16758 results for "sec+and+unspecified+malignant+neoplasm"

in 38.38 milliseconds.

• Raw DNA and RNA data from breast cancer organoids, control samples and biopsies

  Whole genome sequencing data for primary tumors, matching control material from blood and their corresponding organoid. Whole transcriptome data for organoids.

  Dataset EGAD00001003751

• Whole genome sequencing in 1038 index cases reveals novel causative genes in pulmonary arterial hypertension

  Pulmonary arterial hypertension (PAH) is a rare disorder with a poor prognosis. Deleterious variation within genes encoding components of the transforming growth factor-ß pathway underlie the majority of heritable forms of PAH. Identifying the missing genetic contribution is challenging, even with genes of large effect size, since it likely involves mutations in genes confined to small numbers of PAH cases. In this study, we performed whole genome sequencing, comparing 1038 PAH index cases to 6385 subjects with other rare diseases. Rare variant analysis identified mutations in novel causal genes, namely ATP13A3, AQP1 and SOX17, and provided independent validation of a critical role for GDF2 in PAH. We detected mutations predicted to be disruptive of function in most, but not all, previously reported PAH genes. Taken together these findings provide new insights into the molecular basis of PAH, and support a central role for endothelial dysregulation in disease pathogenesis.

  Dataset EGAD00001003423

• The molecular landscape of colorectal cancer reveals genetic mutations（5 cases）

  We collected tumor samples and adjacent nomal mucosae from 5 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

  Dataset EGAD00001003223

• The molecular landscape of colorectal cancer reveals genetic mutations（17 cases）

  We collected tumor samples and adjacent nomal mucosae from 17 patients with colorectal cancer in surgical operation from 2014 to 2016 in the First Affiliated Hospital of Chongqing Medical University (Chongqing, China) and the Research Institute of Surgery, Third Military Medical University (Chongqing, China). the qualified captured library of each sample was then loaded on Illumina HiSeq 2000 (Illumina, San Diego, CA) platforms and subjected to high-throughput sequencing.

  Dataset EGAD00001003224

• Sequencing data for oesophageal and related samples - Xiaodun Li et al (WGS, RNA)

  Data supporting: "Esophageal adenocarcinoma organoid cultures recapitulate human disease heterogeneity and provide a model for clonality studies and precision therapeutics." Li et al. WGS (BAM files) RNAseq (BAM files) Tumours, organoids, normals

  Dataset EGAD00001004007

• Whole Genome, RNA, and ChIP Sequencing of matched brain tumor-normal pairs (ICGC)

  Whole Genome Seq: Illumina HiSeq sequence data (with >30x coverage) were aligned to the hg19 human reference genome assembly using BWA (Li and Durbin, 2009);duplicate reads were removed from the final BAM file. No realignment or recalibration was performed. Paired-end RNA sequencing reads were mapped to the hg19 assembly of the human reference genome using BWA.Each ChIP-seq library was sequenced with two complete lanes on the Illumina HiSeq 2500 in the 101-bases paired-end rapid mode and aligned to hg19 using bwa.This resulted in the following coverage values (genome-wide, after deduplication, including all uniquely mapping reads):GBM103 macroH2A1: 17x H3K36me3: 20xMB59 macroH2A1: 11x H3K36me3: 11x

  Dataset EGAD00001000664

• FinHer Breast Cancer Study

  The purpose of this study is to sequence 500 known cancer genes in 960 newly diagnosed high risk breast cancer patients treated with current standard of care therapies and trastuzumab, for somatic alteration and copy number changes. We will be using next gen sequencing technology to determine the prognostic relevance of these somatic genetic alterations and of teh low frequency events to determine if they are associated with trastuzumab benefit or HER2 positive breast cancer, i.e. treatment interaction. The samples will be analysed adn correlated with clinical variables including outcome.

  Dataset EGAD00001000871

• Direct transcriptional consequences of somatic mutation in breast cancer

  The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation.

  Dataset EGAD00001002237

• MutWP5: CRUK Mutographs of Cancer: Lung: PD38234 (Targeted) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from explanted lung from pulmonary fibrosis 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. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005925

• cfDNA analysis reveals relation of POLR1D amplification to bevacizumab resistance in colorectal cancer patients

  Bevacizumab is an approved anti-angiogenic drug for patients with metastasized colorectal cancer (mCRC) targeting VEGF. The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months and acquired resistance mechanisms are greatly unknown. Using plasma DNA, we studied the evolution of tumor genomes in a cohort of patients with mCRC (n=150) and observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of TCGA data (n=619) suggested an association with later stages, which we confirmed by longitudinal plasma analyses. We defined the minimally amplified region and studied the mechanistic consequences of copy number gain of the involved genes. The amplification of one gene, POLR1D, impacted cell proliferation, resulting in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab. In several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with evolution of therapy resistance. Hence, we describe a novel resistance mechanism against a widely applied treatment in mCRC patients which will impact clinical management .

