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• V(D)J and 5' Gene Expression data on patients with aplastic anemia

  Chromium V(D)J and 5' Gene Expression platform (10X Genomics) was used to study patients with aplastic anemia. CD45+ cells from two patients (patient AA-3: 3 longitudinal samples from bone marrow and patient AA-4: 3 longitudinal samples from peripheral blood) were analysed. The raw data was processed using Cell Ranger 3.0.1 pipelines.

  Dataset EGAD00001006937

• Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC)

  Paired RNA seq of wild type VDH15 cells (3 replicates) - a cell line of oral squamous cell carcinoma (OSCC). RNA was extracted and sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocol. The sequencing was done using Illumina Novaseq 6000.

  Dataset EGAD00001010172

• Spatial Maps of Prostate Cancer Transcriptomes

  A total of 14 samples that has been analyzed with the Spatial Transcriptomics method. H&E stain can be sent if requested.

  Dataset EGAD00001004121

• Molecular analysis of post-colonoscopy CRC (PCCRC)

  Background: Post-colonoscopy colorectal cancers (PCCRCs, i.e. CRC diagnosed after a colonoscopy that excluded cancer) pose a challenge in clinical practice. In a retrospective cohort study, we compared clinical and molecular features of PCCRCs and prevalent CRCs. Methods: PCCRCs were defined according to the WEO classification, as cancers occurring within 10 years after a complete index colonoscopy, which excluded CRC. Whole genome chromosomal copy number changes and mutation status of genes commonly affected in CRC (APC, KRAS, BRAF, FBXW7, PIK3CA, NRAS, SMAD4 and TP53) were examined by low-coverage WGS and targeted sequencing, respectively. MSI and CIMP status were also determined. Results: In total, 122 PCCRCs and 98 prevalent CRCs were examined. PCCRCs are more often located proximally in the colon (p<0.001), non-polypoid appearing (p=0.004), early stage (p=0.009), and poorly differentiated (p=0.006) compared to prevalent CRCs. PCCRCs contain less frequently 18q deletions (p<0.001) than prevalent CRCs. MSI (p=0.029) and CIMP (p=0.014) are more frequently observed in PCCRCs. Conclusion: Although no PCCRC specific pathway could be defined, PCCRCs’ molecular features are more associated with MSI and hypermethylation pathways than canonical CIN pathway. The clinical and molecular features observed in PCCRCs support the hypothesis that sessile serrated lesions and non-polypoid CRNs are contributors to the development of these cancers."

  Study EGAS00001004686

• single cell RNA seq

  A selection of samples was analyzed using single-cell RNA sequencing to explore cellular heterogeneity. 4 inflammatory diseases were chosen for this purpose: Still’s disease, recurrent pericarditis, familial Mediterranean fever (FMF), and chronic non-bacterial osteomyelitis (CNO).

  Dataset EGAD50000002022

• Long-read whole-genome sequencing dataset of aplastic anemia

  This dataset contains long-read whole-genome sequencing data generated from patients with aplastic anemia and RCC. Genomic DNA was prepared for long-read sequencing and sequenced using single-molecule real-time technology on a PacBio platform.

  Dataset EGAD50000002257

• RNAseq following LDC67 or JQ1 treatment

  For RNA-Seq total RNA was isolated following LDC67 or JQ1 treatment. 3’RNAseq libraries were prepared with QUANT SEQ FWD 3´mRNA-Seq Kit (Lexogen, Austria), sequenced on an Illumina HiSeq 4000

  Dataset EGAD00001003464

• Molecular analyses of stage IIIa NSCLC patients treated with neoadjuvant chemmoimmuntherapy

  This dataset comprises molecular and immunogenomic profiles from 60 individual NSCLC patients (30 male, 30 female), with samples collected at multiple timepoints including initial biopsies (IB), resections (RES), and peripheral blood mononuclear cells (PBMC) at different timepoints during treatment. It includes 32 FFPE tumor samples sequenced on Illumina with the FoundationOne panel, 20 FFPE samples sequenced on IonTorrent with the Oncomine Comphrehensive Assay Plus, and 41 samples assessed with IonTorrent via Oncomine Immune Response Research Assay panel for targeted gene expression. T-cell receptor (TCR) repertoire profiling was performed on 62 tumor samples (initial biopsies and resections, Oncomine TCR Beta-SR Assay), and 155 blood-derived samples were sequenced with Oncomine TCR Beta-LR Assay. Data files include processed sequencing results in bam format.

