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• Y_chromosome_mis_segregation_in_the_DLD_1_cell_line

  Study of the well-established DLD-1 colorectal cancer cell line, engineered with an inactivatable Y centromere that leads to mis-segregation. The goal is to gain insights into the mechanism of chromothripsis due to chromosome mis-segration.

  Study EGAS00001002551

• PYDP Papuan Y chromosome Diversity Panel

  The PYDP dataset includes 26 bam files of Y chromosome sequences for Papua New Guinean individuals from different locations, extracted from whole genome sequences. DNA was extrated from saliva samples (Oragen kit). Sequencing libraries were prepared using the TruSeq DNA PCR-Free HT kit. 150 bp paired-end sequencing was performed on the Illumina HiSeq X5 sequencer.

  Dataset EGAD00001008572

• Single Cell Transcriptomic Data from CD4+ T Cells from Children with MIS-C

  Multisystem inflammatory syndrome in children (MIS-C) is a severe complication of SARS-CoV-2 infections in the pediatric population characterized by fever, multi-organ involvement and systemic inflammation. Single-cell RNA sequencing was used to evaluate the transcriptomic signature of CD4+ T cells obtained from the peripheral blood of patients with MIS-C before (n=3) and after (n=5) immunomodulatory treatment, along with pediatric controls (n=4). Compared to controls and treated children with MIS-C, T cells obtained from pre-treatment MIS-C patients upregulated genes associated with activation, such as NF-kB signaling. This single-cell transcriptomic data was used in the context of a larger study entitled, "Notch1-CD22-Dependent Immune Dysregulation in the SARSCoV2-Associated Multisystem Inflammatory Syndrome in Children."

  Study phs003086

• Diagnosis of multisystem inflammatory syndrome in children by a whole-blood transcriptional signature

  To identify a diagnostic blood transcriptomic signature that distinguishes multisystem inflammatory syndrome in children (MIS-C) from Kawasaki Disease (KD), bacterial infections and viral infections. Children presenting with MIS-C to participating hospitals in the United Kingdom and the European Union between April 2020-April 2021 were prospectively recruited. Whole blood RNA Sequencing was performed, contrasting the transcriptomes of children with MIS-C to those from children with KD, definite bacterial and viral infections. Data deposited here comprises samples from patients recruited into the DIAMONDS study.

  Study EGAS00001007409

• Papuan Y chromosome Diversity Panel

  Island Southeast Asia and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ~9.7 Mb of Y chromosome sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this dataset allows us to fully resolve and date the regional Y chromosome phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ~50 kya, and extensive expansions <6 kya. Notably, ~40-25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in Island Southeast Asia, New Guinea and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ~25 kya, at the time of the Last Glacial Maximum. This improved Y chromosome topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and Island Southeast Asia, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the Y chromosome presented here thus enables a detailed exploration of

  Study EGAS00001006025

• Botensilimab, an Fc-enhanced Anti-CTLA-4 Antibody, is Effective Against Tumors Poorly Responsive to Conventional Immunotherapy

  This study explores the genomic landscape associated with a novel Fc-engineered anti-CTLA-4 antibody (botensilimab) in advanced solid tumors. We seek to understand if enhancing the Fc-region affinity of anti-CTLA-4 antibodies can improve anti-tumor efficacy and expand clinical benefit to tumors poorly responsive to conventional immunotherapy. As part of an ongoing open-label, Phase 1, multicenter study, we conducted an exploratory sub-analysis of genomics data. The primary study evaluates the safety, tolerability, pharmacokinetics, and pharmacodynamics of botensilimab monotherapy and in combination with an anti-PD-1 antibody (balstilimab) in participants with advanced solid tumors. RNA from formalin-fixed paraffin-embedded (FFPE) tumor biopsies and matched normal blood samples were isolated and subjected to RNA-sequencing using the Personalis ImmunoID NeXT Platform. We demonstrated that anti-CTLA-4 engineered for enhanced FcγR affinity leverages FcγR-dependent mechanisms to potentiate T cell responsiveness, reduce intratumoral Tregs, and enhance antigen presenting cell activation. This genomic analysis contributes to our understanding of the molecular mechanisms underlying patient responses to Fc-engineered anti-CTLA-4 therapy and may inform future strategies to expand the clinical benefit of immune checkpoint blockade in cancer immunotherapy.

  Study phs003704

• Fgl2 Regulates FcγRIIB+ CD8+ T Cell Responses during Infection

  While the inhibitory receptor FcγRIIB has been shown to be upregulated on activated CD8+ T cells in both mice and humans, its impact on T cell fate during infection has not been fully elucidated. We identified an increase in FcγRIIB-expressing CD8+ T cells in COVID patients relative to healthy controls, and in mouse models of viral infection. Despite its well-known role as an Fc receptor, FcγRIIB also ligates the immunosuppressive cytokine Fgl2, resulting in CD8+ T cell apoptosis. Both chronic LCMV infection in mice and COVID in humans resulted in a significant increase in plasma Fgl2. Further, plasma Fgl2 was directly proportional to CD8+ T cell lymphopenia in COVID patients. To further understand the association of Fgl2 and CD8+ T cell lymphopenia following COVID infection, we assessed the transcriptomic profiles of PBMCs with high (≥ 9.153 ng/ml) vs low (defined as

  Study phs003870

• RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C)

  RNA sequencing data from children with febrile illness and multisystem inflammatory syndrome in children (MIS-C). Samples used were Whole Blood. Febrile illness controls include children with bacterial and viral infections and healthy controls. This dataset contains samples from patients recruited into the DIAMONDS study.

  Dataset EGAD00001011134

• Data Access Committee KCL FC

  Dac EGAC00001000386

• Kbtbd13 knock-down restores muscle function in a human-based mouse model of nemaline myopathy type 6

  Nemaline myopathy type 6 (NEM6) is caused by pathogenic variants in KBTBD13. Patients experience muscle weakness, excessive fatigue and impaired muscle relaxation which significantly impact their daily activities. NEM6 pathophysiology consist of abnormal protein aggregation in muscle cells and a predominance of slow-twitch myofibers, and most patients carry the Dutch founder variant in KBTBD13 (NP_001094832.1: p.Arg408Cys, referred to as KBTBD13R408C). Currently, no specific therapy is available. Here, we used a KBTBD13R408C knock-in mouse model and aimed to identify the molecular changes driving disease pathogenesis and to define a therapeutic window to test a therapeutic intervention. We revealed that the mouse model closely phenocopies the human phenotype at a morphological, functional, and transcriptional level and that the p.Arg408Cys variant causes mis-localization of KBTBD13 within the muscle sarcomere. Our natural history data in the Kbtbd13(R408C) mouse model showed that disease onset occurs between 1-3 months and plateaus by 9 months with little progression at 18 months.