  Dataset EGAD00001005761

• Cryopreservation of human cancers conserves tumour heterogeneity for single-cell multi-omics analysis

  Single-cell RNA-Sequencing of three primary breast cancers, two primary prostate cancers, and a metastatic melanoma sample from Wu et al. (2021) Genome Medicine study. Each tumour was sequenced across different cryopreservation conditions including Fresh Tissue (FT), cryopreserved single-cell suspensions (CCS), cryopreserved solid tissue fragments (CT) and a cryopreserved after overnight cold storage (CO). Data was generated using the Chromium controller (10X Genomics) and sequenced on the NextSeq platform.

  Dataset EGAD00001007030

• Targeted myeloid panel DNA-Sequencing Mutations Matrix Validation Cohort

  Profiling of co-mutations was done by targeted resequencing using the TruSight Myeloid assay (Illumina, Chesterford, UK) covering 54 genes recurrently mutated in AML: BCOR, BCORL1, CDKN2A, CEBPA, CUX1, DNMT3A, ETV6, EZH2, IKZF1, KDM6A, PHF6, RAD21, RUNX1, STAG2, ZRSR2, ABL1, ASXL1, ATRX, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CSF3R, FBXW7, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, JAK2, JAK3, KIT, KRAS, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PTEN, PTPN11, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, TET2, TP53, U2AF1 and WT1. For each reaction, 50 ng of genomic DNA was used. Library preparation was done as recommended by the manufacturer (TruSight Myeloid Sequencing Panel Reference Guide 15054779 v02, Illumina). Samples were sequenced paired-end (150 bp PE) on NextSeq- (Illumina) or (300 bp PE) MiSeq-NGS platforms, with a median coverage of 3076 reads (range 824–30565). Sequence data alignment of demultiplexed FastQ files, variant calling and filtering was done using the Sequence Pilot software package (JSI medical systems GmbH, Ettenheim, Germany) with default settings and a 5% variant allele frequency (VAF) mutation calling cut-off. Human genome build HG19 was used as reference genome for mapping algorithms.

  Dataset EGAD00001008506

• Somatic pathogenic variants in the normal mammary gland of sporadic breast cancer patients

  This dataset contains .fastq files generated by targeted DNA sequencing of 542 cancer-associated and cadidate genes (52 individuals), and targeted duplex sequencing of PIK3CA and TP53 genes (4 individuals).

  Dataset EGAD00001008327

• Southern African Prostate Cancer Study (SAPCS) Ethnic Disparity

  The cohort (n=130) consists of prostate cancer patients from South Africa (n=123) and Brazil (n=7). For each patient, a pair of blood and tumour samples were collected. The sequencing data was mapped to hg38 reference. Blood BAMs are named with “-B” as suffix and tumour BAMs are named with “-T” as suffix.

  Dataset EGAD00001009067

• Distinct embryonic phylogenies and driver events of infant Wilms tumor - RNA

  Cancers of adults typically arise through progressive rounds of clonal diversification and intratumoral selective sweeps which generate a long mutational trunk with shorter subclonal branches. Here, we investigated whether tumors of young children exhibit the same phylogenetic configuration. We studied three infants, including two newborns, with the childhood kidney cancer, Wilms tumour, through whole genome sequencing of bulk tissues, of single cell derived organoids, and of microdissections. All three cancers exhibited unusual driver events, with tumours of newborns harbouring FOXR2 rearrangements, delineating a distinct variant of Wilms tumour. Phylogenetic analyses suggest that tumors were seeded in an early, possibly confined window of development. Unusually, following seeding there was extensive polyclonal diversification with little evidence of clonal sweeps, leading to a distinct phylogenetic configuration more reminiscent of normal tissues rather than of adult cancers. These findings indicate that some childhood cancers may diversify via unorthodox phylogenetic pathways.

  Dataset EGAD00001009813

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (Exome)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010110

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010112

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (WG)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010113

• MutWP5: CRUK Mutographs of Cancer: BRCA Carriers (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 20 women who underwent risk-reducing reduction mastecomies due to germline BRCA1/2. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who had cosmetic breast reduction surgeries and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010115

• MutWP5: CRUK Mutographs of Cancer: Breast: Reduction Mammoplasty (Exome)(Novaseq)

  Sequencing of LCM-derived microbiopsies from 10 women who underwent reduction mammoplasty. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequenctly be sent for whole-genome sequencing. Results from this poriton of the study will be compared to women who are BRCA1/2 germline carriers and those with cancer. . This dataset contains all the data available for this study on 2023-03-08.

  Dataset EGAD00001010116

• MSI-Exome-DAC Team Microsatellites Instability and Cancer, INSERM Hospital Saint-Antoine, Paris 12, France Carte d'identité des tumeurs, French league against cancer, Paris France

  Dac EGAC00001000665

• UCSF Sebaceous Carcinoma DAC for review of sequence data release from manuscript in Nature Communications, based in the UCSF Departments of Dermatology and Pathology

  Dac EGAC00001000850

• Early on-treatment changes in circulating tumor DNA fraction and response to enzalutamide or abiraterone in metastatic castration-resistant prostate cancer - Data Access Committee

  Dac EGAC00001003128

• UTSW KCP DAC

  This DAC manages access to WES and RNA-Seq data from studies approved under the IRBs of KCP principal investigators.

