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• 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

• 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

• 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

• 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

• 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

• 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

• 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

• Deep multi-region WGS of lung cancer tumours

  Deep WGS (germline and 2-5 tumour regions) was performed on 20 patients: 13 lung adenocarcinoma, 5 squamous cell carcinoma, 2 small-cell lung cancers. A total of 68 BAM files are provided, where tumours were sequenced to 60x or 150x depth.

  Dataset EGAD00001005287

• Single cell RNAseq of PBMC from bladder cancer patients

  This dataset contains single cell RNA sequencing data of PBMC samples from 20 bladder cancer patients. cDNAs and single cell RNA libraries were prepared following manufacturer’s user guide (10x Genomics). Each library was sequenced in HiSeq4000 (Illumina) to achieve ~300 million reads following manufacturer’s sequencing specification.

  Dataset EGAD00001006182

• 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

• 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

• 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

• Genomic gain of EBV's LMP-1 in NKTCL

  The study found a high recurrence of genomic gain of LMP1 locus within EBV-associated NKTCL. The pilot data set and extended dataset of 77 WGS NKTCLs found 18/77 tumoral genomes to harbour genomic gain of LMP-1 locus within the EBV viral genomes within NKTCL tumoral sequencing data. The study also found 1/10 NKTCL cell lines to be positive for LMP-1 locus gain within EBV genomes too. This dataset includes solely the confirmatory WGS data of LMP-1 gain from NKYS cell lines using Oxford Nanopore long-read sequencing technology.

  Study EGAS50000000260

• T-cell reconstitution after reduced dose ATLG induction in kidney transplant recipients

  Pre-sensitized kidney transplant recipients have a higher risk for rejection following kidney transplantation and therefore receive a lymphodepletional induction therapy with anti human T-lymphocyte globulin (ATLG). The time course of lymphocyte reconstitution with regards to overall and donor-reactive T-cell receptor (TCR) specificity remains elusive. In this study we aimed to describe the TCR repertoire in a reduced dose ATLG regimen making it possible to evaluate shifts in the shape of the immune repertoire and to detect the reappearance of donor-reactive T-cells following reduced lymphodepletional induction therapy.

  Study EGAS00001005941

• Measurement of SARS-CoV-2 variants fraction in infected alveolar cells

  With the continuous emergence of highly transmissible SARS-CoV-2 variants, the comparison of their infectivity has become a critical issue for public health. However, a direct assessment of the viral characteristic has been challenging due to the lack of appropriate experimental models and efficient methods. Here, we conducted full-length transcriptome sequencing of single human alveolar cells infected by multiple SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1). Using unique mutations of each VOC, we calculated the fraction of VOCs in infected cells.

  Study EGAS00001006730