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• CBD-RAW-SC-VDJ-B: 10X Single-Cell VDJ BCR

  Raw Illumina sequencing data. For further information regarding this dataset, please contact Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007964

• IFN-γ and TNF-α drive a CXCL10+ CCL2+ Macrophage Phenotype Expanded in Severe COVID-19 Lungs and Inflammatory Diseases with Tissue Inflammation

  We explored how the human macrophages response to different inflammatory factors, focusing particularly on the effects of antiviral interferons (IFN-β and IFN-γ), pro-inflammatory cytokines such as TNF-α, and other mediators like IL-4. Co-cultured fibroblasts were a component in some conditions to generate factors produced by resident stroma. We used a single-cell antibody-based hashing strategy to multiplex samples from different stimulatory conditions in one sequencing run. This macrophage transcriptomic data reveals distinct macrophage activation states and polarizations shaped by different tissue-related inflammatory conditions at single-cell resolution. We further performed an unbiased integration between tissue-level macrophages and this stimulated human blood-derived macrophages, which pinpoint an IFN-γ and TNF-α synergistically driven inflammatory macrophage phenotype expanded in severe COVID-19 lungs and other inflamed disease tissues.

  Study phs002780

• Xeroderma Pigmentosum, Complementation Group C, (XPC) and Non-XPC Cutaneous Squamous Cell Carcinoma (cSCC) Mutation Rate Study

  Base mutations occur at higher frequencies within heterochromatin and late-replicating DNA. In this study, we show that regional differences in mutation frequency are absent in portions of the genome that are not transcribed within cutaneous squamous cell carcinomas (cSCCs) with an XPC-\- genetic background. The XPC-\- genetic background predicates a loss of global genome nucleotide excision repair (GG-NER), thus our data shows that regional differences in mutation frequency are a result of differential access of DNA repair protein. Unexpectedly, we also note that greater transcription reduces mutations on both strands of genes in heterochromatin, and only to those levels observed in euchromatin, in a XPC-dependent fashion. Therefore, transcription likely reduces mutation prevalence by increasing access to DNA repair proteins. This tripartite relationship between DNA repair, transcription, and chromatin state shows a new cancer risk factor in human populations.

  Study phs000830

• Long-Read Sequencing to Identify Inherited Mutations Predisposing to Breast Cancer

  We aimed to detect deeply intronic mutations within genes linked to breast/ovarian cancer that are potentially under-reported in clinical testing due to technical limitations. Current DNA and RNA tests typically exclude these regions, which harbor many variants within complex repetitive sequences that short-read sequencing cannot align. By employing targeted long read sequencing together with recent in silico prediction tools, we assessed the implications of rare deep intronic variants in severely affected patients with breast, ovarian, and/or metastatic prostate cancer, who had previously tested negative using standard genomic or cDNA methods. Through this approach, we identified participants who carried deep intronic mutations in tumor suppressor genes, resulting in abnormal transcripts causing premature truncations and loss of gene function. This study underscores the potential of long read DNA and cDNA sequencing in enhancing mutation discovery efforts.

  Study phs003638

• _WGS__Somatic_mutation_in_skin_epidermis__SMS_

  Previously we have sequenced 2mm2 biospies of human epithelia at high depth using a custom bait set. This has identified a range of mutations. Some of the biospies are predicted to be clonal and we would like to perform WGS to give an insight into mutational burden, and CNV which may be associated with these mutations.

  Study EGAS00001004464

• LongVar low-coverage data

  This dataset includes sequencing data from participants of the LongVar study. Specifically, it comprises low-coverage whole genome sequencing (WGS) data which was derived from cell-free DNA from blood samples. These data were generated to compare imputation accuracy. 133 individuals agreed to share their data, and are healthy volunteers.

  Study EGAS50000001114

• Liquid-based genomic profiling in high-risk localized prostate cancer.