  Dac EGAC50000000203

• High throughput profiling of undifferentiated pleomorphic sarcomas identifies two main subgroups with distinct immune contexture, clinical outcome and sensitivity to targeted therapies

  Study EGAS00001004612

• Mutation and Microsatellite Burden Predict Response to PD-1 Inhibition in Children with Germline DNA Replication Repair Deficiency: An Observational Registry Study

  Study EGAS00001005579

• TSO500 on DNA

  Targeted sequencing using the TruSight Oncology 500 DNA probes panel, on samples 162 and 521

  Dataset EGAD50000000270

• BreastCancer_Miroarrays

  Genotyping array data for breast cancer and matched normal mammary gland samples

  Dataset EGAD00010002251

• Gentoypes_Lesotho

  Individuals genotyped on the Illumina GSA v2. Autosome and X chromosome.

  Dataset EGAD00010002468

• BLEMD (arrays set)

  Circulating tumor cells for comprehensive and multiregional non-invasive genetic characterization of multiple myeloma (arrays set)

  Dataset EGAD00010001857

• DNA_Methylation_450K

  BLUEPRINT DNA methylation profiles of monocytes, neutrophils and T cells from healthy donors

  Dataset EGAD00010000850

• RNA-Sequencing generated from 180 human putamen and substantia nigra

  Dataset EGAD00001005526

• RNA-seq data from diagnosis and relapse samples of Down Syndrome acute lymphoblastic leukemia.

  Dataset EGAD00001003280

• Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

  Dataset EGAD00001001096

• RNA Editing Exome

  Exome sequencing data for tumor and matched normal samples of the EGAS00001000495 project.

  Dataset EGAD00001000626

• Comprehensive Characterization of Early Relapse and End-Stage Relapsed Refractory Multiple Myeloma (HIPO K08K/H067/H021+nonHIPO)

  Study EGAS00001007469

• Disorders of growth and insulin action

  Illumina paired-end sequencing of whole- exome pulldown DNA from Severe Insulin Resistant patients.

  Dataset EGAD00001000381

• Multisample2 Amplicon

  Amplicon data of tumor samples generated for validation of WES findings and further sub clonal mapping

  Dataset EGAD00001004020

• Familial CEBPA-mutated AML whole exome sequencing dataset

  Whole exome sequencing data for AML and matched normal samples

  Dataset EGAD00001000996

• Seminoma exome sequencing

  Exome sequencing data for 8 pairs of seminomas and matched normal

  Dataset EGAD00001001002

• Osteosarcoma exome sequencing dataset

  Whole exome sequencing data of primary, secondary and tertiary tumor from a patient.

  Dataset EGAD00001002145

• Melanoma multi site metastases

  These are caveman, pindel, battenberg and brass calls for index patients' metastatic melanoma genomes within this study.

  Dataset EGAD00001005483

• KRAS Mutations in Multiple Myeloma

  Fastq files for 80 Multiple Myeloma Patients and 12 cell-lines

  Dataset EGAD00001005743

• RRBS melanoma biopsies

  RRBS data for melanoma biopsies at baseline and after treatment

  Dataset EGAD00001009060

• ORIENT study

  scRNAseq dataset containing 5 healthy donors and 4 asthmatic donors.

  Dataset EGAD00001009687

• whole genome sequence of liver cancer

  There are six samples with three blood samples and three organids

  Dataset EGAD00001009841

• Whole Exome and Targeted Sequencing in Tourette Syndrome Multiplex Families

  This study consists of 771 individuals from 15 extended, multi-generational Tourette Syndrome (TS) pedigrees collected by the Tourette Syndrome Association International Consortium for Genetics (TSAICG), 213 of whom are affected either with TS or its broader, genetically related phenotype, chronic tic disorder (CT). Prior microsatellite linkage analysis, including 624 individuals from these families, has identified a genome-wide significant TS/CT susceptibility locus on chromosome 2p21-24 with two additional loci meeting criteria for suggestive linkage on chromosomes 6p12-21 and 17p11-q11. Subsequent joint linkage and association analysis, incorporating genome-wide SNP genotyping on the Illumina Hap610 platform from 221 individuals, has strengthened the evidence for a major TS/CT locus on chromosome 2p but did not refine the locus further. In addition, haplotype analyses suggest that multiple TS/CT loci may exist on the short arm of chromosome 2. The goal of the current sequencing study is to use exon-focused sequencing, supplemented with targeted sequencing of additional known functional elements on chromosome 2p, to identify susceptibility variants contributing to the highly penetrant TS/CT phenotype in these families.

  Study phs000415

• Final results and ctDNA analyses from the randomized phase 3 IMpassion031 trial evaluating peri-operative atezolizumab for early-stage triple-negative breast cancer

  In IMpassion031, adding atezolizumab to neoadjuvant chemotherapy significantly improved pathologic complete response (pCR) rate (primary endpoint) for stage II/III triple-negative breast cancer (TNBC). Patients with stage II/III TNBC were randomized 1:1 to neoadjuvant chemotherapy plus peri-operative atezolizumab or pre-operative placebo. Descriptive secondary endpoints included event-free, disease-free, and overall survival. Long-term outcomes favored the atezolizumab group (event-free survival HR 0.76, 95% CI: 0.47–1.21). Among patients without pCR, 14/70 (20%) atezolizumab-treated and 33/99 (33%) placebo-treated patients received additional adjuvant therapy, frequently capecitabine. In exploratory analyses, pCR was prognostic for long-term outcome. Patients with baseline ctDNA-negative status (6%) had excellent long-term outcomes. Most patients (87%) had cleared ctDNA at surgery. ctDNA-positive status at surgery identified a subset of non-pCR patients with poorest prognosis. Long-term safety was consistent with primary results. Adding atezolizumab to chemotherapy for stage II/III TNBC is associated with more favorable long-term outcomes. ctDNA dynamics provide prognostic value beyond pCR. ClinicalTrials.gov identifier: NCT03197935

