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• Systematic Analysis of Coding and Non-coding Elements in Developmental Pathways Implicated in Holoprosencephaly Pathogenesis

  We applied targeted capture to examine 153 genes representative of all the major vertebrate developmental pathways among 340 probands and 285 of their unaffected parents to rank their relative significance as causes for holoprosencephaly (HPE).

  Study phs001653

• Germline Genetic Variants in Cancer-Susceptibility Genes in Patients with Osteosarcoma

  We conducted whole-exome sequencing of germline DNA from patients with osteosarcoma to estimate the frequency of pathogenic/likely pathogenic germline genetic variants in known cancer-susceptibility genes in a large population of osteosarcoma patients unselected for family history.

  Study phs002444

• smallRNA-seq of isolated pancreatic islets

  In this study we performed smallRNA-sequencing, a sequencing method designed for small noncoding RNAs, to investigate the miRNA expression profile of human islets isolated from pancreata of donors without diabetes mellitus (n=3) and donors with type 2 diabetes (n=3).

  Study EGAS50000000865

• scD&D Multiome of GATA1 regulatory network dynamics during erythropoiesis

  Ex vivo differentiation experiments of human CD34+ hematopoietic stem and progenitor cells and profiled cells along the erythropoietic trajectory at multiple timepoints (differentiation days 0, 5, 8, 18, and 24), for simultaneous assessment of transcriptome, chromatin accessibility and GATA1 binding

  Study EGAS50000001606

• Spatially resolved transcriptomics reveals profound subclonal heterogeneity and T cell dysfunction in extramedullary myeloma

  Investigating the spatial architecture and microenvironment of EMD lesions in Multiple Myeloma patients using spatial whole transcriptome sequencing (10X Visium), tomography for spatially resolved transcriptomics (TOMO-seq), and single-cell RNA sequencing (scRNAseq)

  Study EGAS50000000227

• 10X snMultiome (ATAC+GEX) for the study of "SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities"

  10X snMultiome (ATAC+GEX) sequencing of 1 human reactive tonsil sample and 1 DLBCL sample for the study of "SPEN loss drives extra-follicular diffuse large B cell lymphoma with female-specific lethality and TLR pathway therapeutic vulnerabilities"

  Dataset EGAD50000002277

• RNA fastq files and mutation annotation files

  This dataset contains the results of both RNA sequencing and DNA sequencing. For RNA sequencing, it includes data from 12 samples derived from 9 patients, provided as raw sequencing files in FASTQ format. For DNA sequencing, it contains mutation information obtained from targeted panel DNA sequencing, including data from 35 individuals in the mutation annotation file (MAF) format.

  Dataset EGAD50000001768

• Emirati Phased Diploid Trio-Assemblies (27 Individuals, 54 Assemblies)

  This dataset comprises 27 phased diploid genome assemblies (i.e., 54 haplotypes) from Emirati family trios, provided in FASTA format. Sequencing used PacBio HiFi reads generated on the Revio platform at ≥25× coverage for each parent and offspring. Assemblies were produced with hifiasm (trio mode), then scaffolded with NTLink and reference-guided merging via RagTag against CHM13v2. The collection offers haplotype-resolved references suitable for downstream variant discovery and pangenome analyses.

  Dataset EGAD50000001755

• Large deletion predisposes to familial melanoma

  Mutations in CDKN2A and CDK4 account for ~40% of multi-case melanoma families, with another ~10% attributable to BAP1 and genes associated with telomere maintenance. Thus, a substantial proportion of the genetic risk underlying familial melanoma remains unexplained.

  Study EGAS50000001496

• Sequencing data for oesophageal and related samples - Alex Frankell et al (RNA)

  Data supporting: "The landscape of selection in 551 Esophageal Adenocarcinomas defines genomic biomarkers for the clinic." Frankell et al. RNAseq (BAM files) 116 tumours

  Dataset EGAD00001004423

• Mutational_burden_in_skin_following_UV_treatment_Nanoseq

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007681

• Mutational_burden_in_skin_following_UV_treatment_WGS

  We wish to assess the changes in mutational burden in patients under going UV treatment for psoriasis. Using duplex sequencing we will assess mutational burden in traditionally sun exposed (arm) and non-sun exposed (buttock) skin epidermis both pre and post UV treatment.