  In this study, we evaluated the feasibility and performance of tissue and liquid-based genomic profiling in patients with high-risk localized prostate cancer. Genomic DNA from 12 FFPE tissue samples and cell-free DNA from 27 plasma samples were analyzed using Illumina TruSight Oncology (TSO) 500 panels.

  Study EGAS50000001712

• HipSci-RNAseq-healthy volunteers

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sup-study we perform RNAseq on iPS cells generated from skin biopsies from healthy volunteers.

  Study EGAS00001000593

• Pediatric B-cell precursor acute lymphoblastic leukemia samples with very early relapse

  In this study we performed a genomic analysis of diagnosis-relapse pairs of 12 children who relapsed very early, followed by a deep-sequencing validation of all identified mutations. In addition, we included one case with a good initial treatment response and on-treatment relapse at the end of upfront therapy.

  Study EGAS00001005615

• MethylationEPIC_850K

  This dataset includes IDAT files from 160 samples (57 primary prostate cancers, 95 proste-derived brain metastases, and 7 normal tissues). The samples were profiled using the Illumina Infinium MethylationEPIC BeadChips (850K)

  Dataset EGAD00010002372

• The Genetic and Transcriptomic Evolution of Melanoma

  The overarching goal of the study was to better understand the evolution of melanoma. To do this, we collected archival tissue of melanomas adjacent to their intact, remnant precursor lesions. We also collected archival tissue of primary melanomas and their matching metastases. From the formalin-fixed paraffin-embedded (FFPE) blocks, we microdissected non-neoplastic (normal), precursor, and descendent portions of tissue. Both RNA and DNA were extracted from the microdissected tissues and subjected to next generation sequencing. In summary, we performed matched DNA/RNA sequencing of melanoma/precursor/normal trios, allowing us to trace the genetic and transcriptomic evolution of melanoma.

  Study phs001550

• Pulmonary Fibrosis and Telomerase Dysfunction

  This study was used to perform an exome-limited analysis of whole genome sequencing data of patients with idiopathic pulmonary fibrosis (IPF) or familial pulmonary fibrosis. Case cohorts were derived from local centers at University of Southwestern or Columbia University, and subjects were from the IPFnet cohort of clinical trial. Rare damaging mutations in the coding regions of cases were compared to healthy controls, and gene burden analysis was performed to identify enrichment of novel risk genes in the development of pulmonary fibrosis. 

  Study phs002692

• Single cell RNA sequencing of peripheral blood HSPC from patients with sickle cell anemia and healthy donors

  Neutrophils and monocytes are critical contributors to the pathophysiology of sickle cell anemia (SCA) and are persistently elevated in patients' circulation. While chronic hemolysis has been implicated in this leukocytosis, the underlying mechanisms remain incompletely understood. Our data show a myeloid-skewed transcriptional signature in early progenitor populations, including multipotent progenitors (MPPs) and hematopoietic stem cells (HSCs). Notably, we identify upregulation of the type I interferon signaling pathway in HSPCs as a key driver of early myeloid programming in SCA.

  Study EGAS50000001046

• WES of breast cancer patients and controls

  This study assessed the variant profiles of 408 samples from 126 breast cancer patients with various survival outcomes, including paired uninvolved mammary gland samples collected at proximal distances from primary lesions. As a reference, control samples from 15 mammoplasty individuals without cancer history were studied. Whole exome sequencing was performed to identify post-zygotic and germline variants present in the studied samples. Variant annotation in known databases, interpretation, and statistical analyses followed to discern the clinical relevance of called variants.

  Study EGAS50000000539

• Mutational spectrum of highly differentiated, fusion-negative rhabdomyosarcoma (set 1).

  Pediatric PAX-FOXO1 fusion-negative rhabdomyosarcoma represents a diverse spectrum of tumors. In this study, the mutational spectrum of 22 fusion-negative rhabdomyosarcomas with high, rhabdomyoma-like levels of differentiation was evaluated using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 cancer-relevant genes. Corresponding normal tissue was not available. Discarded normal human skeletal muscle, obtained from 7 donors without tumor history, were also included in the sequencing run.

