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• Variant analysis on FFPE specimen from NSCLC patients (OCAPlus)

  This study assessed the presence of somatic variants via the Oncomine Comprehensive Panel Plus panel (ThermoFisher) for commonly mutated cancer genes and measure tumor mutational burden using next-generation sequencing. It was performed on genomic DNA from FFPE tissue of tumor resections. Mutations were used to draw OncoPrints and to assess TMB in relation with response metrics.

  Study EGAS50000001136

• ALLoreactive T-Cell receptOr RePertoire in kidnEy tranSplantation

  A prospective study for investigating the T-cell receptor (TCR) repertoire in T-cell mediated rejection (TCMR) after kidney transplantation. The pre-formed donor-reactive TCR repertoire was tracked in blood and tissue of patients after kidney transplantation and characteristics of TCR repertoires from patients experiencing a rejection were compared to patients with no histopathological signs of rejection.

  Study EGAS00001005299

• Genomic characterization of retinoblastoma (targeted sequencing)

  Retinoblastoma is the most frequent intraocular malignancy in children, originating from a maturing cone precursor in the developing retina. Little is known on the molecular basis underlying the biological and clinical behavior of this cancer. Here, using multi-omics data, we demonstrate the existence of two retinoblastoma subtypes. Subtype 1, of earlier onset, includes most of the heritable forms. It harbors few genetic alterations other than the initiating RB1 inactivation and corresponds to differentiated tumors expressing mature cone markers. By contrast, subtype 2 tumors harbor frequent recurrent genetic alterations including MYCN-amplification. They express markers of less differentiated cone together with neuronal/ganglion cell markers with marked inter- and intra-tumor heterogeneity. The cone dedifferentiation in subtype 2 is associated with stemness features including low immune and interferon response, E2F and MYC/MYCN activation and a higher propensity for metastasis. The recognition of these two subtypes, one maintaining a cone-differentiated state, and the other, more aggressive, associated with cone dedifferentiation and expression of neuronal markers, opens up important biological and clinical perspectives for retinoblastomas. In this study, we performed targeted sequencing of the exonic regions of RB1, BCOR and ARID1A on 37 samples from the series of 102 retinoblastomas. Among them, 23 samples were not subjected to whole-exome sequencing, and 14 samples have the whole-exome sequencing data (deposited in EGAS00001005248).

  Study EGAS00001005550

• DNA Methylation-based diagnostic biomarkers for ESCC in Han Chinese population

  To validate the methylation status of the four candidate tumor suppressor genes (ADHFE1, EOMES, SALL1, TFPI2) in Han Chinese ESCC patients, we recruited 103 patients and obtained the paired tumors(entitled as T) and adjacent normal tissues (entitled as N) as well. Targeted bisulfite sequencing was conducted to detect the methylation profiles of these four genes in these 103 paired tissues. Furthermore, the raw sequence data (fastq files) was aligned using the BSseeker2 and this dataset included all of the bam file after alignment.

  Dataset EGAD00001004288

• Genome Variation among HIV-Resistant People with Hemophilia

  Rare individuals are highly resistant to infection with human immunodeficiency virus (HIV). Studies of candidate genes resulted in the discovery of a 32bp deletion in the CC-chemokine receptor 5 gene (CCR5Δ32), which rendered this critical co-receptor for primary HIV infection to be non-functional. Pharmacologic and vaccine-induced blockade of CCR5 is being pursued to treat and prevent HIV infection and other conditions. The allele frequency of CCR5Δ32 among persons of European ancestry is approximately 10%. CCR5Δ32/Δ32 homozygotes are almost totally resistant to HIV infection. People with severe hemophilia A require frequent replacement with clotting Factor VIII (FVIII) to control hemorrhage. Prior to the discovery of HIV in 1984 and licensure of recombinant FVIII in the late 1980s, people with severe hemophilia A were treated with plasma-derived FVIII and thus were intensively exposed to HIV. Only 5% of such patients were not infected with HIV. Of these, approximately 1/3 were CCR5Δ32/Δ32 homozygotes. The remaining 2/3 of these people who were highly resistant to HIV remain unexplained. This project seeks to discover genome variations among people who are highly resistant to HIV infection. Such variation is likely to serve as a target for reducing the morbidity and incidence of HIV.