  Study EGAS00001007682

• Exome_sequencing_of_UK_Birth_Cohorts___Avon_Longitudinal_Study_of_Parents_and_Children

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001005273

• Exome_sequencing_of_UK_Birth_Cohorts___Born_in_Bradford

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001006978

• Exome_sequencing_of_UK_Birth_Cohorts___Millennium_Cohort_Study

  We propose to exome sequence birth cohorts with near complete population coverage (thus addressing the ascertainment biases of previous studies), which have detailed longitudinal cognitive and educational data on parents and children, and for which genotyping chip data are readily available.

  Study EGAS00001007789

• Transcriptomic response of miRNAs of monocytes to bacterial and viral stimuli assessed by RNA-seq in Africans and Europeans

  The dataset includes raw RNA-seq data (fastq files) for miRNAs of monocytes before and after 6-hour exposure to four different immune stimuli, measured in 200 African- and European-descent healthy donors from Belgium. The stimuli include ligands for TLR4 (LPS), TLR1/2 (Pam3CSK4) and TLR7/8 (R848) and to a human seasonal influenza A virus (IAV).

  Dataset EGAD00001006181

• Improved Sezary cell detection and novel insights into immunophenotypic and molecular heterogeneity in Sézary syndrome

  We performed a prospective investigation in Sézary syndrome by the application of a standardized multiparameter flow cytometry, FACS-cell sorting, and RNA-sequencing for an in-depth immunophenotypic and transcriptional profiling of Sézary cells.

  Study EGAS00001005229

• Set_of_human_mesenchymal_CSA

  51 DNA methylation arrays of human samples initially diagnosed as mesenchymal chondrosarcoma. Microdissection of the cartilage and/or the small round cell component from the same sample may have occurred. As mentioned in the sample descriptions, the diagnoses of four samples have been revised. Additional molecular investigations were conducted for a subset of samples as described in the related publication.

  Dataset EGAD00010002515

• MutWP5__CRUK_Mutographs_of_Cancer__Lung__PD37920__Targeted_

  Sequencing of LCM-derived microbiopsies from explanted lung from COPD patient. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Deep sampling throughout multiple regions of the lung will determine whether there are differences in smoking-related mutation burden in different portions of the lung. Targeted sequencing will be conducted on samples to identify drivers of interest and clonality of the samples, well-performing samples will be sent for subsequent whole-genome sequencing. Results from this portion of the study will be compared to other individuals with smoking-related diseases (COPD, pulmonary fibrosis, lung cancer), and normal, non-smoking lungs.

  Study EGAS00001003321

• Access to "A Spatially Resolved Single-Cell Atlas of the Human Fetal Olfactory System"

  The human nasal region arises from neural crest and placodal lineages, yet its early development remains poorly understood owing to limited fetal tissue access and structural complexity. Here we present an integrated single-nucleus and spatial transcriptomic atlas of the human fetal nasal region, generated from 10 fetuses (males and females) between 7 and 12 post-conceptional weeks. Single-nucleus RNA sequencing resolved 32 distinct cell types, while integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) enabled spatial and temporal mapping of gene expression dynamics across the olfactory epithelium (OE) and adjacent tissues. We identify novel markers of olfactory sensory neuron differentiation and pathways governing epithelial patterning and OE morphogenesis. Notably, spatially organized expression of 169 olfactory receptor genes reveals molecular evidence for the “one neuron-one receptor” principle during the first trimester. Together, this work establishes the first molecular and spatial framework of early human olfactory development and provides a foundational resource for studies of sensory neurogenesis and congenital disorders.