  Study EGAS00001002630

• Mutational spectrum of highly differentiated, fusion-negative rhabdomyosarcoma (set 2).

  Pediatric PAX-FOXO1 fusion-negative rhabdomyosarcoma represents a diverse spectrum of tumors. In this study, the mutational spectrum of 22 fusion-negative rhabdomyosarcomas with high, rhabdomyoma-like levels of differentiation was evaluated using OncoPanel v.2 (OPv2), an Agilent SureSelect custom designed bait set consisting of the coding regions of 504 cancer-relevant genes. Corresponding normal tissue was not available. Discarded normal human skeletal muscle, obtained from 7 donors without tumor history, were also included in the sequencing run.

  Study EGAS00001002771

• Lung_Cell_Atlas__Paediatric_RNA

  Single cell sequencing will be carried out by multiome profiling (RNAseq and ATACseq). Additonal modalities may be examined. Spatial profiling may involve Visium, Curio and other technologies. This data set will feed into a larger analysis of the human lungs over development, that aims to detail all the cell types of the human lungs and airways and will extend current knowledge by providing chromatin accessibility data that will allow us to link GWAS data and identify regulatory networks and then compare these against fetal and adult data sets

  Study EGAS00001008299

• Lung_Cell_Atlas__Paediatric_Spatial

  Single cell sequencing will be carried out by multiome profiling (RNAseq and ATACseq). Additonal modalities may be examined. Spatial profiling may involve Visium, Curio and other technologies. This data set will feed into a larger analysis of the human lungs over development, that aims to detail all the cell types of the human lungs and airways and will extend current knowledge by providing chromatin accessibility data that will allow us to link GWAS data and identify regulatory networks and then compare these against fetal and adult data sets

  Study EGAS00001008300

• Identification of Targetable FGFR Gene Fusions in Diverse Cancers

  In this study, patients with advanced cancer across all histologies were enrolled in our IRB approved clinical sequencing program, called MI-ONCOSEQ, to go through an integrative sequencing which includes whole exome sequencing of the tumor and matched normal, and transcriptome sequencing. Four index cases were identified which harbor gene rearrangements of FGFR2 including two cholangiocarcinoma cases, a metastatic breast cancer case, and a metastatic prostate cancer case. After extending our assessment of FGFR rearrangements across multiple tumor cohorts, including TCGA, we identified FGFR gene fusions with intact kinase domains of FGFR1, FGFR2, or FGFR3 in cholangiocarcinoma, breast cancer, prostate cancer, lung squamous cell cancer, bladder cancer, thyroid cancer, oral cancer, glioblastoma, and head and neck squamous cell cancer. All FGFR fusion partners tested exhibit oligomerization capability, suggesting a shared mode of kinase activation. Overexpression of FGFR fusion proteins in vitro induced cell proliferation, and bladder cancer cell lines that harbors FGFR3 fusion proteins exhibited enhanced susceptibility to pharmacologic inhibition in vitro and in vivo. Due to the combinatorial possibilities of FGFR family fusion to a variety of oligomerization partners, clinical sequencing efforts which incorporate transcriptome analysis for gene fusions are poised to identify rare, targetable FGFR fusions across diverse cancer types.

