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• Rapid response of APC/TP53/KRAS mutated stage IV colorectal cancer under FOLFIRI + Bevacizumab detected by liquid biopsy: a case report

  In our non-interventional liquid biopsy study, a male patient in his fifties diagnosed with stage IV colorectal cancer and polytope liver metastases rapidly progressed after completing chemotherapy and deceased 8 months after diagnosis. Retrospective cell free DNA testing showed that the APC/TP53/KRAS major clone responded quickly after 3 cycles of FOLFIRI + Bevacizumab. Retrospective exome sequencing of pre-chemotherapy and post-chemotherapy tissue samples including metastases confirmed that the APC/TP53/KRAS and other major clonal mutations (GPR50, SLC5A, ZIC3, SF3A1 and others) were present in all samples. After the last chemotherapy cycle,

  Study EGAS00001004088

• SCLC tumor sequencing

  In this study we have sequenced the tumor of 28 Small Cell Lung Cancer patients.

  Study EGAS00001003985

• Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients

  Dataset EGAD00001001421

• Atypical teratoid/rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities

  Atypical teratoid/rhabdoid tumors (ATRTs) represent a rare, but aggressive pediatric brain tumor entity. They are genetically defined by mutations in SWI/SNF chromatin remodeling complex members SMARCB1 or SMARCA4. ATRTs can be subdivided in different molecular subgroups based on their epigenetic profiles. Although recent studies suggest that the different subgroups have distinct clinical features, subgroup-specific treatment regimens have not been developed thus far. This is hampered by the lack of pre-clinical in vitro models representative of the different molecular subgroups. Here, we describe the establishment of ATRT tumoroid models from the ATRT-MYC and ATRT-SHH subgroups. We demonstrate that ATRT tumoroids retain subtype-specific epigenetic and gene expression profiles. High throughput drug screens on our ATRT tumoroids revealed distinct drug sensitivities between and within ATRT subgroups. Our ATRT tumoroids represent the first pediatric brain tumor organoid model, providing representative pre-clinical models allowing for the development of subtype-specific therapies.

  Study EGAS00001006422

• Rare germline variants of acute myeloid leukemia patients

  The dataset (vcf files) consists of rare germline variants of 68 Finnish acute myeloid leukemia patients. We performed exome sequencing and filtered the germline variants against ExAC total MAF<0.01 in two gene panels. The 35 genes in the panels studied here have previously been associated with hematological malignancies and/or solid tumors. The dataset contains only variants of the two gene panels.

  Dataset EGAD00001003894

• shallow Whole-Genome sequencing of 14 TNBC tumor in the MATADOR trial - for in silico spike-in experiment

  14 TNBC tumors with tumor percentage ~90% were selected for in silico spike-in experiment

  Dataset EGAD50000001863

• Dataset to study clonal evolution in TCF3:PBX1 patient SJE2A066 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJE2A066 with 69 high quality cells sequenced (62 blast and 7 normal)

  Dataset EGAD00001011329

• single cell RNASEQ files for Mullighan BiTE RNASEQ3

  single cell RNASEQ files for Mullighan BiTE RNASEQ3 paper titled "Tumor intrinsic and extrinsic mechanisms of response and resistance to blinatumomab in relapsed/refractory acute lymphoblastic leukemia"

  Dataset EGAD00001005733

• Dataset to study clonal evolution in TCF3:PBX1 patient SJE2A063 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJE2A063 with 80 high quality cells sequenced (75 blast and 5 normal)

  Dataset EGAD00001011328

• Dataset to study clonal evolution in TCF3:PBX1 patient SJE2A067 using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJE2A067 with 78 high quality cells sequenced (73 blast and 5 normal)

  Dataset EGAD00001011330

• Dataset to study clonal evolution in iAMP21 patient SJBALL030072using scWGS-seq

  scWGS-seq of flow sorted blast and normal cells from SJBALL030072with 66 high quality cells sequenced (61 blast and 5 normal)

  Dataset EGAD00001010288

• EBV-AID project

  Whole genome sequencing of EBV-transformed B cells in order to determine whether EBV induction of activation-induced cytidine deaminase (AID) produces genome-wide mutations and/or chromosomal rearrangements.

  Dataset EGAD00001001458

• Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer

  Dataset consists of 216 samples, with each sample having a BAM, BAI and VCF file.

  Dataset EGAD00001011297

• Novel manifestations of immune dysregulation and granule defects in gray platelet syndrome

  Gray Platelet Syndrome (GPS) is a rare recessive bleeding disorder resulting from biallelic variants in NBEAL2. As part of a comprehensive evaluation of the phenotype and genotype in 47 patients with GPS, four different blood cell-types (platelets, neutrophils, monocytes, and CD4-lymphocytes) were evaluated using bulk RNA-seq in five patients and five controls. These data are deposited in this archive in FASTQ format.

