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• Dataset for upper_gastrointestinal_tumor-EXON

  Rare cancer sequencing data of 85 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008902

• WGS data of paediatric hyperdiploid B cell acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of two hyperdiploid ALL patients (ALLT-315, ALLT-320). Sequencing libraries were made using PCR free-based WGS library preparation (PCR-), using TruSeq DNA PCRfree library preparation kit v1. Both diagnostic (60x) and remission (30x) samples were sequenced using Illumina HiSeq X.

  Dataset EGAD50000002426

• WGS data of paediatric TCF3::PBX1 acute lymphoblastic leukemia (set2)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one TCF3::PBX1 ALL patient (ALLT-376). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001795

• WGS data of pediatric TCF3::PBX1 acute lymphoblastic leukemia (set1)

  The dataset includes FASTQ and BAM files from diagnostic and matched remission (control) samples of one TCF3::PBX1 ALL patient (ALLT-335). Sequencing library was made using standard PCR-based WGS library preparation (PCR+), using NEB Next® Ultra™ DNA Library Prep Kit. Both diagnostic (90x) and remission (30x) samples were sequenced using HiSeq X.

  Dataset EGAD50000001796

• GATA1 scD&D-seq integrated with Multiome

  Ex vivo differentiation experiments were performed using human CD34+ hematopoietic stem and progenitor cells along the erythropoietic trajectory at multiple timepoints (differentiation days 0, 5, 8, 18, and 24). Simultaneous profiling of transcriptome, chromatin accessibility, and GATA1 binding were performed by integrating D&D-seq with 10X Multiome.

  Dataset EGAD50000002299

• WGS data of paediatric BCR::ABL1 acute lymphoblastic leukemia

  The dataset includes FASTQ and CRAM files from diagnostic and matched remission (control) samples of one BCR::ABL1 ALL patient (ALLT-399). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set Kit (Cat No. PT004). Both diagnostic (90x) and remission (30x) samples were sequenced using NovaSeqX Plus.

  Dataset EGAD50000002185

• WGS data of paediatric B-other B cell acute lymphoblastic leukemia (set5)

  The dataset includes FASTQ and BAM/CRAM files from diagnostic and matched remission (control) samples of two B-other ALL patients (ALLT-396, ALLK-131). Sequencing library was made using PCR free-based WGS library preparation (PCR-), using Novogene NGS DNA Library Prep Set. Both diagnostic (90x) and remission (30x) samples were sequenced using NovaSeqX Plus.

  Dataset EGAD50000002160

• Methylome and transcriptome of memory B cells - Autoproliferation

  Methylome and the corresponding transcriptome of autoproliferating/Dim B cells and resting/hi B cells in Multiple sclerosis patients

  Dataset EGAD50000001236

• T Cell Receptor Sequencing

  The T cell Receptor Sequencing dataset contains 84 files related to T cell receptor sequences obtained using ImmunoSeq by Adaptive Biotechnologies and phenotype metadata from 23 patients enrolled on a phase II clinical trial of neoadjuvant immune checkpoint blockade in high-risk resectable melanoma at MD Anderson Cancer Center (NCT02519322). Included are data on baseline and on-treatment samples from tumor and blood.

  Dataset EGAD00010001608

• Alopecia and Vitiligo

  exome sequencing data captured with agilent v4 (71k) and sequenced on illumina technology. data from a total of 40 samples, of which 14 are vitiligo cases with familial history of vitiligo or immune disease, and the remaining are alopecia areata cases.

  Dataset EGAD00001005289

• CONTAGIOUS trial - COVID-19 16S metadata

  Study metadata, containing the clinical information on samples and patients

  Dataset EGAD00001008006

• DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism

  Plasma samples derived from a study population of control participants (DIGEST: Dietary Influences on Glucuronidation, a Cross-Sectional Study of Diet and Metabolism) were used to profile miRNA circulating in plasma. RNA was isolated from plasma samples using the Qiagen miRNeasy kit. Libraries were prepared using Illumina TruSeq Small RNA Library Prep Kit. Libraries were sequenced on a HiSeq. Data from this sequencing project will be available through dbGaP.

  Study phs003223

• Genetics and Pathobiology of Disorders of Keratinization

  The goal of this study was to identify potential drivers of disorders of keratinization in human. Individuals diagnosed with disorders of keratinization were recruited with no exclusion criteria. Saliva or blood samples were taken from consented patients or family members and DNA harvested immediately. Whole exome sequencing was performed (150-bp paired end reads) to 80X coverage via an Illumina NovaSeq 6000 sequencer. Identification of germline mutations was performed using GATK.

