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• Gentoypes_SouthAfrica

  Individuals genotyped on the Illumina Omni2.5. Autosome and X chromosome.

  Dataset EGAD00010002467

• Panamanian genotype data

  84 Indigenous and admixed individuals from Panama genotyped with Axiom Human Origins (Affymetrix)

  Dataset EGAD00010002473

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

  Dataset EGAD00001001096

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Dublin, Ireland.

  Study EGAS00001005844

• Azienda Ospedaliero-Universitaria di Parma Data Accessibility

  Regulation on the sharing and accessibility of data belonging to Azienda Ospedaliero-Universitaria di Parma

  Dac EGAC50000000239

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Umea, Sweden.

  Study EGAS00001005842

• Whole Exome Sequencing of Bipolar cases and controls performed at the Broad Institute on a cohort from Cardiff, UK (Craddock)

  Study EGAS00001005845

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from Cambridge, UK

  Study EGAS00001005854

• Whole Exome Sequencing of Bipolar cases and matched controls performed at the Broad Institute on a cohort from London, UK

  Study EGAS00001005851

• Whole Exome Sequencing of Spanish Patients diagnosed with rare ophtalmogenetic disorders: Macular Dystrophy, Retinitis Pigmentosa and Leber's congenital amaurosis.

  Study EGAS00001004084

• Integration of metabolomics, genomics and immune phenotypes reveals the causal roles of metabolites in disease

  Study EGAS00001005348

• Analysis of circulating miRNAs for the identification of new prognostic and predictive markers in gastro-entero-pancreatic neuroendocrine tumour (GEP-NET)

  Study EGAS00001007227

• Multi-omics integration reveals only minor long-term molecular and functional sequelae in immune cells of individuals recovered from COVID-19

  Dac EGAC00001002267

• Liquid biopsy-based minimal residual disease monitoring for early risk stratification and decision-making in advanced non-small cell lung cancer

  Dac EGAC50000000832

• Biomarker data

  Biomarker data including the time point of sample collection, tumor content and ERBB2 gene expression.

  Dataset EGAD00001009415

• Melanoma multi site metastases

  These are caveman, pindel and sequenza calls for the metastatic melanoma exomes within this study.

  Dataset EGAD00001005487

• Expression profiles and genetic makeup of agnospheres.

  WES performed on 15 CUP-derived samples

  Dataset EGAD00001006668

• Assessment of genomic copy number alterations in breast cancer

  The aim of this study was to assess genomic copy number alterations in a panel of breast cancer cell lines. These data were used to identify common aberrations associated with breast cancer, and also to identify aberrations associated with response to therapeutic compounds.

  Study EGAS00000000059

• Unmatched WGS from bone marrow samples of 5 chr21 amplified blast phase myeloproliferative neoplasm patients

  We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ~25% of patients (‘chr21amp’). Chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. Here we provide high-depth whole genome sequencing (WGS) in five chr21amp BP-MPN cases, to a median coverage of 81x [range 77-86] and purity 79% [range 58-88%].

  Dataset EGAD00001011280

• Whole Mitochondrial DNA sequencing of Gingivo-buccal Cancer : ICGC-India Project

  This dataset pertains to mitochondrial DNA amplicon sequencing of paired DNA samples from gingivo-buccal oral cancer patients. DNA was isolated from the tumor and blood tissues of 89 patients (178 samples). The sequencing libraries were prepared from whole mitochondrial amplicons using Nextera XT DNA Library Preparation Kit (Illumina) and sequenced in Illumina HiSeq platform. The uploaded BAM files are generated by aligning paired-end reads to the mitochondrial reference sequence (rCRS) using BWA-MEM.

  Dataset EGAD00001004987

• Whole Genome Sequencing of HCC

  The present series corresponds to 24 whole genome sequencing (12 Tumoral/Non-tumoral pairs). Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.

  Dataset EGAD00001003994

• Phase II Trial with Correlative Genomic Analysis of Durvalumab plus Pazopanib Combination in Patients with Advanced Soft Tissue Sarcomas

  This study includes an open-label, phase 2 study to determine the activity of the anti-VEGF receptor tyrosine-kinase inhibitor, pazopanib, combined with the anti-PD-L1 immune checkpoint inhibitor, durvalumab, in unselected advanced sarcomas. We conducted whole exome and transcriptomic sequencing with pre-treatment tissue biopsy to correlate clinical outcomes with molecular and genomic biomarkers to identify patients who would most likely benefit from the combination treatment.