  Study EGAS50000000974

• Rucaparib in patients presenting a metastatic breast cancer with Homologous Recombination Deficiency, without germline BRCA1/2 mutation, pronostic value of high LOH genomic score and predictive value of HRDetect (microarray)

  Breast cancer may present genomic alterations leading to homologous recombination deficiency. PARP inhibitors have proved their efficacy in patients with HER2-negative metastatic breast cancer (mBC) harboring germline (g) BRCA1/2 mutations. We conducted the phase 2 RUBY trial to assess the efficacy of rucaparib in HER2-negative mBC with high genomic loss of heterozygosity (LOH) score or somatic, without gBRCA1/2 mutation. 220 of 711 patients with mBC screened for LOH presented high LOH score which was associated with a higher likelihood of death (HR = 1.39, 95% CI: 1.11-1.75, p = 0.005). The primary objective was not reached with a clinical benefit rate (objective response or SD>16 weeks) of 13.5%. Two LOH-high patients, without somatic BRCA1/2 mutation, presented a complete and durable response (14 and 32 months). HRDetect tended to be associated with response to rucaparib, whithout reaching statistical significance (median HRDetect responders versus non responders: 0.465 versus, 0.040, p = 0.2135). Our data suggests that a small subset of patients with high LOH score could derive benefit from PARP inhibitors.

  Study EGAS00001004755

• Resuscitation Outcomes Consortium Trial of Continuous Compressions Versus Standard CPR in Patients With out-of-Hospital Cardiac Arrest (ROC CCC-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions.Objectives: To compare the rate of survival to hospital discharge after continuous chest compressions versus standard American Heart Association recommended cardiopulmonary resuscitation with interrupted chest compressions in patients with out-of-hospital cardiac arrest.Background: Standard cardiopulmonary resuscitation (CPR) consists of manual chest compressions to maintain blood flow and positive-pressure ventilation to maintain oxygenation until spontaneous circulation is restored. Chest compressions during standard CPR are interrupted frequently by ventilations. These interruptions reduce blood flow and potentially reduce the effectiveness of CPR. In animals with cardiac arrest, the interruption of chest compressions has been associated with decreased survival. Observational studies involving humans with out-of-hospital cardiac arrest of presumed cardiac cause have suggested that continuous compressions are associated with higher rates of survival than interrupted compressions.Participants: Of 35,904 patients with out-of-hospital cardiac arrest who were screened, 26,148 were eligible for participation in the trial and were enrolled in the trial during either the run-in phase or the active-enrollment phase. The active-enrollment phase included 23,711 patients, of whom 12,653 were assigned to the intervention group and 11,058 to the control group.Design: There were 114 participating EMS agencies across the eight participating Resuscitation Outcomes Consortium (ROC) sites, which were grouped into 47 clusters. Clusters of agencies were randomly assigned, in a 1:1 ratio, to perform continuous chest compressions or interrupted chest compressions during all the out-of-hospital cardiac arrests to which they responded. Each cluster was required to begin enrolling patients in a run-in phase to demonstrate adherence to the protocol before entering the active-enrollment phase of the trial. Twice per year, each cluster was crossed over to the other resuscitation strategy.Patients assigned to the group that received continuous chest compressions (intervention group) were to receive continuous chest compressions at a rate of 100 compressions per minute, with asynchronous positive-pressure ventilations delivered at a rate of 10 ventilations per minute. Patients assigned to the group that received interrupted chest compressions (control group) were to receive compressions that were interrupted for ventilations at a ratio of 30 compressions to two ventilations; ventilations were to be given with positive pressure during a pause in compressions of less than 5 seconds in duration. The primary outcome was the rate of survival to hospital discharge. Secondary outcomes included neurologic function at discharge, which was measured with the use of the modified Rankin scale, and adverse events. Conclusions: During the active-enrollment phase, 1129 of 12,613 patients in the continuous chest compression group and 1072 of 11,035 patients in the interrupted chest compressions group survived to hospital discharge.In patients with out-of-hospital cardiac arrest, continuous chest compressions during CPR performed by EMS providers did not result in significantly higher rates of survival or favorable neurologic function than did interrupted chest compressions.