  Study EGAS00001004216

• Bulk-mRNA sequencing comparing hiPSC derived vascular cells from CADASIL patient lines

  CADASIL is a hereditary brain small vessel disease caused by pathogenic variants in the NOTCH3 gene and causes degenration of Vascular Smooth Muscle cells in the brain. We performed bulk-mRNA sequencing and transcriptomic analysis from hiPSC derived vascular cells (hiPSC;Endothelial Cells; Neural Crest Cells; Vascular Smooth Muscle Cells) comparing CADASIL patient lines and respective isogenic-controls.

  Study EGAS50000001507

• Targetable NOTCH1 rearrangements in reninoma - RNA

  Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

  Dataset EGAD00001010889

• Targetable NOTCH1 rearrangements in reninoma

  Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assessed somatic changes in reninoma and found structural variants that generate canonical activating rearrangements of NOTCH1, whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observed excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

  Dataset EGAD00001010887

• Breast cancer topographs

  Whole genome sequencing to identify subclonal variants for subsequent mapping back to fixed tissue specimens. . This dataset contains all the data available for this study on 2023-03-09.

  Dataset EGAD00001010124

• Adoptive Cell Therapy of Autologous T cell Receptor-Engineered T Cells Targeting the p53 Neoantigens in Human Solid Tumors

  Adoptive T cell therapy (ACT) using T cell receptor (TCR)-engineered T cells can mediate regression of advanced human cancers. How TCR-transduced T cells change post-ACT in vivo is currently not well understood. We screened 78 patients for TP53 mutations by whole exome sequencing and whole transcriptome sequencing. Of the 78 patient samples, 49 patient samples were previously reported (phs001003) and 2 additional patients were reported in phs002735. In this accession we report the sequencing data of remaining 23 patients and include 6 additional samples from previously published patients. Additionally, we treated a patient with chemo-refractory breast cancer that expressed mutant p53 R175H with autologous T cells transduced with an allogeneic TCR targeting p53 R175H with human leukocyte antigen (HLA) restriction of A*02. The patient had a partial response for 6 months with 55% tumor regression. The T cells from the infusion product and the peripheral blood T cells at 6 weeks post-ACT were analyzed using 10X single cell transcriptome analysis.

  Study phs002928

• Characterizing the immune and genome landscapes for osteosarcoma

  Osteosarcoma have heavily rearranged genomes and moderate tumor mutation burden, which suggests that the patients may express neoantigens that could be targeted by immune cells. To characterize the immunogenomic landscape of this disease, we performed genome, transcriptome, immune and proteomic profiling of 48 patients comprised largely of relapsed and metastatic cases from both pediatric and adult patients.

  Study EGAS00001003247

• RNA-seq data from 27 glioblastoma samples

  27 Fresh frozen tissue specimens were crushed by mortar and pestle, homogenized using the QIAShredder kit (Qiagen), and genomic DNA and total RNA were extracted using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer’s instructions. RNA libraries were synthesized using 200 ng of total RNA using the Ilumina TruSeq Stranded RNA LT Sample Prep Kit (Illumina), and subsequently sequenced on the NextSeq550 platform to a read depth of 80 million clusters and 160 million paired end reads (75 bp X 75 bp) using V2 chemistry.

  Dataset EGAD00001008362

• Single cell sequencing of human normal luminal cells

  The dataset includes 12 paired FASTQ files (6 samples) with single cell transcriptome sequencing data of normal breast luminal cells from ducts and TDLUs derived from reduction mammoplasties from three patients. Chromium Single Cell 3’ Reagent Kit v2 or v3 (10x Genomics) were used for processing of cells, whereafter sequencing was performed using the Illumina® NextSeq500/550 High Output Kit v2. Cell Ranger was used for generating FASTQ files and files from different lanes were concatenated prior to uploading the data to EGA. "R1" files include the feature barcodes and UMIs, while "R2" files include the reads.

  Dataset EGAD00001008499

• BLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples

  BLLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001001596

• Bleomycin Induced Pneumonitis cohort of Exceptional Responders Program

  This DAC handles access to data from the Bleomycin Induced Pneumonitis cohort of the Exceptional Responders Program of the Garvan Institute of Medical Research (https://www.garvan.org.au/research/collaboration/exceptional-responders-program)

  Dac EGAC50000000791

• Liver Tumours WGS (2020-02-20)

  The aim of this study is to define the mutational landscape of human liver tumours. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005993

• Gene copy number variation in pediatric mental illness in a general population

  We assessed the relationship of gene copy number variation (CNV) in mental health/neurodevelopmental traits and diagnoses, physical health, and cognitive biomarkers in a community sample of 7,100 unrelated European, and East Asian children and youth (Spit for Science). Diagnoses of mental health disorders were found in 17.5% of participants and 27.6% scored in the highest 10% on either or both ADHD and OCD trait measures. Clinically relevant CNVs were present in 3.9% of participants and were associated with elevated scores on a continuous measure of ADHD (p=5.0×10-3), on a cognitive biomarker of mental health (response inhibition (p=1.0×10-2)), and on prevalence of mental disorders (p=1.9×10-6, odds ratio: 3.09). With a rise of mental illness, our data establishes a baseline for delineating genetic contributors in paediatric-onset conditions.