  Dac EGAC50000000688

• The_GENCODE_exome___sequencing_the_complete_human_exome

  We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an addition 5,594 genes and 10.3 Mb compared to current sets which mainly target the CCDS database. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed covers 47.9Mb and performed well in sequence capture experiments with HapMap and clinical samples. Samples within this study are prepared with either the CCDS or GENCODE exome products.

  Study EGAS00001000016

• The Study of Somatic LINE1 Activity in Cancers

  This study focuses exclusively on the quantification of LINE1 mobilization. We analyzed a recent whole genome sequencing data release from multiple Cancer Genome Atlas (TCGA) sub-projects. In addition to the somatic LINE1 insertions (present in tumor and having no support in the matched normal) there are "pseudo-germline" non-reference LINE1 elements identified in tumor tissue and having some support in the matched normal. This dataset reports such "pseudo-germline" LINE1 retrotranspositions. Individual level data for TCGA can be accessed by requesting access to phs000178.

  Study phs003888

• Molecular profiling of DLBCL patients treated in the HOVON84 trial

  Using a comprehensive NGS assay for simultaneous screening of mutations, copy number alterations, and translocations, 5 biology-based risk profiles could be reproduced in a Dutch DLBCL population and validated for outcome prediction. This approach will enable application as a diagnostic tool to select DLBCL patients for risk adapted treatment and help to develop biomarker-driven clinical trials for personalized medicine.

  Study EGAS00001003949

• Isala Cross sectional Flow Meta Data

  This meta data contains extensive meta data from the cross sectional flow of the Isala Citizen Science project. The meta data file contains ENA Accession numbers for 16S Microbiome data, and cleaned responses to questionnaires.

  Dataset EGAD00001009890

• Somatic mutation and selection at epidemiological scale - TwinsUK_ExomeNanoSeq_Buccal

  Exome NanoSeq in buccal swab samples obtained from patients with a wide range of clinical phenotypes. As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations. Some of these clones represent a first step towards cancer whereas others may contribute to ageing and other diseases. However, our understanding of the clonal landscapes of human tissues, and their impact on cancer risk, ageing and disease, remains limited due to the challenge of detecting somatic mutations present in small numbers of cells. Here, we introduce a new version of nanorate sequencing (NanoSeq), a duplex sequencing method with error rates of less than 5 per billion base pairs, which is compatible with whole-exome and targeted gene sequencing. Deep sequencing of polyclonal samples with single-molecule sensitivity enables the simultaneous detection of mutations in large numbers of clones, yielding accurate somatic mutation rates, mutational signatures and driver mutation frequencies in any tissue. Applying targeted NanoSeq to 1,042 non-invasive samples of oral epithelium and 371 samples of blood from a twin cohort, we found an unprecedentedly rich landscape of selection, with 46 genes under positive selection driving clonal expansions in the oral epithelium, over 62,000 driver mutations, and evidence of negative selection in some genes. The high number of positively selected mutations in multiple genes provides high-resolution maps of selection across coding and non-coding sites, a form of in vivo saturation mutagenesis. Multivariate regression models enable mutational epidemiology studies on how carcinogenic exposures and cancer risk factors, such as age, tobacco or alcohol, alter the acquisition and selection of somatic mutations. Accurate single-molecule sequencing has the potential to unveil the polyclonal landscape of any tissue, providing a powerful tool to study early carcinogenesis, cancer prevention and the role of somatic mutations in ageing and disease.

  Dataset EGAD00001015620

• Human Spermatogenesis Methylome

  The dataset contains the methylome EM-sequencing raw data (fastq) of different spermatogenic cells from 5 human males (three controls and two crypotzoospermic). The datasets correspond to the following cell types: undifferentiated spermatogonia, differentiating spermatogonia, 4C spermatocytes, and 1C spermatids (this cell type only for the control individuals)

  Dataset EGAD00001011180

• tRCC UTSW 2024 Cohort

  This submission contains the WES and RNA-Seq raw data for the study titled 'Comparative Genomics of a Translocation Renal Cell Carcinoma Mouse Model Reveals Molecular Mechanisms of Tumorigenesis.