  Dataset EGAD50000001630

• Data generated by the Drier Lab at HUJI

  This Data Access Committee is responsible to all data generated by and deposited by the Drier Lab at the Faculty of Medicine of the Hebrew University of Jerusalem (http://yotamdrier.ekmd.huji.ac.il/)

  Dac EGAC50000000060

• Leptomeningeal melanocytic tumour

  This is the first whole exome sequencing analysis of a primary meningeal melanocytic tumour (MMT) alongside the patients germline. Here we report the CRAM files from the tumour and germline.

  Dataset EGAD00001003750

• Integrated Exome and RNA Sequencing of Dedifferentiated Liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000177

• Analysis of genomic alterations in dedifferentiated liposarcoma

  Multiomics analysis of rare cancers to identify genetic alterations related with pathogenesis and prognosis. To identification of genetics alterations of Dedifferentiated liposarcoma, DNAs and RNAs were extracted from dedifferentiated liposarcoma and paired non-cancer (normal) tissues. NGS libaraies were prepared by using Agilent SureSelect XT Human All Exon V5 + IncRNA kit for whole exome sequencing (WES) and TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit (RNA seq). Sequencing was perfomred by Illumina HiSeq 2500.

  Study JGAS000182

• CUT&Tag sequencing of ZFHX4 and H3K27ac in midbrain dopaminergic neurons.

  CUT&Tag sequencing of the transcription factor ZFHX4 and the histone mark H3K27ac was performed in midbrain dopaminergic neurons (mDANs) derived from induced pluripotent stem cells. This epigenomic approach enabled the identification of ZFHX4 binding sites in this specific cellular context. Comparing the CUT&Tag profiles of ZFHX4 and H3K27ac provided insights into epigenetic landscapes in mDANs and revealed whether ZFHX4 exhibits patterns similar to the active transcription mark H3K27ac. Finally, enrichment analysis of the identified peaks highlighted potential primary targets of ZFHX4 in mDANs.

  Study EGAS50000001112

• WES and RNA-seq of triple-negative breast cancers from the MyBrCa cohort

  The dataset contains a genomics characterization of 35 triple-negative Asian breast tumours from the Malaysian Breast Cancer cohort. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, and RNA-seq of tumour tissue at 40X coverage (>15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a NovaSeq 6000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturer’s instructions and also subjected to paired end 75 sequencing on a NovaSeq 6000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.

  Dataset EGAD00001009311

• Quick Guide for data submission

  Quick Guide This is a quick guide to submit data to the EGA. Please select data type to display the right detailed instructions. Sequence data Array-based data Get your submission account You first need to create your EGA user. Then, once your account has been verified by the Help Desk team, request your submission account and provide details of the data type and platform(s) in your submission. Register Study/DAC Use Submitter Portal to register your study, samples, Data Access Committee (DAC) and Policy. Upload data Encrypt your data files using the and upload it to your inbox using SFTP. Register experiments and runs Associate each data file to a registered sample and study by Linking files to samples. Details of the experimental procedure you followed must be provided. Finalise your submission Group your runs/analysis into datasets and link them to your new or existing DAC and policy using DAC Portal. Data request are done at a dataset level, thus files within a datasets must share release conditions. Release and admin When finalising the submission, set a released date to instruct our Helpdesk to release your study. All registered studies are automatically placed on hold until the named submission or DAC contact instructs our Helpdesk for the study to be released. Get your submission account Fill the submission form and provide details of the data type and platform(s) in your submission. Register Study/DAC Use EGA Programmatic submission to register your study, samples, Data Access Committee (DAC) and Policy. Upload data Encrypt your data files using the EgaCryptor and upload it using default FTP clients or Aspera. Complete the Array-Format (AF) spreadsheet Download the AF spreadsheet and complete all four sections. Return the spreadsheet to the EGA helpdesk. Release and admin Instruct our Helpdesk to release your study. All registered studies are automatically placed on hold until the named submission or DAC contact instructs our Helpdesk for the study to be released.