  Study phs003901

• Whole Genome Sequencing and Variant Calling for Autism Families

  We extracted DNA from whole blood or lymphoblast-derived cell lines and assessed the DNA quality with PicoGreenTM and gel electrophoresis. Whole genome sequencing was performed (Illumina HiSeq2000 and Illumina HiSeq X). WGS reads were mapped to the human reference genome assembly hg19 (GRCh37) using Burrows-Wheeler Aligner v.0.7.12 (TCAG) or Isaac v.2.0.13 (Macrogen). For each genome, we performed local realignment and quality recalibration and detected SNVs and small indels using GATK Haplotype Caller v.3.4.6 without genotype refinement. We detected CNVs using ERDS (estimation by read depth with single nucleotide variants) and CNVnator. We detected structural variants using Manta v.0.29.6. When available by the variant caller (i.e. GATK and Manta), trio-based joint variant calling was conducted for each family.

  Dataset EGAD00001008452

• DAC for the Study EGAS00001006374: Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. snRNAseq of 79 (61 CM patients + 18 controls).

  Dac EGAC00001002804

• BREAKFAST trial DAC

  Data Access Committee for BREAKFAST trial datasets, IFOM-ETS The AIRC Institute of Molecular Oncology and INT Istituto nazionale Tumori Milano, Italy.

  Dac EGAC50000000401

• Baulac Lab - Paris Brain Institute

  Raw 10X single-nucleus RNA-seq data from human postoperative brain samples of patients with epilepsy and cortical malformations.

  Dac EGAC50000000546

• Single cell sequencing reveals expanded cytotoxic CD4+ T cells and two clusters of peripheral helper T cells in synovial fluid of ACPA+ RA patients

  Study EGAS00001005241

• ILC RNAseq dataset

  RNAseq data from ILC (n=168) and IC-NST/IDC (n=79)

  Dataset EGAD50000002527

• CRISPR_perturbations_IRF4_PRDM1_Bcells

  CRISPR perturbations of IRF4, PRDM1, and AAVS1 (within PPP1R12C gene) in activated B cells

  Dataset EGAD50000002113

• DLBCL cfDNA seq

  Sequencing dataset of 290 DLBCL and HGBL cfDNA samples of paired end 150bp sequencing runs.

  Dataset EGAD50000000602

• Whole-exome sequencing of buccal mucosa samples

  40 buccal mucosa samples and a paired blood sample were whole-exome sequenced.

  Dataset EGAD50000000080

• WTCCC2 Pre-eclampsia

  Genotype data from the Affymetrix 6.0 platform for 4,375 Colombian pre-eclampsia cases and controls

  Dataset EGAD00010001647

• dataset_raw_NativesAmericans_LDGH_august2020

  Genome-wide data for 98 Native American individuals from Andes and Amazon

  Dataset EGAD00010001958

• miRNA profiling of human plucked hair follicle

  miRNA profiling of human plucked hair follicle from frontal and occipital scalp

  Dataset EGAD00010001500

• EGAD00010000450

  Genome Wide Genotype Data

  Dataset EGAD00010000450

• Medulloblastoma Illumina RNA-Seq

  Illumina RNA-sequencing of Medulloblastoma primary and relapse tumor.

  Dataset EGAD00001009425

• Medulloblastoma Illumina WGS

  Illumina whole genome sequencing of Medulloblastoma Blood, Primary tumor, and Relapse tumor

  Dataset EGAD00001009424

• Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

  Dataset EGAD00001003778

• RNA Editing Transcriptome

  Transcriptome sequencing data of tumor and 10 matched normal samples of the EGAS00001000495 project

  Dataset EGAD00001000627

• Longitudinal analysis of treatment induced genomic alterations

  Variant call set (vcf) for three (primary and two recurrent) tumors

  Dataset EGAD00001003164

• High-grade meningioma sequencing data

  Whole genome, whole exome, and custom panel sequencing of high-grade meningioma cohort

  Dataset EGAD00001003220

• The UCSF Glioblastoma Genome Project #1

  Dataset contains MeDIP-Seq, MRE-Seq and H3K4me3 ChIP-Seq data on 5 GBM patients.