  Dac EGAC50000000105

• BROCA cancer panel sequencing for 15 samples

  BROCA panel sequencing using the BROCA-HR v8 and BROCA-GO v1 versions of the gene panel

  Dataset EGAD50000000035

• GR@ACE_StageI.CEL_files

  Intensity calculation on the pixel values of the DAT file for 7409 samples genotyped using Axiom 815K Spanish Biobank array (Thermo Fisher)

  Dataset EGAD00010001655

• Exome chip analysis file

  This data set includes the following summary level data file used for the exome chip analysis: exome_chip.sv.assoc.txt: results from single variant association analysis in exome chip

  Dataset EGAD00010001187

• Melanoma post mortem analysis

  We have been applying whole genome and transcriptome sequencing across metastases collected during post mortem. Herein we show the findings for the first such patient.

  Dataset EGAD00001005072

• Hospital for Sick Children Infant Glioma RNA Sequencing

  Whole transcriptome (n=4) and targetted RNA sequencing (n=15) .bam files of infantile glioma samples reported on at the Hospital for Sick Children

  Dataset EGAD00001005092

• T-WGBS for Naive B Cell

  Tagged-WGBS for 3 Naive B Cell samples of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005966

• Human Origins array data for 1510 individuals

  Genotype data typed on the Human Origins array for 1510 individuals published in "Dense sampling of ethnic groups within African countries reveals fine-scale genetic structure and extensive historical admixture."

  Dataset EGAD00001010015

• Data Access Commitee for the project : Methylome profiling of human mesenchymal chondrosarcoma

  Dac EGAC00001003217

• Data Access Committee for the Metastatic Breast Cancer Whole-exome sequencing study

  Dac EGAC00001000434

• DAC for the study of tumor-derived somatic mutation detection in cfDNA

  Dac EGAC00001001569

• Data Access Commitee of the Princess Maxima Center for Pediatric Oncology

  Dac EGAC00001001948

• Single-Cell Atlas of Common Variable Immunodeficiency shows germinal center-associated epigenetic dysregulation in B cell responses

  Common variable immunodeficiency (CVID) is the most prevalent primary immunodeficiency. Here the authors perform single cell omics analyses in CVID discordant monozygotic twins and show epigenetic and transcriptional alterations associated with activation in memory B cells.

  Dataset EGAD00001008575

• Brain Mapping by Integrated Neurotechnologies for Disease Studies: Human Brain Aging Imaging Study

  Compare the MRI data with amyloid PET images and cognitive data.

  Study JGAS000277

• Whole exome sequencing data for two samples

  Whole exome sequencing of two human samples run on the Illumina HiSeq2500 platform. It contains two BAM files aligned to the refrence genoeme GRCh38.

  Dataset EGAD50000000825

• Whole Genome Sequencing of INTERVAL (2019-06-12)

  Whole genome sequencing of participants from the INTERVAL study. . This dataset contains all the data available for this study on 2019-06-12.

  Dataset EGAD00001005084

• CYP2C19 long-read sequencing

  We have assessed the added value of long-read sequencing for PGx focusing on the clinically important and highly polymorphic CYP2C19 gene within 48 samples.

  Dataset EGAD00001009883

• DAC policy The Kids Research Institute Australia

  DAC policy related to the study: Visium CytAssist Spatial Gene Expression analysis for FFPE glioblastoma samples. Committee: Raelene Endersby raelene.endersby@thekids.org.au Anya Jones anya.jones@thekids.org.au Emma Stone emma.stone@thekids.org.au

  Dac EGAC50000000734

• NeoPAL study - RNAseq and Targeted DNA sequencing data

  This dataset is composed of 159 RNAseq data (fastq, bam and count tables) and 35 targeted DNAseq data (fastq).

  Dataset EGAD50000001490

• MGA-NUTM1 fusion in high grade spindle cell sarcoma Data

  There is a total of 4 sample data (2 WGS and 2 RNAseq) belong to 2 patient deposited in this study.