  Documentation submission/quickguide

• Transcriptome sequencing of human colon organoid after co-cultivation with Bifidobacterium longum

  The large intestine has a dense milieu of indigenous bacteria, generating a complex ecosystem with crosstalk between individual bacteria and host cells. In vitro host cell modeling and bacterial interactions at the anaerobic interphase have elucidated the crosstalk molecular basis. Although classical cell lines derived from patients with colorectal cancer including Caco-2 cells are used, whether they adequately mimic normal colonic epithelial physiology is unclear. To address this, we performed transcriptome profiling of Caco-2 and Monolayer cells derived from healthy Human Colonic Organoid (MHCO) cultured hemi-anaerobically. Coculture with the anaerobic gut bacteria, Bifidobacterium longum subsp. longum differentiated the probiotic effects of test cells from those of physiologically normal intestinal and colorectal cancer cells. We cataloged non- or overlapping gene signatures where gene profiles of Caco-2 cells represented absorptive cells in the small intestinal epithelium, and MHCO cells showed complete colonic epithelium signature, including stem/progenitor, goblet, and enteroendocrine cells colonocytes. Characteristic gene expression changes related to lipid metabolism, inflammation, and cell-cell adhesion were observed in cocultured live Bifidobacterium longum and Caco-2 or MHCO cells. B. longum-stimulated MHCO cells exhibited barrier-enhancing characteristics, as demonstrated in clinical trials. Our data represent a valuable resource for understanding gut microbe and host cell communication.

  Study JGAS000740

• Immunogenomics of colorectal cancer response to immune checkpoint blockade

  Molecular and cellular determinants of response to immune checkpoint inhibitors are mostly unknown. Here we use whole exome, RNA and T cell receptor sequencing, imaging mass cytometry, immunohistochemistry and PD1-PDL1 interaction detection to profile 543 regions from 16 colorectal cancers (CRCs) subsequently treated with Pembrolizumab or Nivolumab. Independent of treatment response, CRCs express low levels of PD1 and PDL1 proteins and form less PD1-PDL1 complex than other cancers. Non hypermutated CRCs have no benefit from treatment, show WNT activation and low T cell infiltrates. Among hypermutated CRCs, those with durable benefit have clonal immunogenic alterations, clonally expanded T cells and potential for immune escape through dysfunctional antigen presentation. Responsive tumours are enriched in PD1-expressing cytotoxic and proliferating CD8 T cells and PDL1-expressing antigen presenting macrophages, which form high-density clusters of interacting cells. Our study shows that immune checkpoint inhibitors are most effective in highly infiltrated CRCs where they may release the interactions between macrophages and CD8 T cells thus promoting their priming and expansion in intra-tumour niches.

  Study EGAS00001004438

• Understanding Determinants of Racial Disparities in Lung Cancer Incidence

  This is a nested case-control study designed to evaluate the association between common genetic variants and the risk of lung cancer. The study included 1258 cases and 1252 controls selected from the Southern Community Cohort Study (SCCS), a large, prospective observational cohort. Cases were identified from cancer registries across the catchment area of the SCCS. Cases and controls were frequency matched on age, sex, race, and enrollment site (community health center vs general population).

  Study phs003789

• High Altitude Pulmonary Hypertension

  The Central Asian Kyrgyz highland population provides a unique opportunity to address genetic diversity and understand the genetic mechanisms underlying hypoxia-induced high altitude pulmonary hypertension (HAPH). While a significant fraction of the population is unaffected, there are susceptible individuals who display HAPH in the absence of any lung, cardiac or hematologic disease. We report herein the analysis of the whole genome sequencing of healthy individuals compared with HAPH patients and other controls.