  Study phs000445

• Adipocytes Regulate Fibroblast Function and Their Loss Contributes to Fibroblast Dysfunction in Inflammatory Diseases

  We profiled live synovial cells from 16 individuals with no diagnosed arthritis using single-cell RNA sequencing. Our study was designed to provide a reference single cell RNA sequencing dataset for researchers interested in studying arthritic synovium, providing sequencing data on healthy synovial cells for comparison to cells from diseased synovial tissues. Synovial tissue was collected post-mortem from three different sources between 2019-2021: the National Disease Research Interchange, a collaboration with Rush University and the Gift of Hope, and the Brigham and Women's Hospital Autopsy Department. To be included in the study, patients had to be between the ages of 18 to 72 and have no diagnosed arthritis or autoimmune diseases. Additionally, this study includes bulk RNA sequencing data of cultured primary synovial fibroblasts isolated from three rheumatoid arthritis patents. Cells were stimulated with either cortisol, fat conditioned media, TGFβ, TNFα, fat conditioned media with mifepristone, TGFβ with fat conditioned media, or TNFα with fat conditioned media. Cells were harvested 4 or 22 hours later and lysates collected for sequencing. Data from this study submitted to the Gene Expression Omnibus (GEO) may be accessed via accession number GSE233504.

  Study phs003304

• RNA-seq from B-ALL patients treated on the ALLG ALL09 study

  Dataset contains RNA-sequencing data (fastq files) from 46 patients treated on the Australasian Leukaemia and Lymphoma Group (ALLG) ALL09 study (ACTRN12618001734257). All patients were diagnosed with CD19 positive B-cell acute lymphoblastic leukaemia and were negative for Philadelphia chromosome positive disease. Patient samples (bone marrow or peripheral blood) were taken at diagnosis. mRNA was extracted from lymphoblasts and underwent paired-end sequencing using either the illumina NextSeq (75 bp PE) or MGI DNABSEQ-G400 (100bp PE) platforms. Transcriptomic data was used for identification of genomic drivers of acute lymphoblastic leukaemia (ALL).

  Dataset EGAD50000001603

• DAC Johns Hopkins University - AML scRNAseq study

  This is the Data Access Committee (DAC) from Johns Hopkins University for the study scRNAseq of acute myeloid leukemia

  Dac EGAC50000000242

• CNCD Recall by Genotypes

  This is a DAC to handle recall by genotype studies by the conducted by the Center for Non-Communicable Disease Karachi, Pakistan.

  Dac EGAC50000000937

• MPNST exome and genome

  This is the complete dataset (exome and genome) for the EGAS00001000974 study.

  Dataset EGAD00001001040

• Diverse mutational landscapes in human lymphocytes

  A lymphocyte suffers many threats to its genome, including programmed mutation during differentiation, antigen-driven proliferation and residency in diverse microenvironments. After developing protocols for single-cell lymphocyte expansions, we sequenced whole genomes from 717 normal naive and memory B and T lymphocytes and hematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells – the extra mutations were mostly acquired during differentiation, with burdens higher in memory than naive lymphocytes, although T cells also had a higher rate of mutation accumulation throughout life. Off-target effects of immunological diversification accounted for most of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every one on-target IGV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than stem cells, with ~15% of deletions being attributable to off-target RAG activity. Mutational processes associated with ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory lymphocytes. The mutation burden and signatures of normal B lymphocytes were broadly comparable to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

  Dataset EGAD00001008107

• B cell receptor silencing reveals origin and dependencies of high-grade B cell lymphomas with MYC and BCL2 rearrangements