  Dataset EGAD00001004479

• Indigenous American Diversity and Evolution

  The Indigenous American Genomic Diversity Project (IAGDP) investigates the genomic diversity and evolutionary history of Native American populations, which remain underrepresented in global genomic research. As part of this effort, we generated high-coverage whole-genome sequences individuals sampled across eight Latin American countries. This study provides a resource for investigating population structure, demographic history, and adaptive evolution in Indigenous American populations.

  Study EGAS50000001664

• Genetic regulation of gene expression in human brain cell types

  We leveraged single nuclei RNA-seq from 192 human brain samples to map cis-eQTLs in 8 brain cell types. We found extensive cell-type specific genetic effect on gene expression and integrated our results with GWAS to identify putative novel risk genes for brain disorders and the cell types in which the disease mechanisms are likely active.

  Study EGAS00001006345

• The data access committee for Detecting Liver Cancer Using Cell-Free DNA Fragmentomes

  Dac EGAC00001003279

• DAC for the study of response to EGFR Blockade in Colorectal Cancer

  Dac EGAC00001000360

• Data Access Committee for the Centre National de Recherche en Génomique Humaine (CNRGH)

  Dac EGAC00001000723

• RNA Seq fastq files generated for the "Proteogenomic landscape of medulloblastoma subgroups"

  Dac EGAC00001000792

• DAC for the Canadian Biobank on Respiratory and Allergic diseases (CoBRA)

  Dac EGAC00001000901

• DAC for study: Frequent mutation of the FOXA1 untranslated region in prostate cancer

  Dac EGAC00001000962

• DAC for Enhancer-gene rewiring in the pathogenesis of Quebec Platelet Disorder

  Dac EGAC00001001529

• Cancer Clinical Research Trust DAC for the 23 WES samples of melanoma subtypes

  Dac EGAC00001002402

• The Data Access Committee for Human Olfactory Mucosa Cells (DAC HOM) at UEF

  Dac EGAC00001003404

• This DAC will review all requests for data related to the dataset: EGAD00001015613.

  Dac EGAC00001003562

• Searching for genetic modulators of the phenotypic heterogeneity in Brugada Syndrome

  Study EGAS00001005848

• Comparison Across Multiple Types of Sleep Deprivation

  This study is designed to assess neurobehavioral performance, as well as molecular and physiological changes associated with variations in timing and quantity of sleep. Gene expression changes associated with neurobehavioral (cognitive) performance were assessed in a time-series among individuals randomly assigned to four separate sleep conditions during a 10-day inpatient study: a well-rested control, sleep restriction with nighttime sleep, sleep restriction with daytime sleep to roughly simulate shiftwork schedules, and total (acute) sleep deprivation.

  Study phs003924

• 2014_AML Whole genome sequencing analysis result

  This dataset is belong to 2014 whole genome sequenced AML data which is aligned to human reference(human_g1k_v37.fasta). There are 67 paired CR samples from Chunnam University. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003557

• 2015_AML Whole exome sequencing analysis result

  This data is belong to 2015 whole exome sequenced AML data which is aligned to human reference(human_g1k_v37.fasta). There are 40 paired NR samples from Chunnam University. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001003587

• 2015 AML-ETO WGS analysis result

  This data is belong to 2015 AML-ETO 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 EGAD00001004011

• 2015 AML-ETO WGS additional analysis result

  This data is belong to additional 2015 AML-ETO patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 2 paired tumor/normal samples from SNUH. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001004012

• 2014 sequenced Korean WES-Lung Cancer sample 36 pair

  This data is belong to WES-Lung Cancer patients' genome data which is aligned to human reference(human_g1k_v37.fasta). There are 36 paired tumor/normal samples from Samsung Hospital. All samples has passed QC and recalibration steps while aligning to reference.