  Study EGAS50000001678

• : Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumours

  Study EGAS00001004239

• Somatic mutations in twin breast cancers (2019-04-03)

  The aim of this study is to investigate the somatic mutations in twins with BRCA1/2 negative breast cancer with no strong family history. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004890

• L1 Retrotransposon sequencing in Cocaine Use Disorder - Study 1

  Cocaine Use Disorder (CUD) is a global public health problem, with no effective pharmacotherapies. While CUD is marked by high heritability, discovery of variants associated with risk for CUD has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from medial prefrontal cortex NeuN+ neuronal nuclei from 25 CUD cases and 26 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001966

• Identification of Host Genetic Factors That Are Determinant for the Development of Severe Forms of COVID-19

  We conducted whole exome sequencing (WXS) on 21 cases of Multisystem Inflammatory Syndrome in Children (MIS-C) related to COVID-19 from Brazil. All patients who were hospitalized underwent serum (ELISA) and molecular (RT-PCR) testing for SARS-CoV-2, and the main clinical symptoms associated with SARS-CoV-2 infection were collected. During hospitalization, data on complications, medical interventions, and laboratory findings were also collected. Our results revealed in an unprecedented way the occurrence of several rare loss-of-function variants in the NLRP12 gene among the affected children, and three other SNVs, predicted to be highly pathogenic, were identified in the IL17RC gene. An additional nonsense variant, in the IFNA10 gene, was identified in a single patient. Through in vitro functional analysis, we unequivocally demonstrated that these mutations impact NF-kB activation. These findings are similar to those observed in NLRP12-associated systemic autoinflammatory disorders, characterized by altered innate immune response, with increased NF-κB activation and excessive production of inflammatory cytokines. To our knowledge, our study is the first to provide a plausible molecular mechanism for MIS-C involving inborn errors in NLRP12. We suggest that some patients with MIS-C may benefit from Interleukin (IL)-1 pathway blockade treatments.

  Study phs003512

• MCF10A 12h IL6 classical signaling

  Gene expression after cell culture, 12h IL6+sgp130-Fc stimulated

  Dataset EGAD00010001970

• MCF10A 24h IL6 classical signaling

  Gene expression after cell culture, 24h IL6+sgp130-Fc stimulated

  Dataset EGAD00010001963

• Y chromosome alignment

  Variations on the Y chromosome from 44 samples

  Dataset EGAD00010001573

• Single cell transcriptomes of in vitro differentiated hepatocyte-like cells in comparison to primary human hepatocytes

  Fastq files of deeply sequenced single cell RNA-seq data (Smartseq2, approx. 2 million reads / sample) of hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 3) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as PHH from 3 donors. Each replicate comprises 96 single cells.

  Dataset EGAD00001005946

• Chromatin accessibility analysis of hepatocyte-like cell in vitro differentiation from iPSC in comparison to primary human hepatocytes

  Fastq files of ATAC-seq data of induced pluripotent stem cells (iPSC), definitive endoderm (DE), hepatocyte-like cells (HLC) and primary human hepatocytes (PHH). The dataset comprises data from two different in vitro differentiation protocols: Cellartis (Takara Bio, "CEL", n = 4) and as described by Wang et al. (PMID: 28287600, "HAY", n = 1), as well as from 3 PHH donors.

  Dataset EGAD00001005934

• Human_Evolution_3B

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.

  Study EGAS00001000718

• IYDP Indonesian Y chromosome Diversity Project

  Island Southeast Asia and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic and cultural diversity. We compiled ~9.7 Mb of Y chromosome sequence from a diverse sample of over 380 men from this region, including 126 from Indonesian islands, first reported here. The granularity of this dataset allows us to fully resolve and date the regional Y chromosome phylogeny. This improved Y chromosome topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and Island Southeast Asia, ongoing interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape of today formed. The high-resolution phylogeny of the Y chromosome presented here thus enables a detailed exploration of past isolation, interaction and change in one of the world’s least understood regions.

  Study EGAS00001006028

• Human_Evolution_3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Study EGAS00001000315

• Anthropological dataset 2 for The admixture histories of Cabo Verde

  Datasets used in the article "The genetic and linguistic admixture histories of the islands of Cabo Verde" by Laurent R et al. eLife 2023 (DOI: https://doi.org/10.7554/eLife.79827 - URL: https://elifesciences.org/articles/79827) File name "eGAdeposit_233CaboVerde_GEOcoordFULL_FINAL_01062022.txt" Column 1 corresponds to individual alphanumeric codes as in the "eGAdeposit_233CaboVerde_GenotypeFile_FINAL_01062022.vcf" genotype file Column 2-3 corresponds to X-Y GPS coordinates of individual's interview location in Cabo Verde Column 4-5 corresponds to X-Y GPS coordinates of individual's self-reported residence location at the time of the interview Column 6-7 corresponds to X-Y GPS coordinates of individual's self-reported birth-place location Column 8-9 corresponds to X-Y GPS coordinates of individual's self-reported paternal birth-place location Column 10-11 corresponds to X-Y GPS coordinates of individual's self-reported maternal birth-place location

  Dataset EGAD00001008977

• Sex-biased patterns shaped the genetic history of Roma

  Whole mtDNA sequences and Y chromosomes from Roma and Non-Roma European samples.

  Study EGAS00001004207

• COVID-19-Induced Immune Alterations in Infants

  Although previous studies have described some overlap between COVID-19-induced immune alterations in adults and children, no systematic immune profiling studies have been reported in infants. We applied a multidimensional approach to decipher the immune responses to SARS-CoV-2 infected infants (n=26; 10 mild, 11 moderate and 5 severe) and healthy matched controls (n=14). Single-cell RNA-seq profiling (scRNA-seq) of PBMCs revealed alterations in cell composition upon infection, with most cell types demonstrating an interferon-stimulated gene (ISGhi) state. Our findings shed insight into the immune responses to SARS-CoV-2 in the first year of life.

  Study phs002655

• RNA-seq Revision

  The dataset comprises bulk RNA‑seq libraries generated on the Illumina NextSeq 500 platform, including primary human hepatocytes (four donors), colon tissue (four masked replicates), and a comprehensive set of iPSC‑derived samples from the JHU106, ChiPSC18, ChiPSC22, and H9 lines. The collection covers multiple differentiation stages from iPSC to DE to HLC and cultivation protocols (CEL, HAY, SPH) with at least three replicates per condition. All sequencing data are provided as raw FASTQ files, with colon samples delivered as masked FASTQ in accordance with patient consent requirements.

  Dataset EGAD00001008951

• ZRSR2 Mutant Myelodysplastic Syndromes

  Mutations in splicing factor genes are common in myelodysplastic syndromes but the reason for selection of these mutations remains incompletely understood. This study aimed to identify the effect of minor intron retention due to ZRSR2 mutations in myelodysplastic syndromes. Nine samples from patients with myelodysplastic syndromes bearing ZRSR2 mutations and ten samples from patients with myelodysplastic syndromes not bearing any splicing factor mutations were subjected to transcriptomic analysis for mis-splicing events after RNA-sequencing. 

  Study phs002212

• NGS data of human NES cells and tumors

  Raw RNA-seq data for WT and 2 Gorlin NES cells, tumors derived from MYCN mis-expressed WT NES cells, tumors derived from Gorlin NES cells, and tumors derived from Gorlin NES cells transduced with mutant DDX3X (R351W and R534S) and CRISPR/Cas9 targeting GSE1 (each sample has 3 replicates/tumors except Gorlin NES cell tumors have 4). Raw whole exome sequencing data for WT and Gorlin 1 NES cells, tumors derived from MYCN mis-expressed WT NES cells, and tumors derived from Gorlin NES cells (each sample has 3 replicates/tumors except Gorlin NES cell tumors have 4). Raw data for amplicon sequencing of GSE1 and KDM3B at regions targeted by CRISPR/Cas9 in Gorlin NES cells.

  Dataset EGAD00001004990

• Characterization of a human iPSC-derived endocrine pancreas model

  Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at six stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from two donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs=14.2, p-value=4.9x10-5) and the pancreatic agenesis gene GATA6 (log2 FC=12.1, p-value=8.6x10-5), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to our endocrine pancreas-like cells (log2 FC=5.5, p-value=2.0x10-12), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. "insulin secretion"; odds ratio=4.2, p-value=1.9x10-3): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.