  Study EGAS00001006659

• Improved T Cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer

  This study characterized the evolution of the peripheral immune cell function and composition across the course of standard of care platinum and taxane chemotherapy in ovarian cancer using bulk and single cell transcriptomic approaches. Serial blood samples were collected from ten patients with advanced high-grade serous ovarian cancer treated with chemotherapy. Single cell sequencing was performed on five patients' samples collected before the initiation of chemotherapy and after the third cycle of chemotherapy.

  Study phs002862

• Copy-number signatures and mutational processes in ovarian carcinoma

  This study contains the data underlying our approach for copy-number signature identification in high-grade serous ovarian cancer. The samples studied are part of the BriTROC-1 consortium, a national study into relapsed high-grade serous ovarian cancer. The dataset consists of shallow-whole genome sequencing of 300 samples from 143 patients with match tagged-amplicon sequencing of TP53. The study also contains deeper whole-genome sequencing of 48 cases.

  Study EGAS00001002557

• Immune Checkpoint Blockade for Relapsed Hematologic Malignancy Post-HSCT

  Relapse after allogeneic hematopoietic stem cell transplantation (HSCT) is characterized by poor outcomes and novel therapeutic options are urgently needed. Immune checkpoint blockade using CTLA-4 and PD-1 blocking antibodies are a potential concept for reinstating a dormant graft-versus-leukemia (Gvl) effect. This study investigated transcriptomic changes in biopsies obtained from patients who received immune checkpoint blockade for relapsed hematologic malignancy post-HSCT and elucidated transcriptional programs associated with successful reinvigoration of GvL. Differential gene expression analysis showed evidence of increased T cell infiltration in biopsies of responders to ipilimumab treatment and demonstrated shared gene programs between GvL and GvHD.

  Study phs003291

• CONSERTING: integrating copy number analysis with structural variation detection

  We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection to achieve high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. This study contains all data for "CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data", which was previously split between EGAS00001001202 and EGAS00001001050.

  Study EGAS00001001202

• IMMUcan Lung NSCLC2 cohort

  The goal of IMMUcan is to understand how the immune system interacts with tumors and how therapeutic interventions influence this interaction. This cohort includes patients with non-small cell lung cancer who had surgical resection. This is a subcohort of the EORTC SPECTAlung study. Comprehensive profiling data are integrated with longitudinally collected clinical information. Cellular profiling of the same tumor samples was performed using multiplex immunofluorescence imaging, imaging mass cytometry, and H&E staining.

  Study EGAS50000001558

• Single cell RNA and ATAC sequencing data from GBM patients

  Glioblastoma cells infiltrate and incorporate into the normal brain parenchyma. We conduct unbiased multimodal single-cell and spatial sequencing to capture GBM cells and the surrounding tumor microenvironment using a regional sampling strategy. For each patient, we profile the peritumoral region, tumor edge, and tumor core, providing a comprehensive characterization of the transcriptional and epigenetic landscape of GBM spatial heterogeneity, with a specific focus on infiltrative cells.

  Study EGAS50000000547

• WGBS analysis corresponding to representative cases of iBCP-ALL patients

  This dataset was conceived to characterize the epigenomic landscape of representative iBCP-ALL subtypes. To do so, we performed Whole Genome DNA bisulfite-sequencing on 2 MLL-AF4, 2 MLL-AF9 and 2 non-MLL rearranged leukemias, and also 2 pools of BCPs obtained from fetal liver.

  Dataset EGAD00001005010

• ALK inhibitors in the context of ALK-dependent cancer cell lines

  ALK inhibitors in the context of ALK-dependent cancer cell lines

  Dataset EGAD00001000078

• The landscape of cancer genes and mutational processes in breast cancer

  The landscape of cancer genes and mutational processes in breast cancer

  Dataset EGAD00001000133

• 15x_WGS_HELIC_MANOLIS_

  15x whole genome sequencing in samples from the Cretan Greek isolate collection HELIC MANOLIS

  Study EGAS00001001207

• WGBS data set used in the study, 96 samples

  WGBS data set used in the study, 96 samples

  Dataset EGAD00001007968

• Dutch - BP

  The dataset encompasses 1110 Runs from the WGSPD Project 3 - Genomic Strategies to Identify High-impact Psychiatric Risk Variants Project

  Dataset EGAD50000001738

• Dutch - SCZ

  The dataset encompasses 804 Runs from the WGSPD Project 3 - Genomic Strategies to Identify High-impact Psychiatric Risk Variants Project

  Dataset EGAD50000001739

• SARS-CoV-2 induced alterations of the upper airway DNA methylome exert long-term impacts on ciliary genes involved in ciliary function

  Enzymatic DNA methylome (n=33) and single-cell RNA (n=24) sequencing were performed in nasal cells of COVID-19 patients and controls. In addition, we re-sampled a subset of patients for transcriptome analyses at 3 and 12 months post-infection and followed the expression of differentially regulated genes over time.