  Study EGAS00001003171

• RNA-seq of MPNSTs

  Malignant Peripheral Nerve Sheath Tumors (MPNSTs) are highly aggressive soft-tissue sarcomas with a poor prognosis and a lack of therapeutic options. In this study, we analyse the whole-transcriptome MPNST and combine them with WGS data from a partially overlapping sample set. These analyses and the inclusion of another public dataset allow us to identify three genomic MPNST subgroups with distinct biological and clinicopathological features that can inform management and precision treatments. Published in "Identification of Malignant Peripheral Nerve Sheath Tumor (MPNST) subtypes with distinct genomic identities."

  Study EGAS50000001733

• Somatic mutation in edited cholangiocyte organoids

  Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

  Dataset EGAD00001015457

• Somatic mutation in edited cholangiocyte organoids

  Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

  Dataset EGAD00001015455

• Somatic mutation in edited cholangiocyte organoids

  Primary human cells cultured in organoid format have great promise as potential regenerative cellular therapies. However, their immunogenicity and mutagenic profile remain unresolved, impeding effective long-term translation to the clinic. In this study we report, for the first time, the generation of human leukocyte antigen (HLA)-I and HLA-II knock-out human expandable primary cholangiocyte organoids (PCOs) using CRISPR-Cas9 as a potential ‘universal’ low-immunogenic therapy for bile duct disorders. HLA-edited PCOs (ePCOs) displayed the same phenotypic and functional characteristics as parental unedited PCOs. Despite minimal off-target edits, duplex sequencing approaches demonstrated that ePCOs and PCOs acquire mutations in culture at similar rates, but without evident selection for cancer-driver mutations. ePCOs induced reduced T cell-mediated immunity and donor-dependent NK cell cytotoxicity in vitro and evaded cytotoxic responses with increased graft survival in humanized mice in vivo. Our findings have important implications for assessment of safety and immunogenicity of primary cell-derived organoid cellular therapies.

  Dataset EGAD00001015456

• Dataset for urologic_cancer-EXON

  Rare cancer sequencing data of 112 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008904

• NHLBI TOPMed: African American Sarcoidosis Genetics Resource

  This study aims to comprehensively interrogate the genomes of African American sarcoidosis families. Sarcoidosis is characterized by a hyperimmune response resulting in granuloma formation in multiple organs. It affects African Americans (AAs) more frequently and more severely than whites. While previous linkage, admixture, candidate gene and genome-wide association (GWA) studies show statistically compelling effects, causal variants are still unknown and much of sarcoidosis heritability is yet to be explained. This "missing" heritability likely includes effects of both common (minor allele frequency (MAF)>5%) and rare variants (MAF

  Study phs001207

• Whole Genomes Define Concordance in Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer

  Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis of any common solid epithelial tumour. Multiple failed clinical trials necessitate newer approaches to understand the molecular etiology of this disease. Patient-derived xenografts (PDX) and patient-derived organoids (PDO) may serve as pre-clinical disease models; however, characterization remains largely unaddressed at the whole genome level. We conducted a comprehensive assessment of the genetic landscape of tumours and matched PDX and PDO from patients with PDAC. Our data show that PDX and PDO recapitulate PDAC tumourigenesis with respect to simple somatic mutations and copy number changes, and capture major structural variation events.

  Study EGAS00001002597

• Genomic alterations in MM - CEL

  RNA from the same tumor sample (n=98) was also processed using the 3' IVT kit (Affymetrix) and hybridized to U133 Plus 2.0 arrays (Affymetrix).

  Dataset EGAD00010001577

• Saliva microbiota in Finnish children

  The saliva microbiota of 972 Finnish children, aged 9-14 years was characterized using the 16S rRNA (V3-V4) gene sequencing with Illumina Hiseq platform.