  Study EGAS00001001803

• Anti-TIGIT antibody tiragolumab improves PD-L1 blockade via myeloid and Treg cells

  Tiragolumab, an anti-TIGIT antibody with an active IgG1/kappa Fc, demonstrated improved outcomes in the phase 2 CITYSCAPE trial (NCT03563716) when combined with atezolizumab (anti-PD-L1) versus atezolizumab alone1. However, there remains little consensus on the mechanism(s) of response with this combination2. We found that high baseline intratumoral macrophages and Tregs were associated with better outcomes in patients treated with atezolizumab plus tiragolumab but not with atezolizumab alone. Serum sample analysis revealed that macrophage activation was associated with clinical benefit in patients receiving the combination treatment. In mouse tumor models, tiragolumab surrogate antibodies inflamed tumor-associated macrophages, monocytes, and dendritic cells through Fc gamma receptors (FcɣR), in turn driving anti-tumor CD8+ T cells from an exhausted effector-like state to a more memory-like one. These results uncover a mechanism of action by which TIGIT checkpoint inhibitors can remodel immunosuppressive tumor microenvironments, and suggest that FcɣR engagement is an important consideration in anti-TIGIT antibody development.

  Study EGAS50000000251

• Human_Evolution_3B

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages will be sequenced using the standard whole-genome sequencing followed by filtering out autosomal and X sequences, so that only mtDNA and the Y chromosome would be analysed and released.

  Dataset EGAD00001001374

• Human Evolution 3

  The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released.

  Dataset EGAD00001001373

• Human inflammatory cardiomyopathies following SARS-CoV2 infection and COVID-19 vaccination dataset

  This dataset consists of transcriptome data of 25 human samples with myocarditis, thereof: 8 without COVID-19, 10 post COVID-19, 4 after COVID-19 vaccination and 3 with MIS-C (Multisystem Inflammatory Syndrome in Children, PIMS).

  Dataset EGAD50000001130

• Sardinian Chromosome Y DAC

  Dac EGAC00001000121

• Expression profiling of a human endocrine pancreas iPSC model

  Directed differentiation of stem cells offers a scalable solution to the need for human cell models recapitulating islet biology and T2D pathogenesis. We profiled mRNA expression at six stages of an induced pluripotent stem cell (iPSC) model of endocrine pancreas development from two donors, and characterized the distinct transcriptomic profiles associated with each stage. Established regulators of endodermal lineage commitment, such as SOX17 (log2 fold change [FC] compared to iPSCs=14.2, p-value=4.9x10-5) and the pancreatic agenesis gene GATA6 (log2 FC=12.1, p-value=8.6x10-5), showed transcriptional variation consistent with their known developmental roles. However, these analyses highlighted many other genes with stage-specific expression patterns, some of which may be novel drivers or markers of islet development. For example, the leptin receptor gene, LEPR, was most highly expressed in published data from in vivo-matured cells compared to the endocrine pancreas-like cells (log2 FC=5.5, p-value=2.0x10-12), suggesting a role for the leptin pathway in the maturation process. Endocrine pancreas-like cells showed significant stage-selective expression of adult islet genes, including INS, ABCC8, and GLP1R, and enrichment of relevant GO-terms (e.g. “insulin secretion”; odds ratio=4.2, p-value=1.9x10-3): however, principal component analysis indicated that in vitro-differentiated cells were more immature than adult islets. Integration of the stage-specific expression information with genetic data from T2D genome-wide association studies revealed that 46 of 82 T2D-associated loci harbor genes present in at least one developmental stage, facilitating refinement of potential effector transcripts. Together, these data show that expression profiling in an iPSC islet development model can further understanding of islet biology and T2D pathogenesis.

  Dataset EGAD00001002148

• Indonesian Y chromosome Diversity Commitee

  Dac EGAC00001002533

• An autoinflammatory RIG-I variant causing Singleton-Merten Syndrome associates with small non-coding Y-RNAs

  The RNA sensor RIG-I performs a critical role in surveying the cytoplasm for the presence of viral nucleic acids and initiating the downstream anti-viral type I interferon pathway. Through recognition of specific features, such as the presence of a 5’ di/triphosphate motif or highly structured base-paired regions, RIG-I effectively differentiates between RNA of viral- and self-origin. In Singleton-Merten syndrome (SMS), gain-of-function variants in RIG-I lead to a breakdown in this surveillance system and results in aberrant sensing of self-RNAs and deleterious upregulation of type I interferons. The identity of the self-RNAs binding to gain-of-function RIG-I mutants has remained elusive and would provide a greater understanding of the aetiology of SMS. Here we used an infrared individual-nucleotide resolution UV-crosslinking and immunoprecipitation (irCLIP) approach to determine the RNA profile bound to a previously characterised ATPase-deficient SMS variant, RIG-IC268F. irCLIP identified a broad array of self-RNAs, primarily those transcribed by RNA polymerase III, that were bound to RIG-I. Subsequent native RNA immunoprecipitation confirmed a prominent and specific interaction between RIG-IC268F and Y-RNAs, a family of four structurally similar non-coding RNAs. Manipulation of Y-RNAs alone by targeting either Y-RNA transcripts or Y-RNA stabilising proteins was insufficient to negate RIG-I induce interferon, hinting at a broader profile of RNA polymerase III-derived RNAs being influential in driving the sterile activation of gain-of-function RIG-I variants.

  Study EGAS50000001660

• Papua New Guinean Y chromosome Diversity Commitee

  Dac EGAC00001002531

• Wilm's tumor sequencing data

  No. of samples: 80 (28 ULP-WGS, 26 WES, 26 RNA-SEQ) File types: FASTQ (28 ULP-WGS, 19 WES, 18 RNA) and BAM (7 WES, 8 RNA) Technology used: Sequencing - Illumina Novoseq 6000; Map/Align - Illumina DRAGEN v3.7.5; Genome assembly - GrCh38p13 Filename nomenclature: - SampleName_Passage_SampleType_TissueType_SequencingType - Passage of: PX = unknown; PZ = from patient; P0 = first passage from patient on plastic; P1 = first passage from plastic/PDX/organoid - SampleType: STN = normal; STT = tumor - SampleType STN: 00 = tissue unknown; 01 = adjacent normal; 02 = fibroblast; 03 = germline blood; 21 = cell line from patient tissue; 22 = cell line from PDX; 23 = cell line from patient fibroblast - SampleType STT: 00 = tissue unknown; 01 = primary tumor; 21 = cell line from patient; 22 = cell line from PDX - TissueType: WT = Wilm's tumor; 00 = kidney unknown; 01 = kidney left; 02 = kidney right - SequencingType: 00 = unknown; 02 = ultra-low pass whole-genome sequencing; 20 = whole-exome; 61 = bulk RNA-sequencing

  Dataset EGAD00001011111

• Ribo-depleted RNA-sequencing of II.3, III.1, and III.3

  This datasets contains the Ribo-depleted RNA-sequencing of patients II.3, III.1, and III.3. Libraries were sequenced to a minimum depth of 195 million read pairs (2x75nts) on an Illumina NextSeq500 Midoutput FC.

  Dataset EGAD50000002364

• Y chromosome variability in Polish population

  The aim of the present study was to define the Y chromosome variability in Polish male population. For the first time, the study of Polish population was conducted on such a large number of individuals (n=2705) representing administrative units of both levels of local administration in Poland (voivodeships and counties). Furthermore, the clusters were used as an additional form of population subdivision, corresponding to geographic regions of Poland.