  Dataset EGAD00001000777

• Whole Genome Sequencing of acral melanoma

  Whole Genome Sequencing of 5 acral melanomas and matched normal samples

  Dataset EGAD00001000944

• Transcriptomic profiling of lymphedema

  RNA-seq of skin from human subjects with and without lymphedema

  Dataset EGAD00001006246

• How to encrypt files with EGACryptor

  File preparation Due to the processes used at the EGA for file archival the use of non-alphanumeric characters in a filename will cause issues in archival. By convention whitespaces in filenames are to be avoided and should be replaced with the underscore character (_). Before encrypting your files please make sure that any files that will be uploaded to EGA do not use special characters such as # ? ( ) [ ] / \ = + < > : ; " ' , * ^ | &  Crypt4gh EGACryptor Files encrypted with EGACryptor must be uploaded via FTP EGACryptor The EGACryptor v.2.0.0 is a JAVA-based application which enables submitters to produce EGA compliant encrypted files along with files for the encrypted and unencrypted md5sum for each file to be submitted. The application will generate an output folder that will by default mirror the directory structure containing the original files. This output folder can subsequently be uploaded to the EGA FTP staging area via an FTP or Aspera client. Download EgaCryptor Download EgaCryptor Using the EgaCryptor Using the EgaCryptor Encrypting single file Encrypting multiple files Encrypting all files in folder Points to note Troubleshooting Troubleshooting Download EGACryptor The required jar files can be obtained by downloading EgaCrytptor jar file After the file has been downloaded, extraction of the zipped archive is required. The EGACryptor has been built to work with Java Runtime Environments from version 6 and above and with the OpenJDK Environment. Please refer to the relevant resources for installation guidance. Installing the latest version of the OpenJDK will include the JCE files. If your installation of Java JRE is less than 1.8.0_151 will require the manual installation of the JCE Policy Files. You can verify the version of the Java SE Runtime Environment (JRE) installed by using the command: $ java -version If you need to install the JCE please follow the instructions below: Installing the JCE policy files (due to licensing terms and conditions the required policy files must be downloaded direct from the ORACLE website) : Download the unlimited strength JCE policy files (JRE 6 / JRE 7/ JRE 8) Uncompress and extract the downloaded file. This will create a subdirectory called JCE. This directory contains the following files: README.txt, COPYRIGHT.html, local_policy.jar and US_export_policy.jar Install the two policy JAR files by replacing the existing ones in your java home directory. Install the two policy JAR files by replacing the existing ones in your directory. The standard place for JCE jurisdiction policy JAR files is: /lib/security [Unix] or \lib\security [Win32] Notes: refers to the directory where the Java SE Runtime Environment (JRE) was installed. Additional performance enhancements that have been included in the EGACryptor V2.0.0: The ability to parallelise the processing of datasets through the use of the resources on a system. Multicore systems will allow the user to specify n-1 cores for an n-core system. The use of this feature on clusters may speed up the processing of datasets that have large file numbers but consult your local cluster guide to ensure that there are not monopolising resources that are needed by other system users. The default for this process remains single threaded. 3 levels of system usage can be specified. Full usage within the limits detailed above. A limited mode that will ensure that 50% of the system resources are available for other tasks. Maximum mode is limited to 75% of system resources, this allows encryption to be prioritised but allows for the system to be usable for light alternate tasks. Finally there is a throttling mode that allows you to specify the exact number of computational threads to be used. the EGACryptor is able to ingest a structured directory and will output a directory with the same structure containing the encrypted files along with the md5checksums for the plain and encrypted files. The entire output directory can then be uploaded to the EGA for archival. as with the input path, it is now possible to specify the output path. the options have been updated inline with the upgraded functionality. The tool can only be used via the command line. The EGACryptor is designed to perform a single task, encrypting your data, for upload of these files please refer to our uploading guide Using the EgaCryptor Below are the three ways on how the EGACryptor tool can be used: Encrypting a single file : java -jar ../EGA-Cryptor_2_0_0.jar -i example1.bam Encrypting multiple files : java -jar ../EGA-Cryptor_2_0_0.jar -i "example1.bam,example2.bam" Encrypting all the files within a folder java -jar ../EGA-Cryptor_2_0_0.jar -i path/to/target/directory By default the EGACryptor v2 will create a new output directory containing all encrypted files and the relevant checksums within the target directory. If a specific directory is desired this can be specified by using the -o flag. This can be achieved in a similar manner to the following example: java -jar ../EGA-Cryptor_2_0_0.jar -i /path/to/target/directory -o /path/to/output/directory The tool will output three files per input file: file.gpg ( encrypted file ) file.md5( file md5 sum value file ) file.gpg.md5 ( encrypted file md5 sum value file ) All output files must then be uploaded to your submission account using Aspera or FTP. Further documentation on how to upload files: FTP and Aspera. Points to note Remember to provide the path to EgaCryptor.jar and run the command from within the directory the file/s are located. ECryptor writes files to the source directory of your local file system, as a result you must have write-access permissions for the source directory. Troubleshooting If in doubt about the function of the EGACryptor it is recommended to first consult the built-in documentation. This can be accessessed by using the -h flag as stated in the following table. Built-in Commands Table: list of the command line options built into EGA-Cryptor v2.0.0. Command line Option Action --------------------- ----------- -f Set this option to allow application to create maximum threads to utilise full capacity of cores/processors available on machine -h Use this option to view the bult-in help menu * -i File(s) to encrypt. Provide file/folder path or comma separated file path if multiple files in double quotes -l Set this option to allow application to create maximum threads equals to 50% capacity of cores/processors available on machine -m Set this option to allow application to create maximum threads equals to 75% capacity of cores/processors available on machine -o Path of the output file. This is optional. If not provided then output files will be generated in the same path as that of source file (default: output- files) -t Set this option if user wants to control application to create maximum threads as specified. Application will calculate no. of cores/processors available on machine & will create threads accordingly Encryption Errors UnixFileSystem.createFileExclusively (Native Method) The error is thrown by UNIX ("UnixFileSystem.createFileExclusively(Native Method)"). It appears that the user does not have write-access to the file system where the file to be uploaded is located. EGACryptor always writes MD5 checksums into files before uploading them to the server, and these files are created in the same location where the uploaded file itself resides.Solution: address your directory permission issue and re-run the command. Install JCE Unlimited Strength Jurisdiction Policy files The JCE policy unlimited strength jurisdiction files should be installed according to your current java version If you are still facing difficulty with the EGACryptor v.2 after having consulted the documentation please contact the EGA Helpdesk.