  Study phs004172

• scRNA-seq data of Anti-Her2-CAR T cells treated with immunomodulatory metabolites

  Anti-Her2-CAR T cells produced from T cells derived from healthy human donors were treated with DMSO (control) or either of the immunomodulatory metabolites indole‐3‐carboxaldehyde (ICA), valeric acid (VA) and isovaleric acid (IVA) to assess effects on CAR T cell function. scRNA-seq libraries were generated on a 10X Chromium controller with On-Chip-Multiplexing. The individual samples in a library are distinguished during analysis on the single-cell level via the cell barcode class.

  Dataset EGAD50000002012

• Mate pair whole genome sequencing of 98 AML samples

  This dataset contains bam-files from Mate-pair whole genome sequencing of 98 AML samples. DNA was extracted from either bone marow or peripheral blood from primary AML samples. The libraries were prepared using Illumina Nextera mate pair library preparation kit, generating long-insert (2-8 kb) paired end libraries. These were sequenced on an Illumina NextSeq 500 using 2x76bp paired end chemistry. The fastq files generated by sequencing were aligned to the human hg19 reference genome (ucsc.hg19.fasta from the GATK resource bundle) using bwa (0.7.15-r1140) and duplicate reads were identified using samblaster (0.1.24).

  Dataset EGAD50000001574

• Analysis of Cell-Free DNA to Predict Outcome to Bevacizumab Combination Therapy in Metastatic Colorectal Cancer Patients

  This dataset includes FASTQ files of low coverage whole genome sequencing of normal tissue (n = 8), tumor tissue (n = 55) and cell free DNA from plasma samples (n=101) from patients with metastatic colorectal cancer treated with bevacizumab. A total of 164 samples are present from two different cohorts. The first batch of samples (n = 139, sample names sAPD302T until sAPD502_P0) were collected from the AC-Angiopredict Phase 2 trial (NCT01822444), the second batch of samples (n = 25m, sample names sAPD503_P0 until sAPD527_P0) were collected from the UMM cohort.

  Dataset EGAD50000000176

• Sequencing data for ICGC Oesophageal Adenocarcinoma tissue samples - dcc_release_24_dataset

  WGS sequencing for cases from the ICGC ESAD-UK project Tumours 50x Normals 30x HiSeq X BAM files These samples are all available in ICGC release 24

  Dataset EGAD00001003292

• PCNSL single cell dataset

  Mononuclear cells were isolated as cell suspensions by dissociation in a BD Horizon™ Dri Tumor & Tissue Dissociation Reagent (BD Biosciences) using a gentleMACS dissociator (Miltenyi Biotec). A totalseq-C antibody cocktail (Biolegend) was used, and the cell suspensions were diluted to a concentration of 1,000 cells/μL. Library sequencing was performed using the DNBSEQ-G400 (MGI Tech), Illumina HiSeq 2000, or Illumina NovaSeq 6000 5 (Illumina). The FASTQ files were aligned to the 10x provided reference genome using 10x Genomics Cell Ranger software v7.1.0 to create unique molecular identifier count tables of gene expression of the samples.

  Dataset EGAD50000000685

• Genetic History of Neandertal and Denisovan Introgression into Melanesian Individuals

  This study describes high-coverage whole-genome sequencing of 35 individuals sampled from the Bismarck Archipelago of Northern Island Melanesia, Papua New Guinea as described in PMID: 26989198

  Study phs001085

• Cell-free DNA methylation profiling of sepsis patients

  This data set contains paired-end NGS files (in FASTQ format) generated from a methylation profiling experiment of cell-free DNA derived from the plasma of sepsis patients and healthy controls. Methylation profiling was performed using the TET-assisted pyridine borane sequencing (TAPS) protocol.

  Dataset EGAD50000001505

• 104 CRLM patients RNA-seq

  This dataset consists of RNA-seq data from 104 CRLM patients. Reads were mapped to the GRCh37 genome version using STAR. The data include patients with no treatment, as well as those treated with FOLFOX, FOLFOX-bevacizumab, atezolizumab, and FOLFOX-bevacizumab-atezolizumab.

  Dataset EGAD50000000954

• Multi-omics analysis of cocaine use disorder in postmortem brain tissue of the ventral striatum

  The dataset contains raw sequencing data from miRNA-seq, RNA-seq and single-nuclei RNA-seq experiments to investigate transcriptomic changes in cocaine use disorder.