  Study EGAS00001004111

• Sardinian Chromsome Y 2012 Analysis

  1204 Sardinian males

  Dataset EGAD00001000618

• Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic

  Somatic mutations of RUNX1, which encodes the myeloid and lymphoid transcriptional factor RUNX1, are common in both B- and T- acute lymphoid leukemia (ALL) and are associated with poor prognosis of T-ALL. However, there has been no comprehensive investigation of the pattern or prevalence of RUNX1 germline mutation in both B- and T-ALL. Here we report germline RUNX1 variants in 1.23% of B-ALL and 2.11% of T-ALL, identifying 31 unique variants in 62 B-ALL and 18 unique variants in 26 T-ALL children. The majority of frameshift and nonsense variants affected RUNX1 function in transcriptional regulation, hematopoiesis, and cellular proliferation. We identified JAK3 as the most frequent somatic mutation in T-ALL with RUNX1 variants. These results not only identify RUNX1 as a leukemia predisposition gene but also further underline the importance of germline genetic variants to the development of ALL

  Study EGAS00001005403

• Ychromosome_dataset

  Genotyping of Y chromosome in Polish population

  Dataset EGAD00010001807

• Whole genome sequencing data of paediatric KMT2A-rearranged acute lymphoblastic leukemia

  Whole genome sequencing data from infant (<1 y) paediatric (< 18 y) KMT2A-rearranged acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic and remission (control) samples of 3 patients. Dataset consists of two experiments depending on library preparation method; "Experiment 1" is made using normal WGS library preparation (pcr+), and "Experiment 2" is made using pcr-free library preparation method.

  Dataset EGAD50000001568

• Y-phylogeny-haplogroupDE (2019-04-03)

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004892

• Extracorporeal Life Support Survival in a Pediatric Hematopoietic Cellular Transplant Recipient with Presumed Graft Versus Host Disease-Related Fulminant Myocarditis

  We report the case of a 15-year-old female with hypodiploid pre-B acute lymphoblastic leukemia status post allogeneic hematopoietic stem cell transplantation (HCT) from a matched unrelated male donor who presented on transplant day +75 with cardiac arrest due to ventricular fibrillation associated with fulminant myocarditis. Using conventional diagnostics, an exhaustive search for microbial pathogens in the heart biopsy as well as nasopharynx, blood, urine, and endotracheal aspirate was performed but did not uncover a candidate pathogen. The family consented to a research study for the use of unbiased next-generation genomic sequencing for pathogen identification in the myocardial biopsy. DNA sequencing was performed on 1.5 x 108 sequencing pairs and no microbial pathogens were identified. Interestingly, a significant component of Y-chromosomal human DNA was identified, suggesting infiltration of at least 10 donor leukocytes per host cell. This finding is grossly consistent with the lymphocyte:myocyte ratio in the biopsy according to visual inspection at 40x magnification. This case merits discussion due to (1) her survival after 17 days of veno-arterial extracorporeal life support (ECLS) and (2) the possibility of cardiotropic graft versus host disease (GVHD).

  Study phs001336

• Whole exome sequencing of endometriod ovarian cancer tumours

  Whole Exome sequencing data of tumour samples for 112 patients with endometrioid ovarian carcinoma in FASTQ format. Data was derived as summarized below: Library Preparation: Libraries were prepared from each DNA sample using the Illumina TruSeq Exome Library Prep kit (#FC-150-1002) according to the provided protocol using modifications for working with FFPE sourced material. Libraries were quantified using the Qubit 2.0 Fluorometer and the Qubit DNA HS assay (#Q32854) and the size distribution of fragments was assessed using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Library QC: Exome-captured sequencing library pools were quantified using the Qubit 2.0 Fluorometer and the Qubit DNA HS assay (#Q32854) and the size distribution of fragments was assessed using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Fragment size and quantity measurements were used to calculate molarity for each library pool. Sequencing: Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC-404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002).

  Dataset EGAD00001006389

• A Dose Escalation Study of Efmarodocokin Alfa (UTTR1147A) in Healthy Volunteers and Patients with Ulcerative Colitis

  Background: The interleukin-22 cytokine (IL-22) has demonstrated efficacy in nonclinical colitis models with a non-immunosuppressive mechanism-of-action. Efmarodocokin alfa (UTTR1147A) is a fusion protein agonist that links IL-22 to the crystallizable fragment (Fc) of human immunoglobulin (IgG4) for improved pharmacokinetic characteristics, but with a mutation to minimize Fc effector functions. Methods: This randomized, phase 1b study evaluated the safety, tolerability, pharmacokinetics, and pharmacodynamics of repeat intravenous dosing of efmarodocokin alfa in healthy volunteers (HVs; n=32) and patients with ulcerative colitis (UC; n=24) at 30–90 µg/kg doses given biweekly (Q2W) or monthly (Q4W) (6:2 active:placebo per cohort). Results: The most common adverse events (AEs) were on-target dermatological effects (dry skin, erythema, and pruritus) that were reversible. Dose-limiting non-serious dermatological AEs (severe dry skin, erythema, exfoliation, and discomfort) were seen in two HVs and one patient at 90 ug/kg Q2W. Pharmacokinetics were generally dose-proportional across the dose levels tested, but patients demonstrated lower drug exposures relative to HVs at the same dose. IL-22 serum biomarkers and IL-22 responsive genes in colon biopsies were induced with active treatment. Patients demonstrated changes in microbiota composition following active treatment, thereby reversing baseline dysbiosis. Clinical response was observed in 7/18 active- and 1/6 placebo-treated patients; clinical remission was observed in 5/18 active- and 0/6 placebo-treated patients.

  Study EGAS00001006172

• Peripheral blood DNA transcriptomics of vedolizumab treatment response in patients with Crohn's disease

  Data pertains longitudinal transcriptomic data measured from blood obtained from patients with Crohn's disease that were starting treatment with vedolizumab. Samples were obtained prior to treatment and approximately 26 weeks into treatment during response assessment. At response assessment, patients were classified as responders (R) or non-responders (NR) based on a strict combination of endoscopic, biochemical and clinical criteria: ≥50% reduction in the endoscopic SES-CD score, corticosteroid-free clinical remission (≥3 point drop98 in HBI or HBI ≤4 and no systemic steroids) and/or biochemical response (C-reactive protein (CRP) and fecal calprotectin reduction ≥50% or ≤5 mg/L and fecal calprotectin ≤250 µg/g). Modified response was defined as a combination of corticosteroid-free clinical- (HBI ≤4) and biochemical (CRP ≤5 mg/L and/or fecal calprotectin ≤250 µg/g) remission between week 26-52 without treatment change through week 52. Transcriptomic analyses was conducted through RNA sequencing, wherein mRNA was extracted utilizing the QIAsymphony system, converted into cDNA and sequenced in a paired-end format on the Illumina NovaSeq6000 at the Amsterdam UMC Core Facility Genomics, generating a dataset comprising 40 million 150 bp-reads.

  Dataset EGAD50000000385

• Peripheral blood DNA transcriptomics of ustekinumab treatment response in patients with Crohn's disease

  Data pertains longitudinal transcriptomic data measured from blood obtained from patients with Crohn's disease that were starting treatment with ustekinumab. Samples were obtained prior to treatment and approximately 26 weeks into treatment during response assessment. At response assessment, patients were classified as responders (R) or non-responders (NR) based on a strict combination of endoscopic, biochemical and clinical criteria: ≥50% reduction in the endoscopic SES-CD score, corticosteroid-free clinical remission (≥3 point drop98 in HBI or HBI ≤4 and no systemic steroids) and/or biochemical response (C-reactive protein (CRP) and fecal calprotectin reduction ≥50% or ≤5 mg/L and fecal calprotectin ≤250 µg/g). Modified response was defined as a combination of corticosteroid-free clinical- (HBI ≤4) and biochemical (CRP ≤5 mg/L and/or fecal calprotectin ≤250 µg/g) remission between week 26-52 without treatment change through week 52. Transcriptomic analyses was conducted through RNA sequencing, wherein mRNA was extracted utilizing the QIAsymphony system, converted into cDNA and sequenced in a paired-end format on the Illumina NovaSeq6000 at the Amsterdam UMC Core Facility Genomics, generating a dataset comprising 40 million 150 bp-reads.