  Dataset EGAD50000000114

• IBD dataset

  We performed multi-omics profiling of 38 Crohn's disease and Ulcerative colitis patients across several stimulations (RPMI, LPS, Salmonella, in total 80 samples). Nuclei were profiled using the 10X Multiome protocol which offers paired RNA+ATAC from the same nucleus (e.g. shared barcodes). Per library, the ATAC (I1, R1, R2, R3 reads) and RNA (I1, I2, R1, R2 reads) are provided. Pools are genetically multiplexed across donors. Genotype files are provided to allow genetic demultiplexing.

  Dataset EGAD50000000198

• Clones derived from early passage tumoroids of colorectal cancer

  We obtained different clones from early passage CRC tumoroids to study mutational signatures specific for truncal or private somatic alterations. These whole genome sequences are part of a larger study on the heterogeneity and evolution of DNA mutation rates in microsatellite-stable colorectal cancer.

  Study EGAS50000000107

• Molecular Genetics of Histiocytic Sarcoma

  This is a comprehensive genomic analysis of a rare set of histiocytic sarcomas from the consult service of the Hematopathology section of the Laboratory of Pathology, NCI, NIH. The study identifies two distinct groupings of these tumors based on the site of disease, their mutational spectrum, and proliferation signature.

  Study phs001748

• Whole Genome Sequencing of Two Family Trios with 22q.11.2 Deletion Syndrome

  Two subjects with 22q11.2 deletion syndromes (22q11DS) and their parents were recruited for a whole genome sequencing study to identify candidate genetic modifiers of the various phenotypes seen in 22q11DS. Both probands had a typical 3 megabase deletion on chromosome 22q11.2 but discordant phenotypes.

  Study phs000837

• Multi-Omic Analysis of Von Willebrand Factor Regulation in Endothelial Colony Forming Cells

  This study evaluated the multi-omic analysis of endothelial cells with a focus on von Willebrand factor regulation, and investigated aspects of endothelial regulation in the context of blood disorders. The data available at dbGaP consist of multi-omic analyses of these cells. 

  Study phs002731

• Role of Genetic Factors in the Pathogenesis of Lung Disease

  Three individuals with lymphangioleiomyomatosis (LAM) underwent evaluation for Tuberous Sclerosis Complex (TSC)-associated mucocutaneous and internal findings. Next-generation sequencing (NGS) of cutaneous findings was used to confirm clinical suspicion for mosaic TSC in individuals with LAM. Mosaic mutations in TSC2 were found in these three individuals.

  Study phs003108

• Bulgarian Trio Sequencing Study to Identify de Novo Mutations in Schizophrenia

  The primary aim of this study is to whole exome sequence complete Bulgarian trios to identify de novo mutations in schizophrenic probands. We are investigating the rate of de novo mutations in probands as well as looking for enrichment among previously implicated genes and synaptic gene sets.

  Study phs000687

• Non-coding mutations drive persistence of a founder pre-leukemic clone which initiates late relapse in T-ALL

  T-ALL relapse usually occurs early but can occur much later, which has been suggested to represent a de novo leukemia. However, we conclusively demonstrate late relapse can evolve from a pre-leukemic subclone harbouring a non-coding mutation that evades initial chemotherapy. Data include 19 WGS samples: - 5 cases with presentation, relapse and remission (germline) samples - 2 cases with presentation and relapse samples, but not remission (germline)

  Dataset EGAD50000000174

• Single-cell transcriptomics of PBMC’s from healthy, acute decompensated (AD) and acute chronic liver failure (ACLF) patients.

  This dataset contains the raw sequencing data (fastq-files) of 10 sample libraries. These are 10x genomics single-cell transcriptome libraries of human peripheral blood mononuclear cells (PBMC’s). The samples are taken from healthy, acute decompensated (AD) and acute chronic liver failure ACLF patients. The sequencing was performed on an Illumina NovaSeq6000. This data are related to the paper: "Distinct immunometabolic signatures in circulating immune cells define disease outcome in acute-on-chronic liver failure"

  Dataset EGAD50000000574

• BELLINI clinical trial bulk RNA-Seq data: cohorts A, B & С

  RNA-Seq data of 78 breast cancer primary tumors obtained from 45 unique patients from BELLINI clinical trial. The data includes pre- and post-treatment samples. Patients in cohort A (15 patients, 25 samples) received nivolumab for 4 weeks, patients in cohort B (15 patients, 28 samples) received nivolumab + ipilimumab for 4 weeks, and patients in cohort C (15 patients, 25 samples) received nivolumab + ipilimumab for 6 weeks. The included raw transcriptome sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000808