  Documentation submission/data/file-preparation/egacryptor

• A super-enhancer associated with CD47 links pro-inflammatory signaling to CD47 upregulation in breast cancer

  CD47 is a cell surface molecule that inhibits phagocytosis of cells that express it by binding to its receptor, SIRP&#945;, on macrophages and other immune cells. CD47 is expressed at different levels in normal cells, however, in cancer cells, CD47 transcript and protein expression is aberrantly increased. Here we sought to uncover the regulators of CD47 transcription, including active enhancers that increase its aberrant expression in cancer cells, in order to reveal mechanisms by which different neoplastic cells generate this dominant &#39;don&#39;t eat me&#39; signal. Enhancers are genomic regions, often referred to as "switches", that can turn on or off the transcription of target genes. Recently the discovery of super-enhancers (SEs) has given more insight into the regulatory architecture of key genes that are highly expressed in a specific cell type, during a particular developmental stage or in disease. By analyzing the CD47 regulatory genomic landscape, we discovered: i) A distinct super-enhancer (SE) is associated with CD47 upregulation in breast cancer cells ii) Disruption of CD47 SEs by using the BRD4 inhibitor JQ1 robustly reduces CD47 gene expression; and iii) The TNF-NFKB1 signaling pathway is directly involved in the regulation of CD47 by interacting with a distal downstream constituent enhancer located within a CD47-associated SE specific to breast cancer. Our results describe a novel mechanism that cancer cells have evolved to drive CD47 overexpression to escape immune surveillance.

  Study phs001264

• HuBMAP: A Spatially Resolved Molecular Atlas of Human Endothelium

  The human circulatory system plays a vital role in the proper functioning of every organ in the human body. Because vascular related diseases, such as atherosclerosis, do not occur homogeneously throughout the vascular tree, differences in the endothelium of various organs must exist. There is even evidence of heterogeneity of adjacent endothelial cells. We are studying normal endothelium throughout the body and across individuals of different ages to characterize these differences. The first step will be to procure normal tissue samples from a wide range of organs. From disaggregated samples of these tissues, we will perform single cell combinatorial indexing (sci-) to generate chromatin accessibility (sci-ATAC-seq) and transcriptome (sci-RNA-seq) data from millions of single cells across hundreds of samples.&nbsp; Molecular heterogeneity might correlate with multiple facets of the anatomical distribution of endothelium, including vascular vs. lymphatic, arteries vs. veins, capillaries vs. larger vessels, differences between organs, organ zonation, cell-to-cell differences, etc. Based on heterogeneous markers defined from deep profiling of disaggregated cells, we will employ seqFISH to spatially relate the distinct endothelial subpopulations arising from the single nuclei data to histologic preparations. For example, this will allow us to identify subpopulations with particular markers as arterial, capillary, venous, or lymphatic. The end product will include multiparameter images in which the complete gene expression and chromatin accessibility profile can be interactively visualized for every cell.

  Study phs002267

• Plasma-Seq of patients with metastatic prostate cancer

  Study 1 In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We wanted to make whole-genome analysis from plasma DNA amenable to clinical routine applications and developed an approach based on a benchtop high-throughput platform, i.e. Illuminas MiSeq instrument. We performed whole-genome sequencing from plasma at a shallow sequencing depth to establish a genome-wide copy number profile of the tumor at low costs within 2 days. The genome-wide profiling in the plasma of our patients revealed multiple copy number aberrations including those previously reported in prostate tumors, such as losses in 8p and gains in 8q. High-level copy number gains in the AR locus were observed in patients with CRPC but not with CSPC disease. We identified the TMPRSS2-ERG rearrangement associated 3-Mbp deletion on chromosome 21 and found corresponding fusion plasma fragments in these cases. In an index case multiregional sequencing of the primary tumor identified different copy number changes in each sector, suggesting multifocal disease. Our plasma analyses of this index case, performed 13 years after resection of the primary tumor, revealed novel chromosomal rearrangements, which were stable in serial plasma analyses over a 9 months period, which is consistent with the presence of one metastatic clone. Our approach provides specific genomic signatures within 2 days which may therefore serve as “liquid biopsy”.

  Study EGAS00001000451

• Long-read trio sequencing of unsolved patients with intellectual disability

  Long-read sequencing (LRS) has the potential to comprehensively identify all medically-relevant genome variation, including variation commonly missed by short read sequencing (SRS) approaches. To determine this potential, we performed LRS up to 40x coverage using the Pacific Biosciences Sequel instrument for 5 patient-parent trios with intellectual disability, whose aetiology remained unresolved after SRS exomes and genomes. A first systematic assessment of LRS coverage showed that ~35Mb of the genome was only accessible by LRS and not SRS. Structural variant (SV) calling yielded on average 28,292 SV calls per individual, totalling 12.9 MB of sequence. Trio-based analyses showed concordance for up to 95% of these SV calls across the genome, and 80% of the LRS SV calls were not identified by SRS. De novo mutation analysis did not identify any de novo SVs, confirming these are rare events. Because of high sequence coverage, we were also able to call single nucleotide substitutions. On average, we identified 3 million substitutions per genome, with a Mendelian inheritance concordance of up to 97%. Of these, approximately 100,000 were located in the ~35Mb of the genome that was only captured by LRS. Moreover, these variants affected the coding sequence of 64 genes, including 32 known to cause Mendelian disorders. Although no clinical diagnoses were made in these 5 patients, our data show the potential added value of LRS compared to SRS for identifying medically relevant genome variation.