  High-grade B cell lymphomas with MYC and BCL2 rearrangements (HGBCL-DH-BCL2) represent highly aggressive Germinal center (GC) derived B cell malignancies with dismal prognosis and limited therapeutic options. In the present study, we investigated the expression of BCR complex components, including immunoglobulin (IG) heavy (H) and light (L) chains, and CD79A and CD79B signaling subunits in HGBCL-DH-BCL2, scoring 65% of cases with undetectable IGH immunoreactivity (IGHUND). Transcriptomics (bulk RNA-seq) and genetic (whole exome/genome sequencing) analyses indicated that IGHUND and IGH+ HGBCL-DH-BCL2 lymphomas represent distinct biological entities. Specifically, IGHUND HGBCL-DH-BCL2 exhibit a GC DZ-like molecular program, and select subset-specific gene mutations pointing to distinct evolutionary trajectories respect to the IGH+ counterparts. IG profiling revealed that IGHUND HGBCL-DH-BCL2 preserved potentially productive, hypermutated IGH variable (V) gene rearrangements, indicating a selective advantage conferred to the malignant B cells by residual IGH molecules. Accordingly, disruption of the productively rearranged IGHG1 gene in BCRnull HGBCL-DH-BCL2 cell line model confirmed the dependency on IGH expression for optimal fitness. Using transcriptomics and in situ RNA-scope analysis, we reported that IGHUND HGBCL-DH-BCL2 originated from IG-class switched GC B cells, while IGH-expressing tumors were selected for continuous IGM expression. Moreover, while IGH+ HGBCL-DH-BCL2 favor IGM/IG-Kappa expression, IGHUND counterparts complete IG-Lambda light chain rearrangements. Notably, BCR silencing, caused by accelerated IGH turnover and reduced IGH expression, precedes HGBCL-DH-BCL2 onset, inducing RAG1/2-dependent IG light chain editing and eventually facilitating t(8;22)/IGL::MYC translocations. Finally, IGH silencing observed in HGBCL-DH-BCL2 cell models, which leads to intracellular retention/silencing of CD79B, results in reduced sensitivity to the CD79B-targeting antibody-drug conjugate Polatuzumab-vedotin. Collectively, HGBCL-DH-BCL2 originates from isotype-switched t(14;18)+ GC B cells that undergo IG light chain editing fuelling intra-clonal diversification, BCR silencing, and the acquisition of t(8;22) translocation, while preserving IGH dependency.

  Study EGAS50000001047

• Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X

  Familial colorectal cancer type X (FCCTX) is characterized by clinical features of hereditary non-polyposis colorectal cancer with a yet undefined genetic background. Here, using an integrative genomics strategy, we identify the SEMA4A p.Val78Met germline mutation in an Austrian kindred with FCCTX. Compared with wild-type protein, SEMA4AV78M demonstrates significantly increased MAPK/Erk and PI3K/Akt signaling as well as cell cycle progression of SEMA4A deficient HCT-116 colorectal cancer cells. In a cohort of 53 patients with FCCTX we depict two further SEMA4A mutations, p.Gly484Ala and p.Ser326Phe, and the single nucleotide polymorphism (SNP) p.Pro682Ser. This SNP is highly associated with the FCCTX phenotype exhibiting increased risk for colorectal cancer (OR 6.79, 95% CI 2.63 to 17.52). Our study shows previously unidentified germline variants in SEMA4A predisposing to FCCTX which has implications for surveillance strategies of patients and their families.

  Study EGAS00001000957

• Comprehensive molecular profiling for breast cancer patients and high-risk individuals.

  Although germ-line mutations in BRCA1 and BRCA2 gene are responsible for familial breast and ovarian cancer, the detailed mechanism of tumorigenesis is yet unknown. Here, we performed next-generation sequencing to determine the genomic profiles of familial breast cancer tumorigenesis. Target-capture sequencing of fresh-frozen or formalin-fixed-paraffin-embedded (FFPE) samples of breast cancer or normal breast tissue were performed.

  Study JGAS000368

• ONGOING CHROMOSOMAL INSTABILITY ACROSS ANEUPLOID SUBTYPES OF CHILDHOOD B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA ASSOCIATES WITH DISEASE PROGRESSION

  This is the DAC for the scDNA data on the c-B-ALL datasets

  Dac EGAC50000000005

• Single-Cell Analysis of CD19-Specific CAR T Cell Treatment of Relapsed/Refractory CD19+ Acute Lymphoblastic Leukemia

  By leveraging single-cell transcriptome and T cell receptor (TCR) sequencing, we aimed to track the transcriptional signatures of chimeric antigen receptor (CAR) T cell clonotypes throughout the course of treatment and furthermore identify molecular patterns leading to potent CAR T cell cytotoxicity. The data presented in this study encompass blood and bone marrow samples from patients ≤ 21 years of age with relapsed or refractory B-cell acute lymphoblastic leukemia (B-ALL) participating in the SJCAR19 phase I/II clinical trial (NCT03573700). In brief, patients enrolled in the clinical trial received either 1 x 10^6 (dose level 1) or 3 x 10^6 (dose level 2) per kilogram of body weight following successful generation of autologous CAR T cell products and lymphodepleting chemotherapy. Peripheral blood was drawn from each participant every week until week 4 post-infusion, at week 6 or 8, and month 3 or 6 if feasible. At week 4 post-infusion, blood marrow was also collected from participants. Total T cells (CD3+) were sorted from each post-infusion sample, as well as the pre-infusion CAR T cell products, and processed through 10x Genomics’ single-cell gene expression and V(D)J sequencing platform using the standard protocol. We identified a unique and unexpected transcriptional signature in a subset of pre-infusion CAR T cells that shared TCRs with post-infusion cytotoxic effector CAR T cells. Functional validation of cells with even a subset of these pre-effector markers demonstrated their immediate cytotoxic potential and resistance to exhaustion. The data deposited into dbGaP include all raw single-cell expression and V(D)J sequencing generated from samples obtained from 16 study participants.