  Dataset EGAD00001004027

• Single-cell RNA sequencing of 6 follicular lymphoma tumors

  Follicular lymphoma (FL) is an indolent cancer of mature B-cells but carries increased risk of transformation to a more aggressive histology over time. We present here comprehensive profiling both tumor and immune compartments in 6 diagnostic FL biopsies by single-cell RNA sequencing. This confirmed results from 155 FL tumors characterized by mass cytometry (CyTOF) which revealed two distinct evolutionary trajectories with disparate risk of transformation and alternate biologies.

  Study EGAS00001005257

• Single cell RNA sequencing and Whole Genome Sequencing on different cells from the same sample for a triple negative patient derived xenograft and ovarian cancer cell lines.

  Measuring gene expression of genomically defined tumour clones at single cell resolution would associate functional consequences to somatic alterations, as a prelude to elucidating pathways driving cell population growth, resistance and relapse. In the absence of scalable methods to simultaneously assay DNA and RNA from the same single cell, independent sampling of cell populations for parallel measurement of single cell DNA and single cell RNA must be computationally mapped for genome-transcriptome association. Here we present clonealign, a robust statistical framework to assign gene expression states to cancer clones using single-cell RNA-seq and DNA-seq independently sampled from an heterogeneous cancer cell population. We apply clonealign to triple-negative breast cancer patient derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either DNA-Seq or RNA-Seq alone.

  Study EGAS00001003387

• The taxonomic composition of the human microbiome of healthy donors

  Single homogenized human stool samples from five healthy donors and mix were analyzed by shotgun sequencing to generate a baseline for the establishment of humanized microbiome to be transferred into mice.

  Dataset EGAD50000001119

• Covacta RNAseq counts

  RNA-seq data from PAXgene extracted whole blood of patients enrolled in the COVACTA trial. This dataset includes read counts per gene. Read counts were generated for the Gencode v27 annotation using the summarize Overlaps method from bioC in mode “IntersectionStrict”

  Dataset EGAD00001011164

• Cardiogenics_re_sequencing

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Study EGAS00001000079

• Investigating_low_frequency_variants_in_CAD_MI_cases__controls_and_pedigrees_using_whole_exome_sequencing_and_custom_pulldowns

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Study EGAS00001000043

• Investigating_low_frequency_variants_in_CAD_MI_cases__controls_and_pedigrees_using_whole_exome_sequencing_and_custom_pulldowns

  The Cardiogenics re-sequencing study will consist of three parts: Eight pools of 25 individuals will be sequenced using a Nimblegen hybrid-capture solution specific to miRNA sequences, 80 pools of 25 individuals will be sequenced using a custom Agilent SureSelect array covering genes associated with coronary artery disease (CAD) and myocardial infarction (MI), 10 individuals from families with a history of CAD/MI will be exome sequenced using the Sanger exome array. The experiment will use the early onset patients from the German MI cohort and the UK BHF CAD/MI cohort both of which have strong family history. For controls we will consider individuals from the UKBS and KORA cohorts.

  Study EGAS00001000050

• Roifman_DAC

  This Data Access Committee (DAC) will be set up to review applications, and render decisions for requests submitted to EGA to access data deposited into ega-box-1592 by Dr. Chaim Roifman at the Hospital for Sick Children in Toronto, Canada. Contact: Dr. Chaim Roifman. email:chaim.roifman@sickkids.ca

  Dac EGAC50000000243

• snRNAseq prostate cancer

  single-nucleus RNA seq characterization of human fresh frozen prostate cancer samples and non-malignant controls for the same patients. Biopsies were sectioned in 100 micron thick sections, adjacent to those used for spatial transcriptomics.

  Dataset EGAD50000001633

• Identification of neoantigen from MSI-CRC patient derived organoids and its application for targeting by autologous T cells

  Targeting neoantigens expressed only by tumor cells enable tumor destruction without unexpected damages to healthy tissues. Here, we identified neoantigens from microsatellite instable (MSI) colorectal cancer (CRC) patient-derived organoids by genomics and immunopeptidomics approches. The neoantigens in this study were predicted from frame-shift mutation by whole-genome sequencing and confirmed its presentation on organoids surface class I HLA molecules by mass spectrometry. We utilized these neoantigens to isolate neoantigen-specific CD8 T cells from autologous PBMC, and proved tumor organoids killing ability of the CD8 T cells, whereas it did not attack normal organoids. This study provides a platform to identify neoantigen from patient-derived cancer organoids and a model to validate T cell recognition, which could be useful for adoptive CD8 T cell transfer treatment for MSI-CRC patient.