  Dataset EGAD50000000881

• Disease recurrence after pathologic response

  In this study we aim to gain insight into the mechanisms of immune evasion after initial pathologic response to neoadjuvant immune checkpoint inhibition in macroscopic stage III melanoma by pooling data of the neoadjuvant OpACIN, OpACIN-neo and PRADO trials. Here we used RNAseq data from 21 patients(paired end)

  Dataset EGAD50000000698

• BELLINI clinical trial bulk WES data: cohorts A & B

  WES data of 30 breast cancer primary tumors obtained from 30 unique patients from BELLINI clinical trial (cohorts A & B) and 30 matched blood samples. The data includes pretreatment samples. The included raw WES sequencing data in fastq format was generated using Illumina NovaSeq 6000.

  Dataset EGAD50000000809

• Correction of a Factor VIII genomic inversion with designer recombinases

  PromethION-based whole genome sequencing of endothelial cells differentiated from patient derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, transiently treated with a Cre recombinase, a RecF8 recombinase, and untreated cells. The dataset contains fastq files with all sequencing reads passing the standard quality filtering.

  Dataset EGAD00001007923

• Total RNA sequencing data from the Triple Negative Trial (TNT)

  BAM files from total RNA sequencing of samples from breast cancer patients in the TNT trial. Data includes 186 primary tumour samples and 13 matched recurrence samples.

  Dataset EGAD00001011141

• WGS Data from 42 Multi-Region Sampled IPMN-PDACs and 12 Matched Normal Samples

  This dataset contains whole genome sequencing (WGS) data from 42 IPMN-PDAC and 12 normal samples, with tumours collected from multiple regions within each tumour to capture intra-tumour heterogeneity. Tumour and matched normal samples were sequenced to study somatic mutations, structural variants, copy number alterations, mutational signatures and clonal evolution during IPMN-PDAC progression. The sequencing was performed using Illumina NovaSeq instrument with 150 bp paired-end reads.

  Dataset EGAD50000001687

• TERT rearrangements are frequent in neuroblastoma and identify aggressive tumors

  Whole genome sequencing detected structural rearrangements of TERT in 17/75 high stage neuroblastoma with 5 cases resulting from chromothripsis. Rearrangements were associated with increased TERT expression and targeted immediate up- and down-stream regions of TERT, placing in 7 cases a super-enhancer close to the breakpoints. TERT rearrangements (23%), ATRX deletions (11%) and MYCN amplifications (37%) identify three almost non-overlapping groups of high stage neuroblastoma, each associated with very poor prognosis. This submission contains all newly sequenced samples only.study_refcenter AMC

  Dataset EGAD00001001635

• A Protein Neddylation Inhibitor MLN4924 Suppresses Patient-Derived Glioblastoma Cells via Inhibition of ERK and AKT Signaling

  To identify what factors cause a different reactivity to MLN4924, 15 cells were categorized into high, intermediate, and low MLN4924 resistance groups based on the half-maximal inhibitory concentration (IC50) of MLN4924. PDC1, PCD2, PDC3, PDC4, and PDC5 showed high MLN4924 sensitivity, whereas PDC12, PDC13, PDC14, and PDC15 showed low MLN4924 sensitivity. Whole-transcriptome sequencing of these 9 patient-derived glioblastoma stem cells was performed.

  Dataset EGAD00001005709

• Japanese RIKEN liver cancer WGS

  RIKEN collection of WGS reads for 269 liver cancer tumors and matched normal blood or liver tissue from 258 donors. In total there are 1864 paired fastq sets sequenced on Illumina HiSeq 2000 or Genome Analyzer II instruments with paired reads of 75–101 bp. Quality control and duplication removal has not been performed.

  Dataset EGAD00001001881

• RNA-sequencing data from 195 B-cell precursor acute lymphoblastic leukemias and mate pair whole genome sequencing data from 15 B-cell precursor acute lymphoblastic leukemias

  Fusion genes are potent driver mutations in cancer. In this study, we delineate the fusion gene landscape in a consecutive series of 195 pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL). Using RNA-sequencing, we find in-frame fusion genes in 127 (65%) cases, including 27 novel fusions. We describe a new subtype characterized by recurrent IGH-DUX4 or ERG-DUX4 fusions, representing 4% of cases, leading to overexpression of DUX4 and frequently co-occurring with intragenic ERG deletions. Furthermore, we identify a subtype characterized by an ETV6-RUNX1-like gene expression profile and coexisting ETV6 and IKZF1 alterations. Taken together, this study provides a detailed overview of fusion genes in pediatric BCP ALL and adds new pathogenetic insights, which may improve risk stratification and provide novel therapeutic options in this disease.