  Study EGAS50000000273

• CIAO Clinical Trial

  Whole exome and RNA sequencing for samples from CIAO (Checkpoint Inhibitors Assessment in Oropharynx cancer) (NCT03144778) clinical trial testing neoadjuvant anti-PD-L1 durvalumab with or without the anti-CTLA-4 tremelimumab in oropharynx cancer

  Study EGAS50000001174

• Genetic and expression landscape of Waldenstrom macroglobulinemia

  Exome analyses for the identification of somatic mutation in Waldenstrom macroglobulinemia by comparison of tumor and CD3+(germ line control) population in 16 patients. transcription profiling of a series of Waldenstrom macroglobulinemia samples

  Study EGAS00001003603

• Single-nucleus ATAC sequencing of the human motor cortex

  Single-nucleus ATAC-sequencing of the human motor cortex in patients with ALS, C9ORF72-ALS-FTD, ALS-FTD and unaffected controls.

  Study EGAS50000001563

• Single-nucleus transcriptome sequencing of the human motor cortex

  Single-nucleus RNA-sequencing of the human motor cortex in patients with ALS, C9ORF72-ALS-FTD, ALS-FTD and unaffected controls.

  Study EGAS50000001562

• The evolutionary dynamics of human colorectal cancer using single-gland spatial multi-omic profiling of DNA, RNA and chromatin.

  Deciphering the mechanisms of colorectal cancer growth, progression and dissemination in each individual patient.

  Study EGAS00001005230

• MBL2 genetic variation in critical Covid-19

  The data set includes MBL2 genotypes and clinical phenotypes of a cohort of patients with critical Covid-19. The files included in the data set include a vcf file with single nucleotide variants, and a file with clinical phenotypes.

  Dataset EGAD00001008771

• Multi-omic analysis of SDHB-related PCPG

  Hereditary SDHB-mutant pheochromocytomas (PC) and paragangliomas (PG) are rare tumours with a high propensity to metastasize although their clinical behaviour is unpredictable. To characterize the genomic landscape of these tumours and identify metastasis biomarkers, we performed multi-omic analysis on 94 tumours from 79 patients using six molecular methods including: whole-genome sequencing (WGS) of tumour and matched blood (n=94), whole transcriptome sequencing (RNA-seq) (n=91), small-RNA seq (n=90), DNA methylation profiling (n=93). Droplet-based (10x) single nuclei (sn)RNA-seq and snATAC-seq was applied to 9 and 7 cases, respectively. Additionally snATAC-seq was applied to one sample of normal adrenal medulla.

  Study EGAS50000000346

• Integrative Profiling of T790M Negative EGFR Mutated NSCLC Reveals Pervasive Lineage Transition and Therapeutic Opportunities

  We performed whole exome and transcriptome analysis of 59 first- and second-generation EGFR TKI resistant metastatic EGFR mutated patients to characterize and compare molecular alterations mediating resistance in T790M positive and negative disease. Transcriptomic analysis revealed ubiquitous loss of adenocarcinoma lineage gene expression in T790M negative tumors, orthogonally validated using multiplex immunohistochemistry. There was enrichment of genomic features such as TP53 alterations, 3q chromosomal amplifications, whole genome doubling and non-aging mutational signatures in T790M negative tumors. Almost half of resistant tumors were further classified as Immunehot, with clinical outcomes conditional on immune cell infiltration state and T790M status. Finally, using a Bayesian statistical approach, we explored how T790M negative and positive disease might be predicted using comprehensive genomic and transcriptomic profiles of treatment-naïve patients.

  Study EGAS00001005389

• Accurate Genome-Wide Germline DNA Profiling from Decade-Old Archival Tissue Specimens

  We evaluate the validity of repurposing archival tissue specimens for germline genetic studies. We performed lc-WGS and imputed genotypes on 10 pairs of matching blood and tumor tissue and benchmarked the accuracy of genome-wide genotypes, HLA haplotypes, and several polygenic risk scores (PRSs). The reported results indicate the high accuracy of germline genotypes and haplotypes obtained from archival tissue DNA. Using this methodology, we estimate breast cancer PRS in 36 Ductal carcinoma in situ (DCIS) patients and demonstrate its association with breast cancer subsequent event (BCSE).  

  Study phs002865

• RNA-seq

  The RNA was extracted using the AS1390 PROMEGA kit according to the manufacturer’s instructions. The samples underwent sequencing using a Novaseq 6000 machine, equipped with an SP 200 cycles v1.5 cartridge. The sequencing process varied slightly across batches based on the input RNA and the library preparation kits used.

  Dataset EGAD50000002023

• The genomic landscape of germinal center derived B-cell lymphomas other than follicular, diffuse-large B-cell and Burkitt lymphom

  As part of the ICGC, the ICGC MMML-Seq project performed whole genome sequencing and RNA sequencing of germinal center derived B-cell lymphoma. Analyses were performed in concordance with the guidelines of the ICGC.