  Study phs000602

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - ExomeNanoSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016058

• Polyclonal selection of immune checkpoint mutations in thyroid autoimmunity - TargetedNanoSeq

  Our immune system contains multiple tolerance checkpoints to prevent the activation of self-reactive lymphocytes. How some lymphocytes escape these constraints to cause autoimmune disease remains poorly understood. A long-standing hypothesis in autoimmunity posits that somatic mutations in immune regulatory genes may enable self-reactive lymphocytes to bypass tolerance checkpoints. However, testing this hypothesis has proved challenging due to technical limitations in detecting somatic mutations in polyclonal cell populations. Here, we use deep whole-exome and targeted NanoSeq, a highly accurate single-molecule DNA sequencing protocol, to comprehensively search for driver mutations in autoimmune thyroid disease. This revealed a remarkably high number of B cell clones convergently acquiring loss-of-function somatic mutations in key immune checkpoint genes TNFRSF14 (also known as HVEM) and CD274 (encoding PD-L1), as well as less frequent driver mutations in a diversity of other immune genes. In highly inflamed biopsies, we detected tens to hundreds of independent immune-checkpoint mutant clones. Laser capture microdissection, methylation sequencing, spatial transcriptomics, immunohistochemistry and single-nucleus DNA sequencing localised these mutations to non-naive B cells and revealed frequent co-occurrence of drivers in single cells. We found widespread TNFRSF14 biallelic loss in mutant B cells, and several clones with as many as 4-6 driver mutations. Whilst each clone accounts for a small proportion of cells (typically <1%), the myriad mutant clones in each donor collectively amounted to a substantial fraction of B cells harbouring one or more driver mutations. Our results support the hypothesis that somatic mutations in autoimmune lymphocytes may allow them to escape tolerance constraints through a polyclonal cascade of somatic evolution. These findings provide new insights into the molecular basis of autoimmune disease and suggest novel diagnostic and therapeutic avenues.

  Dataset EGAD00001016059

• Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform

  Ultra low coverage sequencing results from the project 'Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform'. Sequencing data of sample NA12877 and NA12878 generated from 3 nanopore sequencing runs are included in this dataset.

  Dataset EGAD00001004052

• RNA-seq data from the tumor samples of a head and neck cancer patient

  This dataset contains paired-end RNA sequencing data (2x50 bp) from the three synchronous primary tumors and the recurrence of a head and neck cancer patient.

  Dataset EGAD00001006654

• Pre-treatment PD-L1 staining on tumor samples (n=24)

  Data from NABUCCO cohort 1 (NCT03387761). This dataset includes the pre-treatment PD-L1 staining on tumor samples (n=24). Details about the PD-L1 staining can be found on the paper (https://doi.org/10.1038/s41591-020-1085-z)

  Dataset EGAD00001006856

• CITE-seq

  This dataset contains the raw sequencing data (Runs) from all of the 10x Genomics single-cell CITE-seq Experiments, as well as the demultiplexed cell-donor identities matrices which were generated with Vireo (Analysis).

  Dataset EGAD00001009820

• 5 scRNA-seq with TCR Enrichment of Tumour-Involved Lymph Nodes, Malignant Seromas and Patient-Derived Xenografts from 18 T-Cell Lymphoma Patients

  This raw data contains 5' scRNA-seq with TCR enrichment data from 18 individual patients analysing cells taken from tumour-involved lymph nodes (LN), malignant seromas and patient-derived xenografts (PDX) including systemic/nodal ALK+ ALCL (n=3 PDX), BIA-ALCL (n=2 seromas), PTCL-NOS (n=5 nodal tumours), nodal T follicular helper lymphoma - angioimmunoblastic type (nTFHL-AI) (n=1), nTFHL, not otherwise specified (nTFHL, NOS, n=1), TLBL (n=5) and 1 case of Sezary Syndrome (SS, cutaneous tumour). Droplet-based 5’ scRNA-seq with TCR enrichment (10x Chromium platform) was performed for all live cells, or the viable CD45+CD3- and CD45+CD3+ fractions following cell sorting by flow cytometry.