  Dataset EGAD50000000386

• Characterizing the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft model for RNA-based liquid biopsy in a preclinical setting

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model including 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX NOD-scid IL2Rgnull mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either R-CHOP, huCD20-Fc-AFN-CHOP, or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the SMARTer Stranded Total RNA-seq pico v3 kit.

  Study EGAS50000000566

• High titers and low fucosylation of early phase anti-SARS-CoV-2 IgG promote hyper-inflammation by alveolar macrophages

  We show that early phase anti-Spike IgG in serum of critically ill COVID-19 patients induces hyper-inflammatory responses by human alveolar macrophages. We identified that this excessive inflammatory response is dependent on two antibody features that are specific for severe COVID-19. First, inflammation is driven by high titers of anti-Spike IgG, a hallmark of severe disease. Second, we found that anti-Spike IgG from severely ill patients is intrinsically more pro-inflammatory because of different glycosylation of the Fc tail, particularly by low fucosylation. This dataset is linked with the following ArrayExpress Experiment: E-MTAB-10431 - 2020_COVID19_FCGR_MIL10_IgGfucosylation

  Study EGAS00001005206

• Illumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001002598

• ProjectMinE :llumina HiSeqX and HiSeq 2000 whole genome sequence data on 3,001 ALS samples including 212 with known C9orf72 repeat expansions

  Whole genome sequence (WGS) data was generated on 3,001 samples previously quantified for the presence of the C9orf72 repeat expansion (212 expanded and 2,789 wild type), These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer. The repeat expansions were called using ExpansionHunter to demonstrate the ability to call large repeats from high throughput, WGS data. Provided here are all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion in addition to reads aligned in pre-determined off target locations where the aligners are known to mis-align reads.

  Study EGAS00001003383

• dataset1

  Contains test sample 1-26

  Dataset EGAD00010002041

• Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry

  Analysis of the genetic affinity between coastal Pacific and Amazonian natives (i.e. "Y population" ancestry). Here we analyzed a dataset of newly generated data from four Brazilian indigenous communities genotyped in the Axiom Human Origins array combined with publicly available data from other Native American populations.

  Study EGAS00001005022

• Y_phylogeny_haplogroupDE

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001002674

• DAC-2020-03-26-Lemola (DAC-039))

  DAC-2020-03-26-Lemola (DAC-039)), raw data in EGA, metadata in Harvard Dataverse

  Dataset EGAD50000000897

• Gene Expression Study of Individuals with Sex Chromosome Aneuploidies

  Males and females show dramatic differences in their vulnerability to the same diseases. For example, compared to men, lupus is six times more prevalent, thyroid cancer is three times more prevalent, and unipolar depression is twice as prevalent in women. Diseases with a strong male bias include autism (5:1), dilated cardiomyopathy (3:1), and ankylosing spondylitis (5:1). Historically, such differences have been attributed solely to extrinsic factors such as circulating sex hormones or environmental influences. We hypothesized that intrinsic factors - genetic differences between XX and XY cells - have unappreciated biological consequences throughout the body and contribute to sex differences in disease incidence and severity. This hypothesis stems from our long-term effort to sequence the sex chromosomes of diverse mammalian species, which has identified a set of homologous genes on the X and Y chromosomes that are dosage-sensitive, expressed throughout the body, and encode regulators of chromatin modification, transcription, translation, and protein stability. These X- and Y-encoded genes differ in sequence and expression pattern, which likely manifests in genome-wide differences in gene regulation between XX and XY cells and influences all aspects of human biology, including sex differences in disease susceptibility. These hard-wired molecular sex differences have been largely overlooked and understudied, representing a significant gap in our knowledge of human biology.The gene expression study of individuals with sex chromosome aneuploidies takes advantage of natural human variation in sex chromosome number, i.e. sex chromosome aneuploidy, to investigate alterations in genome-wide gene expression that correlate with changes in X- and Y-chromosome dosage. We analyzed samples from 114 individuals with a variety of sex chromosome aneuploidies, including 45,X; 47,XXY; 47,XYY; 47,XXX; 48,XXYY; and 49,XXXXY. We generated lymphoblastoid cell lines (LCLs) from blood samples and, in some cases, fibroblast cultures from skin biopsies. We supplemented our collection with previously-derived cell lines. To evaluate gene expression, we performed deep profiling of the transcriptome (RNA-seq) from these LCLs and fibroblasts. We performed parallel analyses on samples collected from 62 control 46,XX and 46,XY individuals, 6 individuals with trisomy 21, and 14 individuals with structural variations of the X and Y chromosomes. In addition, we performed CRISPRi knockdowns on 3 of the 46,XX and 3 of the 46,XY fibroblast samples for the homologous transcription factors ZFX and ZFY, encoded on the X and Y chromosomes, respectively.In the April 2024 update, we added RNA-seq datasets derived from isolated CD4+ T cells and monocytes from 76 and 72 adults, respectively, with the following sex chromosome constitutions: 45,X; 46,XX; 46,XY; 47,XXX; 47,XXY; 47,XYY. These individuals are largely a subset of the same cohort described above. In addition, we performed RNA-seq on in-vitro stimulated CD4+ T cells with the following sex chromosome constitutions: 45,X; 46,XX; 46,XY; 47,XXY.In the August 2024 update, we added RNA-seq datasets generated from the following: 1) LCLs derived from individuals with AZFa deletions of the Y chromosome, 2) DDX3X and DDX3Y knockdown (via CRISPRi) in XY fibroblasts, and 3) 5-ethyl uridine (5-EU) treatment in XY and XYYYY LCLs.

  Study phs002481

• T cell transcriptional gradient

  There are two datasets: 1. scRNA-seq of human cutaneous immune cells from psoriasis patients. These include pre- and post-Tildrakizumab treated patients and come in a BAM file format. 19006FL-25-01 19006FL-38-01 19006FL-32-01-03 19006FL-33-01 19006FL-28-01-05 19006FL-35-01-01 2. RNA-seq of ZFP36L2 CRISPIR deleted Human T cells are FASTQ files. 19006XR-30-05 19006XR-30-04 19006XR-30-02 19006XR-30-01 19006XR-26-05 19006XR-26-04 19006XR-26-02 19006XR-26-01 19006R-22-04 19006R-22-08 19006R-22-05 19006R-22-01

  Dataset EGAD00001009677

• Cerebrospinal fluid cfDNA sequencing for classification of central nervous system glioma

  Primary central nervous system (CNS) gliomas can be classified by characteristic genetic alterations. In addition to solid tissue obtained by surgery or biopsy, cell-free DNA (cfDNA) derived from cerebrospinal fluid (CSF) is an alternative source of material for genomic analyses. Experimental design: We performed targeted next-generation sequencing (NGS) of CSF cfDNA in a representative cohort of 85 patients presenting with with suspicion of primary or recurrent glioma at two neurooncological centers. Copy-number variation (CNV) profiles, single nucleotide variants (SNVs), and small insertions/ deletions (indels) were combined into a molecular-guided tumor classification. Comparison with the solid tumor was performed for 38 cases with matching solid tissue available. Results: Cases were stratified into four groups: glioblastoma (n = 32), other glioma (n = 19), non-malignant (n = 17) and no confirmed diagnosis available (n = 17). We introduce a molecular-guided tumor classification, enabling identification of tumor entities and/ or cancer specific alterations in 75.0 % (n = 24) of glioblastoma and 52.6 % (n = 10) of other glioma cases. The overlap between CSF and matching solid tissue was highest for CNVs (26-48 %) and SNVs at pre-defined gene loci (44 %), followed by SNVs/indels identified via uninformed variant calling (8-14 %). A molecular-guided tumor classification was made 23.5 % (n = 4) of cases with no confirmed diagnosis available. Conclusions: We developed a workflow for targeted sequencing of CSF cfDNA as well as a strategy for interpretation and reporting of sequencing results based on a molecular-guided tumor classification in glioma.