  Study EGAS00001002422

• A Multimodal Atlas of Human Brain Cell Types

  "A multimodal atlas of human brain cell types" includes sample data targeting two cell types that show species differences between mouse and human. First, it includes a detailed transcriptomic, morphological, and electrophysiological characterization of cell types in layer 1 of human middle temporal gyrus, focusing primarily on different inhibitory cell types. This project also includes gene expression data collected from nuclei in layer 5 of human fronto-insula, with a goal of identifying transcriptomic signatures of Von Economo neurons. Control samples collected as part of the same experiment are also included in the data set. This study was conducted as part of a collaboration between the Allen Institute for Brain Science, the University of Szeged, and the J. Craig Venter Institute. Collaborators request that publications resulting from these data cite their original publication: Transcriptomic and morphophysiological evidence for a specialized human cortical GABAergic cell type (PMID: 30150662).

  Study phs001791

• ILyAD (Indolent Lymphoma And vitamin D)

  Indolent non-Hodgkin lymphomas are incurable diseases, and require intermittent and often morbid and expensive therapy during their prolonged natural history. Lower intensity and better-tolerated, cost-effective treatment strategies are needed for these patients. Low vitamin D levels at diagnosis of indolent lymphomas are strongly associated with inferior outcomes to treatment. Standard therapy for low tumor burden, indolent lymphoma includes a single agent monoclonal antibody (rituximab). In our double-blind, placebo-controlled, randomized trial we evaluated if vitamin D supplementation with 2000IU oral cholecalciferol daily for three years improved the progression-free survival of patients with indolent lymphoma treated with single agent rituximab. Stratification factors for randomization included histology and Follicular Lymphoma International Prognostic Index (FL-IPI) prognostic score. The primary endpoint of the trial was progression-free survival over three years; secondary endpoints included response at 13 weeks, and overall survival. Eligible participants were adults with biopsy proven follicular lymphoma (grades 1-3a), small lymphocytic lymphoma, marginal zone lymphoma and mucosal-associated lymphoid tissue with no prior anti-lymphoma systemic therapy. Participants had Ann Arbor stage II or greater, measurable disease defined by Lugano criteria. Participants with osteoporosis requiring prescription treatment, symptomatic primary hyperthyroidism, hypercalcemia, creatinine greater than 1.5 times the upper limit of normal or a history of calcium-related kidney stones were excluded. Germline DNA was isolated from saliva samples obtained from participants at baseline. Whole exome sequencing was performed and SNPs were analyzed using the Agilent SureSelectXT Human All Exon V6 +UTR array. SNP data from 185 participants are available through dbGaP.

  Study phs003503

• Transcriptome of periadrenal and subcutaneous fat in patients with hyperaldosteronism in comparison to patients with non-functional adenomas

  This study analyzed subcutaneous fat (SCF) and periadrenal fat (PAF) from patients with aldosterone-producing adenomas (APAs) and, as controls, non-functional adrenal adenomas (NFA) (SCF, n = 7; PAF, n = 5).

  Study EGAS50000001095

• Transcriptome data of periadrenal and subcutaneous fat in patients with hyperaldosteronism in comparison to patients with non-functional adenomas

  We analyzed subcutaneous adipose tissue (scAT) and periadrenal adipose tissue (paAT) from patients with Aldosterone-Producing Adenomas (APA) and, as controls, non-functional adrenal adenomas (NFA). RNA sequencing and immunohistochemistry of AT was performed (IHC, only on scAT). IHC markers included adipokines (leptin, adiponectin) and transcription factors (eg, c-jun, CaMKII)

  Dataset EGAD50000001590

• RNA-Seq of novel miR (nmiR-1 and nmiR-2) overexpression and knockdown in BL

  After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets.

  Dataset EGAD00001001612

• Cholangiocarcinoma whole genome sequencing data 12 samples

  This dataset contains whole genome sequencing FASTQ data for 12 cholangiocarcinoma tumor samples, and their matched normal samples. These 12 samples are in addition to 59 samples available in dataset EGAD00001001988, and consist of patients from Thailand, Romania, and Singapore. Paired-end sequencing data was generated by Illumina Hiseq 2000 and 2500, with insert sizes of 170 and 350.

  Dataset EGAD00001003834

• Whole genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

  The dataset comprises of an aggregate level VCF (version 4.1), containing the somatic point and indel mutations found across the glioblastoma cohort (SweGBM-1, n=38 samples). The VCF file is in accordance with the HTS format specifications (https://samtools.github.io/hts-specs/).

  Dataset EGAD00001006084

• Neoplastic pancreatic cysts and associated cancers

  Data from a study of 148 samples from IPMNs, MCNs, and small associated invasive carcinomas from 18 patients using whole exome or targeted sequencing. Sequencing data from 77 samples out of the 148 samples in the complete study are available in this dataset, based on the permissions given by the participating patients and the informed consents.

