics; dbGaP phs000237, phs000297, phs000360, phs000368, phs000888, and phs000948) project.

  Study phs000984

• Integrative Analysis of Tumor Biopsies on Sequential CTLA-4 and PD-1 Blockade Reveals Markers of Response and Resistance

  Blockade of T cell coinhibitory molecules such as CTLA-4 and PD-1, can activate T cell antitumor response. Although these immune checkpoint blockades (CTLA-4 blockade and PD-1 blockade) have shown durable response, response rate is modest. Therefore, there is a need to find stable biomarkers predictive of response to immune checkpoint blockades and to understand underlying resistance mechanisms. We collected longitudinal tumor biopsies from a cohort of metastatic melanoma patients treated with sequential immune checkpoint blockades and performed whole exome sequencing of this cohort. The comprehensive genomic characterization of tumors enabled identification of higher copy number loss burden as a resistance mechanism and clonal T cell repertoire as a predictive biomarker.

  Study phs001425

• Next Generation Mendelian Genetics: Malignant Hyperthermia

  Malignant hyperthermia (MH) is a genetic disorder that causes a profound metabolic derangement following exposure to certain anesthetics. While approximately half of all cases are associated with ryanodine receptor-1 gene (RYR1) mutations, many cases have an unknown genetic cause. We sought to identify rare variants in novel MH candidate genes by sequencing the protein-coding regions of the genomes of individuals whose disease was either ruled in or out by the gold-standard diagnostic test. We also carefully selected individuals from well-characterized families to use gene-sharing information and maximize efficiency in the study design. Exome sequencing has helped identify the causes of over a dozen Mendelian disorders, has high power at low sample sizes, and is cost-efficient compared to whole-genome sequencing.

  Study phs000405

• Early Onset and Progression of Primary Ciliary Dyskinesia Lung Disease Prior to 10 Years of Age

  Primary Ciliary Dyskinesia (PCD) is a genetic defect in airway host-defense, and typically results in chronic infection of the airways. Patients with PCD have chronic lung, sinus and ear infections. This longitudinal study is designed to define the rate of progression of PCD lung function in participants prior to 10 years of age using special lung function tests, which help to track lung impairment and prognosis in other disorders of the airways such as cystic fibrosis. This longitudinal protocol will also systematically track other specific outcomes, including pathogens infecting the airways (assessed by respiratory cultures), and age at onset and progression of airway damage and bronchiectasis [assessed by high-resolution computerized tomography (HRCT) of the chest].

  Study phs001310