  Study EGAS00001006633

• HIV-phyloTSI: BEEHIVE

  This dataset includes sample numbers TSI_0203 to TSI_0315 for the BEEHIVE cohort of the study. Samples were sequenced using the Illumina NovaSeq system and the veSEQ-HIV method (see Bonsall, Golubchik et al 2020, DOI: 10.1128/JCM.00382-20). Each sample has a BAM file, and its associated reference file.

  Dataset EGAD50000001310

• Exome sequencing in bipolar disorder families

  In the present study two large, multiply affected bipolar disorder families from Cuba were investigated using whole exome sequencing (Illumina HiSeq2500 v4). The variant calling files (VCFs) of 15 individuals provided here were generated using the Varbank exome pipeline from the Cologne Center for Genomics (CCG, https://varbank.ccg.uni-koeln.de).

  Dataset EGAD00001004276

• Bulk RNAseq with monocyte spike-ins

  This dataset contains bulk transcriptomes from the operable cohorts of the LUD2015-005 study (NCT02735239, EudraCT 2015-005298-19), used to verify the deconvolution method used for the scRNA-seq dataset.

  Dataset EGAD00001010306

• 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

• Single-cell RNA sequencing on 5063 single T cells isolated from peripheral blood, tumour and adjacent normal tissues from six hepatocellular carcinoma patients.

  Single-cell RNA sequencing on 5063 single T cells isolated from peripheral blood, tumour and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional properties of these individual cells, coupled with the assembled T cell receptor (TCR) sequences, were used to delineate the molecular subtypes, lineage, and functional properties of each T cell group. For five HCC patient, the exome-seq data of matched normal/tumor and bulk RNA-seq data of tumor are also available.

  Study EGAS00001002072

• HYPERMUTATION AND MALIGNANT PROGRESSION IN LOW-GRADE GLIOMA PATIENTS

  While patients with primary glioblastoma (GBM) have benefited from increased overall survival due to treatment with the alkylating chemotherapy temozolomide (TMZ), the benefit ofTMZ for patients with diffuse low-grade gliomas (LGG) remains unknown. To further explore the relationships among TMZ treatment, hypermutation and malignant progression, we studied tumor evolution in an expanded cohort of untreated and TMZ-treated patients by exome-sequencing of paired IDH1/2-mutant LGGs and their post-TMZ recurrences. Together, these findings further our understanding of the molecular features and clinical behavior of hypermutated clones.

  Study EGAS00001002368

• DAC for genomic data obtained within the Micrometastasis (Oslo1) project from Oslo, Norway

  Dac EGAC00001000558

• Data Access Committee for the project: Epic arrays from human OB and their mimics

  Dac EGAC00001002482

• The Data Access Committee for Human Olfactory Mucosa Cells (DAC_HOM) at UEF

  Dac EGAC00001002527

• The EMC-NICHE DAC considers appeals for hematopoietic/niche-related data sets.

  Dac EGAC00001001897

• Translational Gastroenterology Unit, University of Oxford Data Access Committee for the EPIC-CD study

  Dac EGAC00001003481

• Data access committee for datasets generated by the Tampere University Computational Biology research group

  Dac EGAC50000000177

• Mesothelima_OSCHP_Files

  Oncoscan CHP files for the Mesothelemia Project

  Dataset EGAD00010001540

• Epigenetic Changes in Immune Response and Oncogenesis Related Genes Caused by Heavy Metal Long-Term Exposure