  Study EGAS50000000060

• WGS of Multiple Myeloma/MGUS/SMM cases (germline) - VCF files (SNPs)

  WGS - PCR-free library preparation (whole blood gDNA), paired-end (2x100bp) sequencing on DNBseq sequencing platform (BGI) Number of samples: 26

  Dataset EGAD50000001800

• ATAC-seq

  ATAC-seq data for 26 CLL samples (7 controls, 19 tumor) of the CancerEpiSys-PRECiSe project.

  Dataset EGAD00001005967

• MutWP1: CRUK Grand Challenge Mutographs of Cancer: kidney (2019-03-26)

  This dataset contains all the data available for this study on 2019-03-26.

  Dataset EGAD00001004867

• Relation between transcriptome, karyotype and age in cases of sex chromosome aneuploidies.

  Why women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that transposable element (TE) repression declines with age, potentially leading to detrimental effects such as somatic mutations and disrupted gene expression, which may accelerate the aging process. Given that the Y chromosome is rich in repeats, age-related increases in TE expression could be more pronounced in males, likely contributing to their reduced longevity compared to females. In this work, we first studied whether TE expression is associated with the number of sex chromosomes in humans. We analyzed blood transcriptomic data obtained from individuals of different karyotype compositions: 46,XX females (normal female karyotype), 46,XY males (normal male karyotype), as well as males with abnormal karyotypes, such as 47,XXY, and 47,XYY.

  Study EGAS50000001009

• Relation between transcriptome, karyotype and age in cases of sex chromosome aneuploidies.

  Why women live longer than men is still an open question in human biology. Sex chromosomes have been proposed to play a role in the observed sex gap in longevity, and the Y male chromosome has been suspected of having a potential toxic genomic impact on male longevity. It has been hypothesized that transposable element (TE) repression declines with age, potentially leading to detrimental effects such as somatic mutations and disrupted gene expression, which may accelerate the aging process. Given that the Y chromosome is rich in repeats, age-related increases in TE expression could be more pronounced in males, likely contributing to their reduced longevity compared to females. In this work, we first studied whether TE expression is associated with the number of sex chromosomes in humans. We analyzed blood transcriptomic data obtained from individuals of different karyotype compositions: 46,XX females (normal female karyotype), 46,XY males (normal male karyotype), as well as males with abnormal karyotypes, such as 47,XXY, and 47,XYY.

  Study EGAS00001007462

• scRNA-seq analysis of HGSC tumors, including immune TME, before and after NACT

  Gene expression profiles of single cells from 26 tumor and ascites samples samples from 17 patients

  Dataset EGAD50000000862

• Resequencing candidate genes for male spermatogenic impairment

  This study aims to identify novel candidate variants from human Y-chromosomal genes DAZ, BPY2 and CDY1/2 by resequencing the coding regions of these genes from male patients with spermatogenic impairment. The coding regions of the genes plus a selection of phylogenetically informative Y-chromosomal markers have been amplified by standard PCR, amplicon lengths range from 178 to 486 bp. Amplicons were quantified by gel electrophoresis and pooled in approx. equimolar concentrations per patient. For each of the 480 submitted samples, approx. 1 microgram of amplified DNA pool was provided in a total volume of 120 microlitres. The samples were indexed and libraries prepared for PE250bp Illumina MiSeq runs. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ .

  Dataset EGAD00001006784

• IYDP Indonesian Y chromosome Diversity Project

  The IYDP dataset includes BAM files of 126 Y chromosomes extracted from whole genome sequences. These are from individuals from a broad range of Indonesian islands - communities close to mainland Asia through to New Guinea. The original whole genome sequencing libraries were prepared using TruSeq DNA PCR-Free and TruSeq Nano DNA HT kits depending on DNA quantity. 150 bp paired-end sequencing was performed on the Illumina HiSeq X sequencer. Individuals were sequenced to expected mean depth of 30x, with an achieved median depth of raw reads across samples of 43x.

  Dataset EGAD00001008573

• H3Africa H3AChipDesign TrypanoGEN1

  26 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004393

• Integrating molecular imaging and transcriptomic profiling in advanced HER2-positive breast cancer receiving trastuzumab emtansine (T-DM1): an analysis of the ZEPHIR clinical trial

  Purpose: The ZEPHIR clinical trial evaluated the role of [89Zr]trastuzumab-PET/CT (HER2-PET/CT) and 2-[18F]fluoro-2-deoxy-D-glucose PET/CT ([18F]FDG-PET/CT) in predicting outcomes in patients with advanced HER2-positive breast cancer treated with trastuzumab emtansine (T-DM1). Here, we combined molecular/metabolic imaging and transcriptomic data to investigate the biological processes associated with [89Zr]trastuzumab and [18F]FDG uptake, and to dissect the mechanisms involved in T-DM1 resistance. Experimental design: RNA was extracted from metastasis biopsies obtained at study inclusion in the ZEPHIR trial. HER2-PET/CT and [18F]FDG-PET/CT imaging data of biopsied lesions were integrated with RNA sequencing data. Lesions were compared based on the level of [89Zr]trastuzumab uptake (dichotomized into high/low classes) as well as on the presence/absence of metabolic response, defined comparing baseline and on-treatment [18F]FDG-PET/CT. Results: We analyzed matched transcriptomic and molecular/metabolic imaging data for 24 metastases (one lesion/patient). Pathways involved in extracellular matrix (ECM) organization, glycosylphosphatidylinositol synthesis, and collagen formation were enriched in lesions presenting low [89Zr]trastuzumab uptake. [18F]FDG uptake at baseline correlated with proliferation and immune-related processes. Hypoxia and ECM-related processes were enriched in lesions that showed no metabolic response to T-DM1. Interestingly, immune-related processes (e.g., Fc gamma receptor activation, complement cascade) were associated with high [89Zr]trastuzumab uptake and metabolic response. Conclusions: To our knowledge, this study represents the first correlative analysis between [89Zr]trastuzumab tumor uptake and gene expression profiling in humans. Our findings point toward a role of ECM in impairing [89Zr]trastuzumab tumor uptake and T-DM1 metabolic response in advanced HER2-positive breast cancer, and highlight the potential of molecular imaging to depict tumor microenvironment features.

  Study EGAS50000000470

• Aligned reads from specific genomic locations derived from Illumina HiSeqX and HiSeq2000 whole genome sequence data

  This dataset includes bam files from 3,001 samples. These bam files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these bam files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001003513

• Chromosome Y Philogeny in Sardinia

  Genetic variation within the male specific portion of the Y chromosome (MSY) can clarify the origins of contemporary populations, but previous studies were hampered by partial genetic information. Population sequencing of 1,204 Sardinian males identified 11,763 MSY single nucleotide polymorphisms (SNPs), of which 6,751 have not previously been observed. We constructed a MSY phylogenetic tree containing all main haplogroups found in Europe along with many Sardinian-specific lineage clusters within each haplogroup. The tree was calibrated with archaeological data from the initial expansion of the Sardinian population ~7,700 years ago. The ages of nodes highlight different genetic strata in Sardinia and reveal presumptive timing of coalescence with other human populations. We calculate a putative age for coalescence of ~180-200,000 years ago, consistent with previous mitochondrial DNA (mtDNA) based estimates.