  Study EGAS00001004319

• Identification of the mutational consequences of precancerous liver disease (including alcohol abuse) on the genomes of human adult stem cells.

  Stem cells are believed to be the cells-of-origin cancer. Nevertheless, their genome remains remarkably stable during life. To increase insight into how these cells can drive tumorigenesis, we set out to determine the genomic integrity of human adult stem cells from patients with liver disease associated with increased cancer risk. To this end, we characterized genome-wide mutation profiles of single ASCs from livers of patients with alcoholic liver disease, non-alcoholic liver disease and primary sclerosing cholangitis. The patients included in our study received a liver transplant due to their liver disease. Strikingly, we found that ASCs in these livers maintain a stable genome and have comparable mutation rates as healthy human liver ASCs. We did observe more nonsense and nonsynonymous mutations in COSMIC cancer genes that are hit by dominant mutations in tumors in comparison to healthy ASCs (n.s.), including two ASCs in alcoholic liver disease patients with a nonsense mutation in PTPRK. Next, we sequenced 5 biopsies of an alcoholic tumour to identify the mutational patterns in the tumour-initiating ASC. We found that the mutational patterns are, again, similar to healthy liver, but the mutational load is slightly higher. This suggests that the increased cancer risk in the liver disease patients is not caused by an increased mutational load, but rather that the precancerous liver environment promotes outgrowth of cells that would normally be selected against.

  Study EGAS00001002983

• ITER-FIISC Data Access Committee (Sepsis)

  DAC for Whole-exome variant calling of individuals from the study of sepsis and acute distress respiratory syndrome in Spain.

  Dac EGAC50000000641

• JKLab, SNU College of Medicine

  JKLab, Lab of Cellular Translational Medicine, Department of Anatomy and Cell Biology, Seoul National University College of medicine.

  Dac EGAC50000000288

• Adrenal scRNA sequencing data access

  Raw sequencing datasets for manuscript "Hybrid untargeted and targeted RNA sequencing facilitates genotype-phenotype associations at single-cell resolution".

  Dac EGAC50000000869

• Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

  Study EGAS00001003886

• Preeclampsia InterPregGen Consortium: GWAS meta-analysis summary statistics for European fetal preeclampsia cases versus controls and GWAS genotype data for European fetal preeclampsia cases

  Study EGAS00001001048

• MPNST study - LCM WGS data

  LCM WGS data from one MPNST patient, including one primary and five recurrence regions

  Dataset EGAD50000002568

• SMPaeds tumour tissue lcWGS

  Low coverage whole genome sequencing (0.5-4X) for both relapse and archival diagnostic tumour tissue.

  Dataset EGAD50000000784

• RNAseq for 4 pdx and 1 cell-line

  RNAseq for #1049, #111, #1217, #206, COV362

  Dataset EGAD50000000032

• Methylation_PBL_UC_Tofacitinib

  Longitudinal whole-genome DNA methylation profiling of PBL obtained from UC patients categorized as responders and non-responders

  Dataset EGAD00010002590

• Groupe_case

  Illumina EPIC arrays of human osteoblastomas and their mimics

  Dataset EGAD00010002279

• Whole transcriptome and 850k methylome profiling of human MBM

  Assessment of methylation status of ~850,000 sites

  Dataset EGAD00010002281

• Batch1-2_Genotypes_PostQC

  Combined genotypes for Batch 1 and 2 after quality control. All individuals included in analyses.

  Dataset EGAD00010002127

• Methylation_monocytes_female_CD

  Whole-genome DNA methylation profiling of CD14+ monocytes obtained from CD-active, CD-remissive and non-CD individuals

  Dataset EGAD00010001846

• ADME_gene_expression

  Gene expression for 303 ADME and ADME related genes (averaged log2 signal intensities using Human-WG6v2 Expression BeadChip)

  Dataset EGAD00010001709

• Illumina_450K

  Primary renal cell carcinoma (RCC), RCC metastases and cell lines by Illumina 450K

  Dataset EGAD00010001001

• 450K_DKFZ_CLL_NB

  CLL and normal B cell samples using 450K

  Dataset EGAD00010000871

• TCR β-chain repertoire characterization of regulatory and conventional T cells in breast tumors from breast cancer patients.

  Dataset EGAD00001006428

• Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

  Dataset EGAD00001001602

• ChIPseq data

  ChIPseq data for H3K4me1 and H3K9me3 in HT29; H3K4me1, H3K27me3, H3K9me3, H3K36me3 in LoVo.

  Dataset EGAD00001003258

• 20180221_EGA_OESO

  Illumina platform sequencing of whole genome libraries prepared from normal, Barrett's oesophagus and oesophageal cancer samples from 44 donors

  Dataset EGAD00001003996

• Dataset of PPB

  Whole exome sequencing and miRNA-seq data of PPB.

  Dataset EGAD00001000822

• Maastricht Irritable Bowel Syndrome metagenomic sequencing

  Metagenomic shotgun sequencing of Irritable bowel syndrome patients and matched controls

  Dataset EGAD00001002668