  Dataset EGAD00001006229

• Programs, Origins, and Immunomodulatory Functions of Myeloid Cells in Gliomas

  Gliomas are challenging malignancies characterized by an immunosuppressive microenvironment filled with myeloid cells, whose roles in immune modulation are not fully understood. In this study, we utilized single-cell RNA sequencing (scRNA-seq) data from 85 primary human glioma tumors, related blood samples, and brain tumor organoid models. We found that nearly all glioma-associated myeloid cells express at least one of four distinct immunomodulatory activity programs. These programs include:1. Scavenger Immunosuppressive Program2. Complement Immunosuppressive Program3. Microglial Inflammatory Program4. Systemic Inflammatory ProgramAll four programs are found in both lower-grade and high-grade gliomas and are expressed across various myeloid cell types, whether derived from blood or resident origins. We validated the remarkable plasticity of myeloid cells by showing that the introduction of peripheral blood monocytes into glioma organoid models can induce the emergence of identities resembling microglia, macrophages, and dendritic cells, as well as all four immunomodulatory programs. Our study provides a valuable resource and a new framework for understanding the role of immunomodulatory myeloid cells in gliomas, laying the groundwork for developing effective immunotherapy strategies for glioma patients.

  Study phs003756

• Sputum RNA-Seq from Asthmatic Patients for Microbes and Genes

  RNA-seq files and other data associated with an investigation of the relationship between microbes, genes and immune cells present in the sputum of humans with asthma.

  Study phs002224

• DigiPico sequencing data for the study of active mutational processes in HGSOC

  The dataset contains Bam files from DigiPico runs as well as bulk sequencing data used in the "A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes" publication.

  Dataset EGAD00001005118

• Total RNAseq in the sporadic ALS and healthy control motor cortex

  The motor cortex is the earliest affected brain region in ALS. This dataset contains total RNA sequencing (stranded, 2x101bp) data derived from the motor cortex of 11 sporadic ALS patients and 8 healthy controls.

  Dataset EGAD00001006022

• Edinburgh Naevi Cohort (2018-08-03)

  In this project we have sequenced the exome of skin moles (melanocytic naevi) and also normal skin from young and old people. We are interested in looking at the clonality of these lesions and the burden of UV mutations . This dataset contains all the data available for this study on 2018-08-03.

  Dataset EGAD00001004273

• Leukemic evolution of donor-derived cells harboring IDH2 and DNMT3A mutations after allogeneic stem cell transplantation

  An individual with acute myeloid leukemia (AML) received peripheral blood stem cell (PBSC) transplantation, but later experienced relapse. Whole-exome sequencing of bone marrow cells obtained from different stages of this patient as well as PBSC of the donor revealed that relapsed AML was not the regrowth of the original leukemic clones, but donor cell leukemia (DCL). Interestingly, some of the oncogenic mutations found in DCL were already present at a low frequency in the donor PBSC. Target deep sequencing of these genes indeed confirmed this observation, and revealed that the emergence of additional oncogenic mutations triggered leukemic evolution.

  Study JGAS000017

• Linked-read based analysis of Medulloblastomas

  Medulloblastoma (MB) is the most common type of malignant pediatric brain tumor with group 4 medulloblastomas (G4 MBs) accounting for 40% of cases of medulloblastomas. The molecular mechanisms that underlie this subgroup are still poorly understood. Point mutations are detected in a large number of genes at low incidence per gene while the detection of complex structural variants (SVs) in recurrently affected gene typically requires the application of long-read technologies. Here, we applied linked-read sequencing, which combines the long-range genome information of long-read sequencing with the high base pair accuracy of short read sequencing and very low sample input requirements.

  Study EGAS00001007064

• Whole scRNA-seq from pre frontal cortex patient biopsy

  The single- cell RNA-seq prefrontal cortex sample was selected from a cohort of patients with hydrocephalus ≥18 years of age planning to undergo CSF diversion surgery either with a ventriculoperitoneal shunt placement (VP) or ventriculocisternostomy (VCS). The tissue was dissociated followed by red cell and debris removal and counting of the cells to be sequenced with (scRNA-seq; 10x Genomics kit v2). After dissociation only non neuronal cells were retrieved.

  Dataset EGAD50000001542

• WES patient 368

  Whole Exome Sequencing of blood and FFPE tumour of patient #368.  150–300 ng of DNA was fragmented to approximately 200 bp using a focal acoustic device. Libraries were prepared with the Kapa Hyper Prep Kit and SureSelectXT adaptors. Hybridisation capture was performed with SureSelect Clinical Research Exome V2 baits following the SureSelectXT recommended protocol (Agilent). Indexed libraries were sequenced on an Illumina NovaSeq 6000 to generate paired-end 150 bp reads with average of 70-fold base coverage for the germline sample and 330-fold coverage for tumour sample.

  Dataset EGAD00001011272

• RCC Infiltrated Macrophages and Monocytes

  Tumor infiltrated Macrophages and Monocytes were sorted on Aria II (Becton Dickinson) into TRIzol LS and flash frozen. RNA was extracted with chloroform. Isopropanol and linear acrylamide were added, and the RNA was precipitated with 75% ethanol. Total RNA (0.649–1 ng) with RNA integrity numbers 6.8 to 10 underwent amplification using the SMART-Seq v4. Ultra Low Input RNA Kit (Clontech; cat. #63488). Amplified cDNA (15 ng) was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems, KK8504) using 8 cycles of PCR.

  Dataset EGAD00001009393

• A Novel APP p.V742L variant in a patient with ischemic small vessel disease enhances FE65 signalling

  We identified a novel variant in the APP gene associated with cerebral ischemic strokes, which is not seen before with APP variants. This results in increased affinity of APP for FE65, APP’s most important intracellular interactor that regulates gene transcription.