  Study EGAS00001000532

• Refractory Classic Hodgkins Lymphoma (cHL) sWGS

  Associated with the study: Blood-based Monitoring of Relapsed/Refractory Hodgkin Lymphoma Patients Predict Responses to Anti-PD-1 Treatment. 26 ctDNA Samples from 4 patients followed longitudinally. sWGS performed for copy number aberration (CNA) analysis.

  Dataset EGAD50000001163

• RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

  DAC for RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

  Dac EGAC50000000627

• Germline RUNX1 Variation and Predisposition to Childhood Acute Lymphoblastic

  Somatic mutations of RUNX1, which encodes the myeloid and lymphoid transcriptional factor RUNX1, are common in both B- and T- acute lymphoid leukemia (ALL) and are associated with poor prognosis of T-ALL. However, there has been no comprehensive investigation of the pattern or prevalence of RUNX1 germline mutation in both B- and T-ALL. Here we report germline RUNX1 variants in 1.23% of B-ALL and 2.11% of T-ALL, identifying 31 unique variants in 62 B-ALL and 18 unique variants in 26 T-ALL children. The majority of frameshift and nonsense variants affected RUNX1 function in transcriptional regulation, hematopoiesis, and cellular proliferation. We identified JAK3 as the most frequent somatic mutation in T-ALL with RUNX1 variants. These results not only identify RUNX1 as a leukemia predisposition gene but also further underline the importance of germline genetic variants to the development of ALL

  Dataset EGAD00001007793

• RNA-seq of high grade serous ovarian tumours

  Somatic RNA for 40 samples matched to the WGS was extracted using the Qiagen Qiasymphony RNA protcol (cat no 931636). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including DNase digestion). The resulting RNA the underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as measures of RNA purity. A260/280 had to be 2.0 and A260/230 had to be 2.0-2.2. Then RNA was quantified using LifeTechnologies Qubit RNA BR kit (cat no Q10210). RNAseq was carried out by the Edinburgh Clinical Research Facility on an Illumina NExtSeq500. Total RNA samples were assessed on the Agilent Bioanalyser (Agilent Technologies, #G2939AA) with the RNA 6000 Nano Kit (#5067-1512) for quality and integrity of total RNA, and then quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q32855). Libraries were prepared from total-RNA sample using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760S) with the NEBNext rRNA Depletion kit (#E6310) according to the provided protocol. 400ng of totalRNA was then added to the ribosomal RNA (rRNA) depletion reaction using the NEBNext rRNA depletion kit (Human/mouse/rat) (#E6310). This step uses specific probes that bind to the rRNA in order to cleave it. rRNA-depleted RNA was then DNase treated and purified using Agencourt RNAClean XP beads (Beckman Coulter Inc, #66514). RNA was then fragmented using random primers before undergoing first strand and second strand synthesis to create cDNA. cDNA was end repaired before ligation of sequencing adapters, and libraries were enriched by PCR using the NEBNext Multiplex oligos for Illumina set 1 and 2 (#E7500). Final libraries had an average peak size of 271bp. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC- 404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). Libraries were combined in an equimolar pool based on the library quantification results and run across 5 High-Output Flow Cell v2.5.

  Dataset EGAD00001009048

• RNA-seq of high grade serous ovarian tumours

  Somatic RNA for 37 samples was extracted using the Qiagen Qiasymphony RNA protcol (cat no 931636). The tissue was initially homogenised using a Qiagen Bioruptor, followed by the manufacturers recommended protocol (including DNase digestion). The resulting RNA the underwent quality control as follows: firstly, A260 and A280nm were measured on a Denovix DS-11 Fx to qualitatively illustrate A260/280nm and A260/230nm ratios as measures of RNA purity. A260/280 had to be 2.0 and A260/230 had to be 2.0-2.2. Then RNA was quantified using LifeTechnologies Qubit RNA BR kit (cat no Q10210). RNAseq was carried out by the Edinburgh Clinical Research Facility on an Illumina NExtSeq500. Total RNA samples were assessed on the Agilent Bioanalyser (Agilent Technologies, #G2939AA) with the RNA 6000 Nano Kit (#5067-1512) for quality and integrity of total RNA, and then quantified using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific Inc, #Q32866) and the Qubit RNA HS assay kit (#Q32855). Libraries were prepared from total-RNA sample using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina (#E7760S) with the NEBNext rRNA Depletion kit (#E6310) according to the provided protocol. 400ng of totalRNA was then added to the ribosomal RNA (rRNA) depletion reaction using the NEBNext rRNA depletion kit (Human/mouse/rat) (#E6310). This step uses specific probes that bind to the rRNA in order to cleave it. rRNA-depleted RNA was then DNase treated and purified using Agencourt RNAClean XP beads (Beckman Coulter Inc, #66514). RNA was then fragmented using random primers before undergoing first strand and second strand synthesis to create cDNA. cDNA was end repaired before ligation of sequencing adapters, and libraries were enriched by PCR using the NEBNext Multiplex oligos for Illumina set 1 and 2 (#E7500). Final libraries had an average peak size of 271bp. Libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626). Sequencing was performed using the NextSeq 500/550 High-Output v2 (150 cycle) Kit (# FC- 404-2002) on the NextSeq 550 platform (Illumina Inc, #SY-415-1002). Libraries were combined in an equimolar pool based on the library quantification results and run across 5 High-Output Flow Cell v2.5.

  Dataset EGAD00001010139

• Dataset of BAM files of three trio members

  This dataset contains whole genome sequencing data, based in BAM files of three trio members. These BAM files contain information of chromsomes 21, X, Y and mitochondrial.

  Dataset EGAD00001008095

• Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

  Gene expression profiles of single cells from 26 chemo-naïve and IDS tumor tissue and ascites samples from 17 HGSC patients

  Study EGAS50000000607

• dataset1

  Contains 14 control samples and 26 case samples.

  Dataset EGAD00001008576

• BLUEPRINT release August 2015, ChIP-Seq for CD8-positive, alpha-beta T cell, on genome GRCh38

  ChIP-Seq data for 5 CD8-positive, alpha-beta T cell sample(s). 26 run(s), 26 experiment(s), 26 alignment(s) on human genome GRCh38. Part of BLUEPRINT release August 2015. Analysis documentation available at http://ftp.ebi.ac.uk/pub/databases/blueprint/releases/20150820/homo_sapiens/README_chipseq_analysis_ebi_20150820

  Dataset EGAD00001001513

• MeDALL epigenetics study

  MeDALL- (Mechanisms of the Development of ALLergy) is a collaborative project supported by the European Union under the Health Cooperation Work Programme of the 7th Framework programme (grant agreement number 261357).MeDALL epigenetics study includes illumina 450k methylation measurements from 4 cohorts: Infancia y Medio Ambiente (INMA), Etudes des Déterminants pré et postnatals précoces du développement et de la santé de l’ENfant (EDEN), Children’s Allergy Environment Stockholm Epidemiology study(BAMSE), and Prevention and Incidence of Asthma and Mite Allergy (PIAMA)

  Study EGAS00001002169

• C9orf72 region reads of 3001 samples

  This dataset includes cram files from 3,001 samples. These cram files include all read pairs where at least one of the reads aligns within 1kb of the C9orf72 repeat expansion. Additionally, these cram files also contain reads that are aligned to any of 29 pre-determined off target locations where the aligners are known to mis-align reads associated with this repeat expansion. These samples were sequenced using a combination of 2x100bp reads on an Illumina HiSeq2000 and 2x150bp reads on an Illumina HiSeqX sequencer and aligned using the Isaac aligner.