  Dataset EGAD00001004145

• Total RNA sequencing in M1911

  The dataset comprises total RNA sequencing data obtained from two samples of testicular tissue from the individual M1911, who was diagnosed with meiotic arrest.

  Dataset EGAD00001008639

• Determinants of Asthma Following RSV Bronchiolitis in Early Life

  The goal of the RSV Bronchiolitis in Early Life (RBEL) study is to determine how specific genetic, biologic, and immunologic characteristics interact to predispose individuals to develop asthma. Participants were carefully recruited by selecting a prospective cohort of 206 infants with severe respiratory syncytial virus (RSV) bronchiolitis who were at substantial risk of developing asthma.

  Study phs001009

• Genomic evolution of pancreatic cancer at single-cell resolution

  This project assesses genomic evolution of pancreatic cancer using the Mission Bio Tapestri platform and Whole Exome Sequencing. The Mission Bio Tapestri platform is a single-cell DNA sequencing platform using a targeted gene panel to assess SNV/CNV. Several samples, including primary and metastatic tissue, were used to investigate changes at single-cell resolution.

  Study EGAS50000001351

• RNAseq and ATACseq on HGSC lines, pre- and post-treatment with an epigenetic drug

  This study looked to determine changes in gene expression and chromatin accessibility of five HGSC cell lines, following treatment with a novel epigenetic drug. The epigenetic drug, HKMTi-1-005, is a compound with dual activity against H3K27 and H3K9 methylation. The cell lines used were PEO1, PEO4, PEA2, OVCAR5, OVCAR8.

  Study EGAS50000000047

• Abnormal_foetal_development_exome_trios

  This project is to explore the contribution of de novo mutations to severe structural malformations diagnosed prenatally using ultrasound. These malformations include heart, CNS, renal and GI abnormalities. In this pilot project we aim to exome sequence 30 parent-foetus trios to ~50X mean coverage and identify de novo functional variants using an algorithm developed in the Hurles group

  Study EGAS00001000167

• Defective mitophagy and enhanced oxidative stress dictate regulatory T cell impairment in autoimmunity

  Regulatory T cell (Treg) impairment is a common denominator of autoimmune pathologies. Despite the extensive characterization of Treg cell phenotype in autoimmunity, the molecular mechanisms underlying their deterioration remain ill defined. To investigate Treg dysfunction during autoimmunity we performed transcriptomic analysis of CD4+CD25highCD127- Treg cells from peripheral blood of patients with autoimmunity.

  Study EGAS00001004470

• Methylation data

  To ellucidate methylation activity in mRCC, methylation data was generated as part of the EuroTarget study

  Dataset EGAD50000002295

• Molecular and functional profiling of plasmablastic lymphoma

  Plasmablastic lymphoma (PBL) represents a rare and aggressive lymphoma subtype frequently associated with immunosuppression. Clinically, patients with PBL are characterized by poor outcome. The current understanding of the molecular pathogenesis is limited. A hallmark of PBL represents its plasmacytic differentiation with loss of B-cell markers and, in 60% of cases, its association with Epstein-Barr virus (EBV). Roughly 50% of PBLs harbor a MYC translocation. Here, we provide a comprehensive integrated genomic analysis using whole exome sequencing (WES) and genome-wide copy number determination in a large cohort of 96 primary PBL samples. We identify alterations activating the RAS-RAF, JAK-STAT, and NOTCH pathways as well as frequent high-level amplifications in MCL1 and IRF4. The functional impact of these alterations is assessed using an unbiased shRNA screen in a PBL model. These analyses identify the IRF4 and JAK-STAT pathways as promising molecular targets to improve outcome of PBL patients.