  Study EGAS50000001283

• Target sequencing of 8 hereditary prostate cancer genes in Japanese

  We performed a case control association study for variants in coding regions of 8 hereditary prostate cancer genes in 7,636 male unselected prostate cancer patients, 12,366 male controls of Japanese ancestry. The 8 genes were ATM, BRCA1, BRCA2, BRIP1, CHEK2, HOXB13, NBN, and PALB2.

  Study JGAS000203

• Integrative Analysis of Lung Adenocarcinoma in EAGLE (Phase 2)

  We performed whole genome sequencing and whole exome sequencing of 31 lung adenocarcinoma (LUAD) samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study.

  Study phs001239

• ADCC Pilot RNAseq Study on Posterior Cingulate Astrocytes in Alzheimer's Disease

  In this study, RNA sequencing was performed on astrocytes microdissected from the posterior cingulate cortex of Alzheimer's disease subjects and healthy elderly controls.

  Study phs000745

• Whole-exome variant calling of individuals from the study of familial pulmonary fibrosis in the Canary Islands

  Research study of rare genetic variants associated with familial cases of pulmonary fibrosis in patients and relatives from Canary Islands, Spain.

  Study EGAS50000000782

• SNP array data for 140 individuals from 5 populations in Pakistan

  We have genotyped 140 individuals from 5 populations in Pakistan, using the OmniExpressExome-8 array, which includes approximately one million autosomal SNP markers.

  Study EGAS00001002965

• CD8+ Tumor-Infiltrating Lymphocyte Abundance is a Positive Prognostic Indicator in Nasopharyngeal Cancer

  This retrospective tissue study explores the prognostic significance of tumour-infiltrating lymphocyte (TIL) populations in NPC, using a combination of RNA sequencing and immunohistochemistry.

  Study EGAS00001006396

• My Pediatric and Adult Rare Tumor (MyPART) Natural History Study of Rare Solid Tumors

  The goal of this study is to comprehensively and longitudinally evaluate the natural history of patients with rare solid tumors or tumor predisposition syndromes, estimating and defining their clinical spectrum (e.g. disease course and survival). Clinical data, patient reported outcomes (PROs), and biospecimen associated data are collected. Clinical data includes response to treatment, tumor pathology, and imaging. PROs include measures of pain, depression, anxiety, mobility, and cognitive functioning. Biospecimen data includes next-generation sequencing [RNAseq, whole exome sequencing (WES), whole genome sequencing (WGS), EPIC methylation array data, and TruSight Oncology 500 gene panel sequencing], cytokine analysis of plasma, immune phenotyping of circulating peripheral blood mononuclear cells.

  Study phs003143

• Finnish - THL SUPER

  The dataset encompasses 852 Runs from the WGSPD Project 3 - Genomic Strategies to Identify High-impact Psychiatric Risk Variants Project

  Dataset EGAD50000001466

• Analysis of chromosomal background of cancerous mutations using a long-read sequencer

  In our previous study detecting cancerous complex SVs, we performed whole-genome sequencing of lung cancer clinical samples using PromethION. In this study, its depth and quality was substantially enriched and we conducted the phasing analysis in human lung cancer genomes. In addition, long read and short read RNA-seq was performed for transcriptome analysis.

  Study JGAS000349

• CD79B expression in DLBCL

  This study proposes a novel association between CD79B expression and cell-of-origin subtypes of DLBCL. Integrative single-cell analyses also revealed a distinct association between germinal center B-cell physiology and the pattern of CD79B expression, which is potentially a key explanation for the variable CD79B expression in DLBCL.

  Study EGAS50000000363

• Indonesian RNA-seq data

  Transcription data were collected to study patterns of functional variation across the broad geography of Indonesia. The region has extremely diverse populations, with very different demographic histories and multiple genetic ancestries. This dataset reports high-throughput RNA-sequencing data for individuals from three islands spanning this geographical region: Mentawai, Sumba and West Papua.

  Study EGAS00001003671

• Bone marrow single cell genomics from blood cancer samples

  The overall goal of this study was to characterize bone marrow cells based on their transcriptome, surface protein expression and BCR- and TCR VDJ-profile for accurate identification of clinically relevant cell states. This project has received funding from the European Union Horizon 2020 research and innovation programme under grant agreement No 824110 (EASI-Genomics)

  Study EGAS00001007332

• Transcriptome sequencing of hepatocellular carcinoma biopsies

  RNA-sequencing of 122 hepatocellular carcinoma biopsies and 15 normal liver biopsies. RNA-seq library prep was performed with 200 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to manufacturer’s specifications. Single-end 126-bp sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry at the Genomics Facility Basel according to the manufacturer’s guidelines. Primary data analysis was performed with the Illumina RTA version 1.18.66.3.