• Genotype variables of the 61 COVID-19 patient cohort used in the main project of data integration

  We selected SNPs with a minor allele frequency (MAF) higher than 10% in the Caucasian population from the Ensembl database. Specifically, we selected ACE2 (rs2285666), MX1 (rs469390), and TMPRSS2 (rs2070788) for the present analysis. For more information, please refer to:

  Study EGAS50000000589

• Long Read sequencing data from 4 tumor/germline samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). Additionally, tumor/germline samples from 4 patients were sequenced using Oxford Nanopore technology. This dataset contains 8 BAM files corresponding to the Long read sequencing data.

  Dataset EGAD50000000731

• RnaSeq data from 414 tumor samples with non muscle invasive bladder cancer

  A better understanding of the molecular landscape of non-muscle-invasive bladder cancer (NMIBC) is essential to improve risk assessment and identify potential therapeutic targets. Here, we perform a comprehensive genomic analysis of patients diagnosed with NMIBC based on whole-exome- (n=438), shallow whole-genome- (n=362), and total RNA-sequencing (n=414). This dataset contains 414 BAM files corresponding to the full total RNA-sequencing dataset.

  Dataset EGAD50000000733

• MDS 5q exomes

  This project aimed to study the somatic alterations present in myelodysplastic syndromes patient with isolated chromosome 5q deletion. It was emphasized in analysing TP53 alterations, including mutations and copy number alterations affecting chromosome 17. Exome data from five patients that were included in this project are shared in this submission.

  Study EGAS50000000649

• snRNA-seq on patient tumours

  snRNA-seq performed on patient tumours (n = 6 patients, one biopsy sample each sequenced) using the 10x technology. Single nuclei were acquired from six frozen mCRPC biopsies (4 lymph node, 2 liver metastases) obtained from consenting patients treated at the Royal Marsden Hospital between 2018 and 2023 under an institutional review board approved research protocol (Research Ethics Committee approval number: 04/Q0801/60). All six patients had previously received androgen-receptor signalling inhibitor(s) and five of six patients had previously received taxane(s).

  Dataset EGAD50000000874

• RNA-Seq data from study: Molecular underpinnings of dedifferentiation and aggressiveness in chromophobe renal cell carcinoma

  The ChRCC study RNA-Seq dataset contains raw whole transcriptome sequencing data of 16 tumor and 6 adjacent normal samples from 7 UTSW patients, who have consented to depositing their genomic data to public repository. RNA-Seq was performed using 50bp single-end on a HiSeq2500 platform (Illumina, San Diego, CA, USA). 50M reads per sample on average. The raw data is in fastq format.

  Dataset EGAD50000000416

• Illumina GSA-MD v3 genotyping arrays for 183 samples

  Genotyping arrays for 183 samples from patients with a neuroendocrine tumor of the small intestine. All samples have been hybridized on Illumina GSA-MD v3 arrays with standard automated protocols. Reading of the chips was performed on Illumina iScan+ scanners and this file is the result of primary analysis done using Illumina GenomeStudio software. It contains data for 147 tumors, 2 adenomas, 1 lymph node, 19 mesenteric nodules, 6 liver metastasis and 8 normal ileum samples.

  Dataset EGAD50000000905

• WES for CNV-verified CTCs enriched by high-throughout microfluidic device from entire cancer patient leukopak

  WES analysis (illumina platform, PE150, 100x coverage) was performed on a pool of copy number variation (CNV)-verified CTCs that were enriched using high-throughout microfluidic device from entire leukopak from patients with metastatic prostate cancer (GU-1 and GU-2).

  Study EGAS50000000724

• Cohort B spatial transcriptomics sequencing

  Cohort B includes IDH-wild type, EGFR amplified, surgically derived glioblastoma tissue samples from male and female individuals. FFPE tissues for each sample in cohort B were analyzed with the 10X Genomics Visium CytAssist protocol. Processed data is available on the NCBI Gene Expression Omnibus database with accession GSE242352.

  Study EGAS50000000956

• Low-coverage Single-cell Whole Genome Sequencing Data from Paired Meningioma Samples

  This dataset comprises low-coverage (~0.5X) whole genome sequencing data from 179 single cells isolated from paired meningioma samples (88 cells from initial grade II and 91 cells from recurrent grade III tumor from the same patient). The single-cell libraries were constructed using Primary Template Amplification and ResolveDNA protocol, with libraries subsequently sequenced on NextSeq 1000 using 2x150bp paired-end reads targeting 8M reads per cell. This dataset includes the sequencing data in Fastq format.