  Study EGAS00001004659

• RNA Dataset

  The RNA dataset includes 5 samples analyzed with the Oncomine Comprehensive Assay (OCA) panel. After library preparation, sequencing was performed on the Ion Torrent S5 System, generating FASTQ files. The analysis captures gene fusions and splice variants relevant to oncogenic processes. (idem)

  Dataset EGAD50000002502

• bulk Exome-seq of the 5 HCC patients which also have the single cell T cell RNA-seq data

  bulk Exome-seq data of the 5 HCC patinets. Single cell RNA seq data of these patients was under the accession number EGAD00001003337

  Dataset EGAD00001004149

• SCANDARE MACARON project

  Among gynecological cancers, high-grade serous ovarian cancer has the highest prevalence and more than 75% of patients have advanced stage at diagnosis with a 5-year survival of 40%. When the initial complete surgical removal is not possible (60% of patients), an interval surgery can be considered after three to four cycles of neoadjuvant chemotherapy to reduce the tumor mass. However, in approximately 50% of cases the tumor has little or no response to neoadjuvant chemotherapy. Therefore, identification of potential drug targets, biomarkers and/or pathways whose modulation can help in the prevention, interception, or curing of the disease is essential to address the unmet need. Therefore, MACARON project aims to address these issues through the identification of shared neoantigens arising out of somatic alterations and aberrant transcriptional programs in ovarian cancer DNA/RNA datasets.

  Dac EGAC50000000104

• Type 2 Diabetes Starr County GWAS and Exome Sequencing

  The T2D Seq GWAS Starr County Cohort is utilized in the following dbGaP sub-studies. To view genotypes, other molecular data, and derived variables collected in these sub-studies, please click on the following sub-studies below or in the "Sub-studies" section of this top-level study page phs001166 T2D Seq GWAS Starr County Cohort. phs000143 CIDR T2D Hanis phs001099 T2D GENES Starr County

  Study phs001166

• Pseudotime_ordering_of_cell_cycle_state

  We will be using G&T method to sequence single cell genome and transcriptome derived from FS13B iPSCs cell line. The cell cycle state of each of the single cells is known. Hence, we will be analysing the genome and transcriptome of single cells from each of the cell cycle state to generate a copy number profile and transcriptome profile per given cell cycle stage: G1, S, G2, S.

  Study EGAS00001003293

• A GWAS of Progression in Multiple Sclerosis

  This is a genome wide association study (GWAS) of disease progression in multiple sclerosis (MS). The study involved a total of 12584 cases recruited from multiple centres around the world and tested at 7.8 million common autosomal single nucleotide variants. The data from the European cases (n=4853) are included in this EGA submission in 10 country specific data sub-sets.

  Study EGAS00001007162

• Targeted sequencing of patients with neurodegenerative diseases

  A targeted gene panel that covers coding, noncoding, and short tandem repeat regions improves the diagnosis of patients with neurodegenerative diseases

  Dataset EGAD00001005114

• Screening Protocol and Longitudinal Study of Bone Marrow Failure Syndromes and Cytopenias

  The purpose of this study is to characterize patients with Bone Marrow Failure Syndromes (BMFS) and to track the clinical course of patients with these diseases over time. An exact and comprehensive diagnosis at presentation is essential. Due to the sporadic nature of BMFS (aplastic anemia, myelodysplastic syndrome, paroxysmal nocturnal hemoglobinuria, pure red cell aplasia, amegakaryocytic thrombocytopenic purpura and large granular lymphocyte leukemia) most diseases have not undergone systematic long-term outcome studies. Individual diseases, combined under the collective entity of bone marrow failure syndromes, frequently overlap and evolve from each other. The frequency of complications, associations with other diseases, and genetic factors such as allelic polymorphisms are not well studied. Some of these syndromes are likely mediated by the cellular immune system. However, while target antigens are likely to be expressed on early hematopoietic cells, their identification has been unsuccessful. Hypothesis: Clinical and epidemiologic studies may, through etiologic clues and intricate laboratory testing, facilitate the understanding of the pathophysiology of BMFS and ultimately lead to implementation of better diagnostic tools and more targeted and rational therapies.