  Dataset EGAD00001008205

• Aligned reads from specific genomic locations derived from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 3,001 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these bam files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001003513

• Tumor and normal exomes for 95 PMBCL cases

  Whole-exome sequencing for 95 PMBCL cases (including 21 with matching normal DNA) was performed using a targeted capture approach with the SureSelect Human All Exon V6+UTR bait (Agilent Technologies) followed by massively parallel sequencing of enriched fragments on the HiSeq2500 platform (Illumina). Five libraries were pooled per lane and a 125bp paired-end mode was used. Tumor and normal DNA samples were sequenced to an average of 115X (SD 24X). All reads were aligned to the human reference genome (hg19) using bwa-mem version 0.7.5a29 with optical and PCR duplicates removed using the Picard tool.

  Dataset EGAD00001005780

• Genome-wide Identification of Variants Affecting Early Human Brain Development

  This is a genome-wide association study (GWAS) of global brain tissue volumes in human infants. The published study for this project includes 561 infants, and 239 parents gave consent for data sharing through dbGaP. An intronic single-nucleotide polymorphism (SNP) in IGFBP7 (rs114518130; GeneID: 3490) met genome-wide significance for gray matter volume (P=4.15x10-10). An intronic SNP in WWOX (rs10514437; GeneID: 51741) neared genome-wide significance for white matter volume (P=1.56x10-8). Additional loci with small P-values include psychiatric GWAS associations and transcription factors expressed in the developing brain. Genetic risk scores for schizophrenia and ASD, and the number of genes affected by rare copy number variants (CNV burden) did not predict global brain tissue volumes. Integrating these results with large-scale GWAS in adolescents [Philadelphia Neurodevelopmental Cohort (PNC)] and adults [Enhancing Neuro Imaging Genetics through Meta-Analysis version 2 (ENIGMA2)] suggested minimal overlap between common variants impacting brain volumes at different ages.

  Study phs001122

• Transcriptomic characterization of the histopathological growth patterns in breast cancer liver metastases

  20 fastq files of RNA-sequencing of the 2 main histopathological grow patterns observed in liver metastases.

  Dataset EGAD50000000331

• DAC for "Identification and characterization of tertiary lymphoid structures in brain metastases"

  This is the DAC for the study "Identification and characterization of tertiary lymphoid structures in brain metastases" of Prof. Dr. Guido Reifenberger (Guido.Reifenberger@med.uni-duesseldorf.de)

  Dac EGAC50000000369

• DAC for "Drug Development against Tumor Microtube Networks in Glioblastoma"

  This is the DAC for the study "Drug Development against Tumor Microtube Networks in Glioblastoma" of Dirk C. Hoffmann, Dirk.Hoffmann@dkfz.de and Frank Winkler, Frank.Winkler@med.uni-heidelberg.de

  Dac EGAC50000000326

• Pulldown_cytosine_deaminases

  We are looking at the causal factors behind hyper-mutator phenotypes found in previous Breast Cancer sequencing studies.

  Study EGAS00001000233

• Germline sequencing

  Detection of SNVs/indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants.

  Study EGAS00001006254

• Germline sequencing

  Detection of SNVs/ indels in the germline of pediatric cancer patients with a focus on CHEK2 germline variants

  Study EGAS00001006705

• HEMOGLOBIN HAPLOTYPES IN ABIDJAN

  This is a prospective study with 100 participants. The enzymatic digestion profiles after conventional PCR allowed the identification of different haplotypes of hemoglobin in Abidjan.

  Dataset EGAD00001008546

• RNAseq data set used in the study, 10 samples

  RNAseq data set used in the study, 10 samples

  Dataset EGAD00001007967

• Amplicon–Based Metagenomic Analysis.

  Amplicon-based fungal metagenomic sequencing for the identification of fungal species in brain tissue from Alzheimer's disease. The study consists in 14 samples, sequenced using Illumina's paired-end technology.

  Dataset EGAD00001003196

• Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER

  Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER

  Dataset EGAD00001015411

• FHIR Test Study BETA

  FHIR Test Study BETA. This study was created with 3 consent groups to simulate an actual study for FHIR API testing project. The data herein is simulated and are intended for development of FHIR representation of dbGaP phenotype data.

  Study phs002410

• Developmental Maturation of Hematopoietic Stem and Progenitor Cells Mediated by Lin28b/Let-7/Cbx2

  This study encompasses two human cell lines used to profile polycomb repressive complex markers during hematopoietic maturation.  This study includes epigenomic mark sequencing data obtained via the CUT&RUN protocol.

  Study phs002507

• MOSAIC Window Glioblastoma Data

  This dataset will include Spatial Transcriptomics, Single-Cell RNA-Seq, Bulk RNA-Seq, Clinical data, WES, and H&E data from 10 Glioblastoma (GBM) Cancer patients. Researchers from private or public institutions outside the MOSAIC Consortium will be able to apply to access this data and, pending approval, use the data for their research.

  Dataset EGAD50000001352

• Epigenomic analysis of human androgenetic trophoblast stem cells derived from complete hydatidiform mole

  A complete hydatidiform mole (CHM) is an abnormal pregnancy caused by genetic fertilization disorders. The aim of this study is to establish human trophoblast stem (TS) cell lines from CHMs and elucidate their pathogenesis.

  Study JGAS000207