  Study EGAS00001001795

• TOTHER3

  Patritumab deruxtecan in HER2-negative breast cancer: part B results of the window-of-opportunity SOLTI TOT-HER3 trial and biological determinants of early-response

  Dac EGAC50000000255

• Finding structural variation and functional consequences from primary acute myeloid leukemia cells with complex karyotype (CK-AML) at the single-cell level

  Study EGAS00001007436

• Transcriptional and functional profiling defines human small intestinal macrophage subsets

  Macrophages (Mf) are instrumental in maintaining immune homeostasis in the intestine, yet studies on origin and heterogeneity of human intestinal Mf are scarce. Here, we identified four distinct Mf subpopulations in human small intestine (SI). Assessment of their turnover in duodenal transplants revealed that all Mf subsets were completely replaced over time; Mf1 and Mf2, phenotypically similar to peripheral blood monocytes (PBMo), were largely replaced within 3 weeks, whereas two subsets with features of mature Mf, Mf3 and Mf4, exhibited significantly slower replacement. Mf3 and Mf4 localized differently in SI; Mf3 formed a dense network in mucosal lamina propria, whereas Mf4 was enriched in submucosa. Transcriptomic analysis showed that all Mf subpopulations subsets were markedly distinct from PBMo and dendritic cells (DC). Compared to PBMo, Mf subpopulations showed reduced responsiveness to proinflammatory stimuli, but were proficient at endocytosis of particulate and soluble material. These data provide a comprehensive analysis of human SI Mf population and suggest a precursor-progeny relationship with PBMo.

  Study EGAS00001002093

• Inherited chromosomally-integrated human herpesvirus 6A/B (HHV-6A/B) genome sequences in the Japanese population

  The deposited sequences represent inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) genomes identified from 10 BioBank Japan (BBJ) subjects based on the analysis of the whole-genome sequencing (WGS) data. In brief, we re-aligned unmapped reads from the WGS to HHV-6A genome (Genbank accession number: KJ123690.1) using BWA-MEM algorithm. Ten out of 3,256 subjects were identified with high depth of coverage of HHV-6. We further distinguished subjects with integrated HHV-6A subtypes from those with integrated HHV-6B based on phylogenetic analysis of concatenated sequences of three viral genes (U27/U43/U83, which show high divergence between viral species). We reconstructed the HHV-6 viral genome of 10 subjects. First, reads that mapped to a reference HHV-6A genome (KJ123690.1) were further aligned against the integrated HHV-6A genome derived from a Japanese individual NA18999 (GenBank Accession number: KY316047.1) using BWA-MEM. Based on the alignment, variant calling was performed using freebayes (version: v1.2.0-2-g29c4002) with parameters ploidy = 1 and min-alternate-fraction = 0.8 {Garrison, 2012}. We generated subject-specific iciHHV-6 viral sequences by applying the resulting variants to the KY316047.1 reference genome using the FastaAlternateReferenceMaker function in the Genome Analysis Toolkit (GATK) v3.7. Please note that HHV-6B-specific variants are unlikely to be sensitively reconstructed using this method.

  Study JGAS000240

• CALGB 80303:Genome-Wide Association Study of Advanced Pancreatic Cancer Patients - A Randomized Phase III trial of Gemcitabine Plus Bevacizumab versus Gemcitabine Plus Placebo in Patients with Advanced Pancreatic Cancer

  CALGB 80303 was a randomized, phase III study in advanced pancreatic cancer patients treated with Gemcitabine plus either Bevacizumab or placebo. No difference in overall survival (OS) was observed between the two arms. We prospectively collected germline DNA and conducted a genome-wide association study (GWAS).

  Study phs000250

• Myelodysplastic Syndrome (MDS) in Humanized Mice

  This study was to develop a faithful pre-clinical MDS patient-derived xenotransplantation model in cytokine-humanized immunodeficient "MISTRG" mice. We performed targeted genome sequencing on bone marrow from patients with MDS or AML and from bone marrow of mice engrafted with the respective patient bone marrow. Cytokine-humanized immunodeficient mice faithfully replicate human MDS.

  Study phs001778

• Immunoreactive_p53_areas_in_human_skin_2

  Previous work has suggested that in mice there may be a difference in mutational burden between areas expressing stabilised p53 protein and others. We wish to see if this observation holds true in human sun-exposed epidermis. We will take 0.25mm punch biopsies from peeled human skin epidermis which will be submitted to the low input pipeline prior to sequencing.