  Study phs002966

• Single cell whole genome sequencing of luminal breast epithelial cells from wildtype and BRCA mutation carriers

  Single cell whole genome sequencing was done using DLP+ (https://doi.org/10.1016/j.cell.2019.10.026) on luminal breast epithelial cells from wildtype and BRCA mutation carriers. Each BAM file is a merged BAM from single cells from a single sample, and the cells can be uniquely identified by their @RG group. Only high quality cells were kept, thus there are large differences in BAM sizes. The same sample/patient can be found across multiple BAM files to accumulate more cells, sometimes the same patient will have multiple FACS sorted cell types also split by BAMs.

  Dataset EGAD50000000883

• Single-cell and spatial atlas of steatotic liver disease-related hepatocellular carcinoma

  This study consists of the spatial transcriptomics data generated by : 1. Visium CytAssist Spatial Gene Expression for FFPE (10x) for steatotic liver disease-associated hepatocellular carcinoma (SLD-HCC) (n=7) and non-SLD-HCC (n=5) 2. CosMxTM Human Universal Cell Characterization RNA Panel (1000-plex); NanoString, USA for n=4 SLD-HCC and n=4 non-SLD-HCC. The goal of this data is to compare SLD-HCC vs non-SLD-HCC as well as response to immunotherapy

  Study EGAS50000001034

• Solve-RD Solving the Unsolved Rare Dieseases

  Solve-RD – solving the unsolved rare diseases is a research project funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257 from 1 January 2018 to 31 March 2024. Six European Reference Networks (ERNs; ERN-RND, -ITHACA, -EuroNMD, -GENTURIS, -RITA and -EpiCare) contributed data and samples to one or more of the four cohorts for data re-analysis and novel omics. For more information see https://solve-rd.eu/results/solve-rd-data/.

  Study EGAS00001003851

• Whole exome and targeted DNA sequencing data for formalin-fixed paraffin embedded tissue from de novo small cell prostatic carcinoma cases

  This dataset consists of 44 compressed paired fastq files, 15 of which are generated from whole exome sequencing, and 29 of which are generated from DNA sequencing using a targeted gene panel capturing the exonic regions of 73 prostate cancer driver genes. Targeted DNA sequencing was performed on an Illumina MiSeq (v3 600 cycle kit), and exome sequencing was done using an Illumina HiSeq 2500 (v4 250 cycle kit) machine. The fastq files are named in accordance with the sample aliases provided, which reflect the pathology of interest to this study (small cell prostatic carcinoma--SCPC), whether it was sequenced using an exome or targeted gene panel, whether the FFPE sample was sourced from tumor or benign tissue (labeled T or B, respectively), and whether there exists multiple samples belonging to a single patient.

  Dataset EGAD00001004139

• Capturing sex-specific and infertility-linked effects of assisted reproductive technologies on the cord blood DNA methylome