  Dataset EGAD50000001254

• ProstOmics - DNA methylation v1

  Bulk methylation array data from 64 prostate tissue samples from 16 patients (5 with post-surgery relapse). Methylation data were acquired using the microarray kit Illumina Infinium MethylationEPIC BeadChip (n=64 ). The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Dataset EGAD50000000605

• ProstOmics - DNA methylation v2

  Bulk methylation array data from 32 prostate tissue samples from 8 patients (3 with post-surgery relapse). Methylation data were acquired using the microarray assay Illumina Infinium MethylationEPIC v2.0 Kit. The individual samples have information on patient origin and sample type (cancer, cancer-adjacent field-effect normal or normal sample far from cancer). Patient metadata include information of age at surgery, time (months) until reported relapse, pre-surgery PSA and post-surgery T-stage.

  Dataset EGAD50000000606

• RNAseq data from 112 samples of benign or malignant ovarian tumours

  This dataset contains ~1.2 TB RNA sequencing data in fastq format from 112 samples of fresh-frozen ovarian tumours from a total of 111 women, two samples being replicates. The samples were collected from the U-CAN collection at Uppsala Biobank and include both benign (n = 18) and malignant (n = 94) tumours. The RNA sequencing samples were sequenced using paired-end sequencing (2x150 bp) on an Illumina NovaSeq 6000 instrument at the SciLifeLab National Genomics Infrastructure (NGI) in Uppsala.

  Dataset EGAD50000001521

• Dataset belonging to the article "Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples"

  This dataset consists of raw sequencing data from targeted next generation sequencing of samples from patients with chronic lymphocytic leukaemia. These samples were used to validate an approach for detection of sample mislabelling and swapping in clinical cohorts using single nucleotide polymorphisms (SNPs), as described in the associated article. The data are divided into two parts - data from the initial validation experiment (discovery cohort) and data from an additional independent cohort.

  Dataset EGAD50000000757

• CMV infection during pregnancy

  This study aims to characterize the transcriptional diversity, clonal composition, and viral target antigens of CMV-specific CD8 T cells among pregnant women with different anti-CMV serological patterns. Single-cell RNA sequencing (scRNA-seq) combined with MHC-peptide dextramers were performed using CD8 T cells from pregnant donors.

  Study JGAS000728

• Broad utility of ultrasensitive analysis of circulating tumor DNA (ctDNA) dynamics across solid tumors treated with immunotherapy

  Here, we applied a whole-genome, tumor-informed approach to study ctDNA in more than 202 advanced-stage cancer patients treated at VHIO. This study demonstrates the efficacy of ultrasensitive ctDNA as a broad biomarker in a large pan-cancer discovery and validation cohort, spanning 24 tumor types treated with diverse immunotherapy modalities. It demonstrates ctDNA’s potential for early response assessment, survival prediction, and distinguishing true progression from pseudoprogression, enhancing its clinical relevance. This dataset captures the plasma sequencing data from the project.

  Dataset EGAD50000001813

• Transcriptional data of human isogenic iPSCs

  This dataset contains bulk RNA-seq data from 12 autosomally isogenic human iPSCs. Three biological replicas from XXY (sample ID 419295-7), XX (sample ID 419298-419300), XY (sample ID 419302, 419305-6), and XO (sample ID 419308, 419310, 419312) hiPSC. RNA for this dataset was collected using Trizol method, and polyA library type was implemented. The libraries were sequenced using Illumina device. The sample reads are deposited as fastq files. Analysis have been done using reference alignment to GRCh38 reference genome.

  Dataset EGAD50000001361

• Long-read single-cell RNA-seq in COVID-19

  We report the first application of long-read single-cell RNA sequencing on nasopharyngeal swabs from COVID-19 patients and healthy controls to resolve transcript-level changes across cell types. Samples were collected from three patients with moderate COVID-19, six patients with critical COVID-19, and three healthy controls. Single-cell libraries were generated using the 10x Genomics Chromium 3' protocol, producing unfragmented cDNA. Libraries were sequenced on the Oxford Nanopore Technologies PromethION platform. Basecalling was performed with Guppy (v1.6), generating a single FASTQ file per sample.

  Dataset EGAD50000001836