  Study EGAS00001004463

• Poland WES - The Genomic Map of Poland in Open Access

  This project used NGS (next generation sequencing), using Illumina NOVASEQ 6000 and Illumina DRAGEN aligner. The dataset includes BAM and BAM.BAI files from Whole Exome Sequencing of 450 samples (227 female, 223 male, Poland from POPULOUS collection). Library Construction Protocol: Illumina DNA Prep with Enrichment. Reference Genome: GRCh37.

  Dataset EGAD50000000130

• RNAseq_Pulldown_

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. In this experiment cDNA derived form Breast Cancer Cell lines was used in an Agilent whole exome pulldown experiment.

  Study EGAS00001000230

• Triple_Negative_Breast_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Triple negative breast cancer through generation of comprehensive catalogues of somatic mutations in 500 cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses. This study will use a bespoke bait set to pulldown regions of interest found in whole genome sequencing to validate mutations found.

  Study EGAS00001000426

• Analysis of Complex Genomic Rearrangements of Lung Adenocarcinomas

  Lung adenocarcinomas (LADC) are heterogeneous disease with distinct etiology. A majority of tumors are related with tobacco smoking, and some tumors arise from never-smoking or young patients, whose clinical history do not support the environmental carcinogen-induced oncogenes. Here we analyzed complex rearrangements in lung adenocarcinomas including tumors with distinct etiologies.

  Study EGAS00001002801

• Exome sequencing of matching primary tumor and venous tumor thrombus (VTT) renal cell carcinoma (RCC) samples

  We performed multiregion whole exome sequencing of a total of 37 samples from five consecutive patients (normal tissue, n=5; primary tumors, n=16; tumor thrombi, n=16) to >35-fold target coverage. Matching primary tumor and venous tumor thrombus samples were analyzed. Four patients had a clear cell RCC, one patient had a poorly differentiated type II papillary RCC (RCC-VTT-04). The latter patient had a friable thrombus, the others were of solid consistency.

  Dataset EGAD00001004887

• Cell-free DNA and bone marrow samples from myelodysplastic syndromes

  We have assessed the molecular profile of a cohort of 70 patients with MDS by next-generation sequencing (NGS) using cfDNA and compared the results to paired bone marrow (BM) DNA.

  Dataset EGAD00001008567

• Targeted Germline Sequencing of the Leeds Melanoma Cohort

  In this project we performed targeted sequencing of known and suspected melanoma susceptibility genes in a cohort of melanoma patients and matched controls. Our aim was to identify variants that predispose to melanoma development. The melanoma cases used in this study were population ascertained.

  Dataset EGAD00001007520

• Mitochondrial-Nuclear Mutational Cross-Talk Drives Recurrence of Localized Prostate Cancer

  Prostate cancer remains the most prevalent non-skin cancer in men, but has a remarkably quiet mutational profile. Exome sequencing studies have revealed few recurrent somatic single nucleotide variants (SNVs). Whole-genome sequencing studies have not yet identified highly recurrent driver non-coding SNVs (ncSNVs) or genomic rearrangements (Grs). As a result, the underlying events that drive this frequent disease remain unknown. While mitochondrial mutations have been linked to several tumour types, including prostate cancer, their global frequency and impact has remained unknown. To determine if mitochondrial mutations might drive some prostate cancers, we analyzed the mitochondrial genomes of 216 tumours from patients with the most commonly diagnosed form of prostate cancer. We developed a pipeline that conservatively identified only mitochondrial SNVs (mitoSNVs) that differed in the heteroplasmy fraction as compared to their paired-normal by at least 20%. We identified several features of the mitochondrial genome that were correlated with nuclear genomic mutations, as well as features that were significantly associated with biochemical recurrence.

  Study EGAS00001001782

• Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma

  Dataset EGAD00001010049

• The UCSF Low Grade Glioma Genome Project #2"

  Dataset contains WES data from 3 astrocytoma patients: blood as control, primary tumor and recurrent tumor

  Dataset EGAD00001001305

• Single cell multi modal dataset of bone marrow samples from follicular lymphoma patients at diagnosis et one year post treatment

  This dataset contains transcriptome, BCR, TCR and HTO data at the single cell level from follicular lymphoma bone marrow samples at diagnosis (n=19) and one year post rituximab therapy (n=16).

  Dataset EGAD50000001843

• Clonal_analysis_Bcell_activation

  We developed a B cell stimulation protocol that allowed us to expand a smaller number of naive B cells in culture (2,000 B cells at day 0). On day 6, we performed single-cell RNA-and BCR-sequencing on the entire culture, preserving both clonal diversity and size.

  Dataset EGAD50000002114