  Study phs000592

• Post-liver transplant recurrent human hepatocellular carcinoma study (RHCCS)

  The whole exome sequencing showed that HERC5 deletion and under-expression associates with shorter: time to tumor recurrence, progression-free, and overall survival in hepatocellular carcinoma (HCC) in two independent studies (p1=0.004, HR1=1.80; p2=0.018, HR2=3.31) totaling 286 HCC patients. Matched primary and recurrent tumors indicated a clonal selection advantage in somatic single nucleotide and copy number variants (CNVs) in recurrent compared to primary tumors of Chinese HCC patients with Wnt signaling most activated.

  Study phs000782

• Whole-Genome Sequencing Reveals Complex Genomic Features Underlying Anti-CD19 CAR T-Cell Treatment Failure in Lymphoma

  We performed Whole-Genome Sequencing (WGS) on 100 tumor and matched germline samples from 49 CD19-directed chimeric antigen receptor (CAR-19)-treated diffuse large B cell lymphoma (DLBCL) patients. We found that the presence of complex structural variants, APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide) mutational signatures, and genomic damage from reactive oxygen species predict CAR-19 resistance. BAM files will be available through dbGaP.

  Study phs003023

• Intercellular nanotube-mediated mitochondrial transfer enhances T-cell metabolic fitness and antitumor efficacy

  We found that bone marrow-derived mesenchymal stromal cells (MSC) establish nanotubular connections with T cells in a Talin 2 (TLN2)-dependent manner and leveraged these intercellular highways to supply new mitochondria to CD8+ T cells. In this experiment we analyzed the transcriptional profile of T cells co-cultured with MSC containing MSC derived Mitochondria (MitoPositive), T cells co-cultured with MSC not containing MSC derived Mitochondria and control T cells.

  Study EGAS00001007356

• NHLBI TOPMed: Pulmonary Hypertension and the Hypoxic Response in SCD (PUSH)

  During Visit One, the PUSH Study will perform echocardiography on 600 children and adolescent with patients with sickle cell disease (SCD) and 100 control children and adolescents at three Field Centers, namely Howard University, Children's National Medical Center and University of Michigan. Patients or their parents will be approached and asked to give informed consent. If they appear to have a difficult reading, reading of the consent will be offered. Patients or their parents not appearing to comprehend the consent will not be eligible. As a part of this visit, each participant or parent will sign informed consent, complete a Participant Contact Information Form, complete a Medical History Form, undergo physical examination with completion of a Physical Examination Form and have blood drawn. Each participant must have echocardiography performed with measurement of Tricuspid Regurgitant Jet Velocity (TRV). In addition, attempts will be made 1) to perform a six-minute walk test, 2) to collect information from a recent (within six months) Transcranial Doppler Study (TCD) or to perform TCD, and 3) to perform pulmonary function tests. Study personnel will review all forms for completeness and conduct phlebotomy. Blood will be shipped to the Central Lab. Results of all procedures and tests will be transmitted to the Data Manager at Howard University. Sequencing was only done on sickle cell participants.

  Study phs001682

• Studies of a Targeted Risk Reduction Intervention through Defined Exercise (STRRIDE)

  The STRRIDE study is the combination of three interventional trials to evaluate dose and intensity of physical activity on cardiometabolic health. The three component studies are Peripheral Effects of Exercise on Cardiovascular Health (STRRIDE I, ClinicalTrials.gov Identifier: NCT00200993), Effects of Resistence and Aerobic Exercise on Cardiovascular Health (STRRIDE II, ClinicalTrials.gov Identifier: NCT00275145) and Exercise Dose-Response Effects in Prediabetes (STRRIDE-PD, ClinicalTrials.gov Identifier: NCT00962962).

  Study phs001855

• Human pan-genome analysis

  The reference human genome is still incomplete, and several non-reference sequences have derived from diverse populations. With the available of whole genome sequencing data from multiple individuals, we could construct the pan-genome sequence. Here we provide high quality genome sequencing (~30x coverage) from 185 Han Chinese individuals. All samples were sequenced using Illumina HiSeq X10 sequencer and paired-end 150-bp reads were produced.

  Study EGAS00001003657