  Our study investigated methylation changes in CpG islands located in immune response and oncogenesis related genes in humans induced by long-term environmental heavy metal exposure. We assessed the methylation levels of 654 CpG sites located on NFKB1, CDKN2A, ESR1, APOA5 and IGF2/H19 genes by targeted bisulfite sequencing (target enrichment by 48.48 Access Array Integrated Fluidic Circuit (Fluidigm, USA) in a cohort of 40 subjects living near a metal mining area (the Kapan mining region, Armenia) and 40 unexposed subjects. We performed linear regression on our data to find differentially methylated positions with adjustment for gender, age, BMI class, smoking, and plasma concentrations of 21 essential and non-essential metals detected by ICP-MS. Our study showed hypomethylation of five CpG sites in the NFKB1 promoter region in the exposed group. According to our findings, the methylation changes of CpG sites in NFKB1, CDKN2A, IGF2 and ESR1 genes are associated with multiple and specific metal exposures. Targeted bisulfite sequencing data obtained for 80 subjects who participated in this study are available through dbGaP. The tables contain information about age, sex, BMI, smoking and exposure status, as well as race and ethnicity of the study participants.

  Study phs003392

• A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

  Here we describe a method to target, multiplex and sequence full-length, native single-molecule the human mitochondrial genome utilizing the RNA-guided DNA endonuclease Cas9.

  Study EGAS00001006203

• Evaluation of the Efficacy and Safety of a Clinical Grade Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Patch: A Pre-Clinical Study

  Cardiomyocyte-derived induced pluripotent stem cells (iPSCs) may represent a promising therapeutic strategy for severely damaged myocardium. This study aimed to assess the efficacy and safety of clinical grade human iPSC-derived cardiomyocyte (hiPSC-CM) patches and conduct a pre-clinical proof-of-concept analysis.

  Study EGAS50000000188

• Single cell resolution of human CNV body map (2019-10-02)

  12 tissues from the warm autopsy are selected for this project. Using 10X Chromium technology we will generate ~1000 single cell/nulei genomic libraries per tissue. Each tissue will be whole genome sequenced (~2 lanes per 1000 cells) on hiseq X10. per single cell we will generate CNV profile and we investigate the level of genomic heterogenity with in tissue and across different tissues. . This dataset contains all the data available for this study on 2019-10-02.

  Dataset EGAD00001005372

• Picuris Pueblo Genomic Project – Modern Dataset

  Please refer to the Supplemental Materials of the paper for more information.

  Dataset EGAD50000001245

• GSA reference

  reference whole exome sequence serving as a reference of individuals. Includes the raw GSa files and the called variants in vcf format merge for all individuals (S1-S5).

  Dataset EGAD50000000481

• 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

• ORCADES 15x (2019-07-23)

  15x whole genome sequencing in samples from the isolated population of Orkney. This dataset contains all the data available for this study on 2019-07-23.

  Dataset EGAD00001005194

• FPKM expression values of the CUP/reference/validation cohort (H021)

  FPKM expression values of the CUP/reference/validation cohort used for tissue-of-origin prediction based on transcriptomic data

  Dataset EGAD00001008638

• WGS of all Patients Listed within this Study

  This dataset contains WGS from whole blood of patients II.2, II.3, III.1-4 and WGS from fibroblasts of patients III.2 and III.3. All WGS was performed on an Illumina NextSeq2000 to a minimum depth of 250 million read pairs (2x150nts).

  Dataset EGAD50000002362

• RNA-seq dataset of salivary gland tumor samples

  This dataset contains paired-end RNA-seq data of salivary gland tumor samples from 94 patients. Sequencing was performed on Illumina HiSeq 2500, HiSeq 4000, HiSeq X Ten or NovaSeq 6000.

  Dataset EGAD50000001191

• Sequencing data of primary uveal melanomas and their matched metastases

  We performed targeted DNA sequencing of primary uveal melanomas and their matched metastases from 35 patients, analyzing a total of 124 tissues. Sequencing was performed on an Illumina HiSeq 2500 instrument using a panel of 538 genes commonly involved in cancer. 124 BAM files were generated.

  Dataset EGAD00001004453