  Background: Children conceived through assisted reproduction are at an increased risk for growth and genomic imprinting disorders, often linked to DNA methylation defects. It has been suggested that assisted reproductive technologies (ART) and the underlying parental infertility can induce epigenetic instability, specifically interfering with DNA methylation reprogramming events during germ cell and preimplantation development. To date, human studies exploring the association between ART and DNA methylation defects report inconsistent or inconclusive results, likely due to population heterogeneity and the use of technologies with limited coverage of the epigenome. In our study, we explore the epigenetic risk of ART by comprehensively profiling the DNA methylome of 73 human cord blood samples from singleton pregnancies (n=36 control group, n=37 ART/infertility group) from a human prospective longitudinal birth cohort, the Design, Develop, Discover (3D) Study using a high resolution sequencing based custom capture panel that interrogates over 2.4 million autosomal CpGs in the genome. Results: the main findings We identified striking sex-specific effects of ART on cord blood DNA methylation patterning both genome-wide and for imprinted genes. When compared to less invasive procedures such as in utero insemination, more invasive ARTs (IVF, ICSI, embryo culture) resulted in more marked and distinct effects on the cord blood DNA methylome, including targeting of loci involved in development. Background: Children conceived through assisted reproduction are at an increased risk for growth and genomic imprinting disorders, often linked to DNA methylation defects. It has been suggested that assisted reproductive technologies (ART) and the underlying parental infertility can induce epigenetic instability, specifically interfering with DNA methylation reprogramming events during germ cell and preimplantation development. To date, human studies exploring the association between ART and DNA methylation defects report inconsistent or inconclusive results, likely due to population heterogeneity and the use of technologies with limited coverage of the epigenome. In our study, we explore the epigenetic risk of ART by comprehensively profiling the DNA methylome of 73 human cord blood samples from singleton pregnancies (n=36 control group, n=37 ART/infertility group) from a human prospective longitudinal birth cohort, the Design, Develop, Discover (3D) Study, using a high resolution sequencing based custom capture panel that interrogates over 2.4 million autosomal CpGs in the genome. Results: We identified striking sex-specific effects of ART on cord blood DNA methylation patterning both genome-wide and for imprinted genes. When compared to less invasive procedures such as in utero insemination, more invasive ARTs (in vitro fertilization (IVF), intracytoplasmic sperm injection (ICSI), embryo culture) resulted in more marked and distinct effects on the cord blood DNA methylome, including targeting of loci involved in development. Conclusions: Our study highlights the ability of a sensitive, targeted, sequencing based approach to uncover DNA methylation perturbations in cord blood associated with infertility and ART and influenced by offspring sex and ART technique invasiveness.

  Study EGAS00001006643

• Cellular and Molecular Investigations of Human Hearts

  We aim to discover gene regulatory networks that govern heart morphogenesis in the early fetal heart. To this end, we have performed single-nucleus ATAC-seq on cells derived from 2 human hearts at 15 weeks post conception to define the chromatin profiles and genomic regulatory networks for these in vivo specific cardiomyocyte lineages during development, from which the FASTQ files are available through dbGAP. This information will help us understand the process of heart morphogenesis early in development and may further our understanding of how congenital heart disease impacts development.

  Study phs003473

• Test Study for EGA using data from 1000 Genomes Project - Big CRAM, BAM, VCF and BCF files used for testing

  This is a test study for EGA using data from 1000 Genomes Project, specifically created to add more diversity to the existing dataset EGAD00001003338. This Test Study should NOT be confused with the real study of 1000 Genomes Project - Phase 3. Specifically, this study encompasses 4 CRAM, 4 BAM, 2 VCF and 2 BCF files, of different sizes (all above 1 GB), used for testing downloads and monitoring services. It also contains their respective indexes: crai for crams, bai for bams, tbi for vcfs and csi for bcfs.

  Study EGAS00001006718

• Transcriptomic profiling of proximal and distal regions of human long head biceps tendon

  Tendinopathy is a prevalent musculoskeletal disorder marked by extracellular matrix disorganization, collagen remodeling, vascular ingrowth, and pain, yet its underlying molecular mechanisms remain insufficiently defined. The long head of the biceps tendon (LHBT) is particularly prone to mechanical overload and early degenerative changes, making it a relevant model for studying tendon pathology. In this study, we aimed to characterize region-specific gene expression changes along the LHBT to better understand the molecular basis of degeneration. We collected paired proximal and distal LHBT tissue from patients undergoing rotator cuff repair surgery and performed bulk RNA sequencing. This approach enables the identification of degeneration-associated transcriptional signatures while minimizing inter-patient variability.

  Study EGAS50000001454

• Autoimmunity_and_immunodeficiency_COVID19

  Cell Atlas of COVID-19 patients with Pre-existing Autoimmunity and Immunodeficiency conditions COVID-19 disease is characterized by hyperinflammation of the lungs and poor immune response against the virus, leading to acute respiratory distress syndrome. Patients with pre-existing medical conditions strongly correlated with poorer clinical outcomes upon SARS-CoV-2 infection. This study aims to characterize the cellular response to SARS-CoV-2 infection in controls and in patients with primary immunodeficiency and autoimmune disease. 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 EGAS00001004489