  Dataset EGAD00001004834

• Sequencing files for "Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy"

  Files from whole exome sequencing of 26 tumors and two matched normals from one melanoma patient. The 26 tumors include the untreated primary, cutaneous metastases and distant metastases to internal organs.

  Dataset EGAD00001003200

• Non-coding mutations reveal cancer driver cistromes in luminal breast cancer

  A dataset of ER+PR+ breast tumor samples that were analyzed in order to identify mutation enrichment in cis-regulatory elements and cistrome. The repository includes sequencing data from 88 patients. 26/88 were sequenced using ATAC-seq

  Dataset EGAD00001007650

• GenomeDenmark Phase 2 - variants called on chrY for 62 males.

  Variants on the Y chromosome for 62 danish males in VCF format from the GenomeDenmark Phase 2 cohort. Variants were called using reference based approaches such as the haplotype-caller module from GATK and using alignment of denovo assemblies to the reference using ASMvar.

  Dataset EGAD00001003186

• High-throughput transcriptome data of paediatric ETV6-RUNX1 acute lymphoblastic leukemia

  High-throughput transcriptome sequencing data from paediatric (&lt;18-y) ETV6-RUNX1 fusion positive acute lymphoblastic leukemias. Dataset includes fastq and BAM files from diagnostic samples of 33 patients.

  Dataset EGAD00001010164

• Phenotype information

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model in-cluding 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either rituximab, cyclophosphamide, doxorubicin, vincris-tine, and prednisone (R-CHOP), CD20-targeted human IFNα2-based AcTaferon combined with CHOP (huCD20-Fc-AFN-CHOP), or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the using the SMARTer Stranded Total RNA-Seq Kit v3.

  Dataset EGAD50000000806

• Long-read data (PacBio)

  The goal of this project was to perform long-read RNA sequencing (LR-seq, PacBio) in combination with short-read RNA-seq for systematic characterization of the isoform diversity in primary breast tumor samples. We sequenced the full-length transcriptomes of 26 breast tumors and 4 normal breast samples.

  Dataset EGAD00001006597

• Sahel Data Access Committee

  Genome-wide genotype array data of Fulani populations presented in Fortes-Lima et al. 2025. Citation: Population History and Admixture of the Fulani People from the Sahel. Cesar A. Fortes-Lima, Mame Y. Diallo, Václav Janoušek, Viktor Černý, and Carina M. Schlebusch. American Journal of Human Genetics 112(2), February 6, 2025. doi: https://doi.org/10.1016/j.ajhg.2024.12.015

  Dac EGAC50000000290

• Drug Perturbation of Primary Lymphoma Patient Samples and RNA Sequencing

  This submission contains 3'-end-based shallow-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule drugs (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). The samples were sequenced after 48 hours. The total data set consists of 1476 RNA sequencing samples from 6 batches (pilot, batch 1, batch 1 replicate, batch 2, batch 3, batch 4).

  Study EGAS50000001500

• Bladder Cancer Organoids as a Functional System to Model Different Disease Stages and Therapy Response

  The study 'Bladder Cancer Organoids as a Functional System to Model Different Disease Stages and Therapy Response' reports the genomic characterization at the single allele level upon Whole Exome Sequencing of Bladder Cancer (BLCa) Patient Tumor (PT) samples obtained from 18 patients and corresponding Patient Derived Organoids (PDOs), implementing the SPICE pipeline (Ciani Y et al). Our cohort included 21 PTs and 22 PDOs. In this study, we generated a unique biobank resource of BLCa organoids that encompasses a broad spectrum of disease stages. We demonstrated that PDOs retain cancer heterogeneity and mutational burden. Furthermore, we observed that BLCa PDO can have different morphologies which may reflect tumor-specific features. Indeed, a solid morphology may be associated with more advanced tumors, as supported by the high PDO genomic burden and high primary tumor stage. Moreover, with our drug screening pipeline, we demonstrated the clinical relevance and feasibility of using a BLCa PDO-based drug assay for comparing the standard of care (SOC) drugs with compounds not currently in use for BLCa. Response to SOC was highly heterogeneous with approximately 50% of non-muscle invasive bladder cancer and 33% of muscle invasive bladder cancer PDOs showing no or minimal response. The most effective targeted therapy was lapatinib. We used an integrative analysis of drug response profiles with matched PDO genomic analysis to determine enrichment thresholds for candidate markers of therapy resistance and sensitivity. Importantly, by assessing the clinical history of longitudinally sampled cases, the clonal evolution of the disease could be determined and matched with PDO drug response profiles.

  Study phs003149

• Lymphoma_primary_patient_drug_perturbed_RNASeq_samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET-762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dac EGAC50000000578

• scMultiome (snRNA + snATAC) data of 26 regionally sampled GBM tissue from 6 patients

  This dataset contains snRNA-seq data of 26 regionally sampled GBM tissue (peritumoral region, tumor edge, and tumor core). Regionally sampled GBM patient tissue was dissociated and nuclei were processed unsorted or by sorting with 7AAD to remove debris and dead cells. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit. Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit, nuclei were barcoded and RNA and ATAC libraries were constructed, allowing for simultaneous capture of transcriptome and epigenome from the same cells.

  Dataset EGAD50000001838

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Dataset EGAD00001002262

• INSPIRE - Investigator-initiated Phase 2 Study of Pembrolizumab Immunological Response in Metastatic Solid Tumors

  Whole exome and RNA sequencing source data for: Clouthier, D.L., Lien, S.C., Yang, S.Y.C. et al. An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE). j. immunotherapy cancer 7, 72 (2019). https://doi.org/10.1186/s40425-019-0541-0 Bratman S*, Yang SYC*, Iafolla MAJ, Liu Z, Hansen AR, Bedard P, Lheureux S, Spreafico A, Razak AA, Shchegrova S, Louie M, Billings P, Zimmerman B, Sethi H, Aleshi A, Torti D, Marsh K, Eagles J, Cirlan I, Hanna Y, Clouthier D, Lien SC, Ohashi PS, Xu W, Siu LL, Pugh TJ. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nature Cancer. 2020:1:873-881. https://doi.org/10.1038/s43018- 020-0096-5. Yang SYC, Lien SC, Wang BX, Clouthier DL, Hanna Y, Cirlan I, Zhu K, Bruce JP, El Ghamrasni S, Iafallo MAJ, Oliva M, Hansen AR, Spreafico A, Bedard PL, Lheureux S, Razak A, Speers V, Berman HK, Aleshin A, Haibe-Kains B, Brooks DG, McGaha TL, Butler MO, Bratman SV, Ohashi PS, Siu LL, and Pugh TJ. Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. Nature Comm 2021:12, 5137. https://doi.org/10.1038/s41467-021-25432-7

  Study EGAS00001003280

• WES in muscle-invasive bladder cancer (MIBC) treated with durvalumab plus olaparib in the neoadjuvant setting: NEODURVARIB trial

  This submission contains the metadata derived from the whole exome sequencing of 70 samples from 26 patients who developed advanced urothelial carcinomas. The patients were enrolled in the Neodurvarib clinical trial, which compares the molecular profiles at diagnosis and after neoadjuvant treatment with Durvalumab and Olaparib. In this regard, the analyzed samples include: normal tissue and tumoral tissue obtained from the transurethral resection of the bladder (TURBT, a procedure performed prior to neoadjuvant therapy) from the 26 patients (52 samples), as well as tissue obtained from the radical cystectomy (a procedure performed after treatment with the aforementioned drugs; 18 samples).

  Study EGAS50000000791

• Whole Exome Sequencing of gliomas

  Dataset EGAD00001001614