  Dataset EGAD00001015703

• Phylogenetic reconstruction of adult blood cancer reveals early origins and lifelong evolution - TGS

  Mutations in cancer-associated genes drive tumour outgrowth. However, the timing of driver mutations and dynamics of clonal expansion that lead to human cancers are largely unknown. We used 580,133 somatic mutations from whole-genome sequencing of 1013 clonal haematopoietic colonies to reconstruct the phylogeny of haematopoiesis, from embryogenesis to clinical disease, in 12 patients with myeloproliferative neoplasms which are blood cancers more common in older age. JAK2V617F, the pathognomonic mutation driving the majority of these cancers, was acquired in utero or childhood, with upper estimates of age of acquisition from 33 weeks gestation to 10.8 years, in all 5 patients in whom JAK2V617F was either the only or the first driver event.  Driver mutations associated with age-related clonal haematopoiesis occurred prior to or following JAK2V617F,  as independent clonal expansions in JAK2V617F-mutated patients, and as large clonal expansions in JAK2V617F-unmutated patients . These mutations were also acquired in utero or childhood, with DNMT3A mutations occurring by 8 weeks of gestation to 7.6 years across 4 patients, and PPM1D mutation occurring by age 5.8yrs in a patient with MPN lacking phenotypic driver mutations. Sequential driver mutation acquisition was common, separated by decades across life, and often outcompeted ancestral clones. The mean latency between JAK2V617F acquisition and clinical presentation was 30 years (range 11-54 years). Rates of clonal expansion were inferred from phylogenetic trees and varied substantially (3% to 190% expansion/year), were affected by additional driver mutations, and were predictive of latency to clinical presentation. Driver mutations and rates of expansion would have been detectable in blood one to four decades before clinical presentation. This study reveals how driver mutation acquisition early in life with life-long growth and evolution underlie adult myeloproliferative neoplasms, providing opportunities for early detection and intervention and a new paradigm for cancer development.

  Dataset EGAD00001007715

• Characterization of mutational signatures in human cancer cell lines reveals episodic APOBEC mutagenesis

  Multiple signatures of somatic mutations have been identified in human cancer genomes. To investigate whether mutational signatures continue to be generated, and if so their temporal patterns of activity, subsets of cell lines were cultured in vitro for extended periods and subjected to single cell cloning and whole genome or exome sequencing or directly to single cell whole genome sequencing. As expected, signatures of past exogenous exposures, such as tobacco smoke and ultraviolet light, were not generated in vitro. In contrast, signatures of normal and defective DNA repair and replication continued to be generated at essentially constant mutation rates. Signatures of APOBEC cytidine deaminase DNA-editing activity exhibited a distinctive pattern with substantial fluctuations in mutation rate over time and episodic bursts of mutations. The initiating factors for these bursts are unclear although retrotransposon mobilisation may play a role. This cell line set now constitutes a comprehensive resource of live experimental models of mutational processes of both known and unknown aetiologies potentially retaining the patterns of activity and regulatory influences operative in human cells in vivo.

  Dataset EGAD00001004203

• Decoding Human Endogenous Retrovirus Expression in Liver Metastatic Colorectal Cancers: Implications for Diagnosis and Prognosis

  The association between Human Endogenous RetroVirus (HERV) expression and cancer can be considered to both reflect the epigenetic deregulation of cancer and facilitate oncogenesis through its promoter/enhancer action on genes. More than 50% of colorectal cancers develop liver metastases and HERV has never been studied in this setting. We collected 400 RNAseq samples from more than 200 patients with primary and liver metastases from published and unpublished databases. We corroborated our findings with tandem mass spectrometry from primary colorectal cancer and single-cell RNAseq from liver metastatic colorectal cancer (lmCRC). We identified global stability in HERV expression between liver metastases and primary colorectal cancers, suggesting an early oncogenic footprint. Therefore, we proposed a list of seventeen HERV loci for lmCRC characterization with ERV-derived peptides but no expression in normal tissues. Among them, we discovered six prognostic markers after surgical resection of lmCRC. Four of them, HERVH_Xp22.32a, HERVH_20p11.23b, HERVH_13q33.3, HERVH_13q31.3, showed poor prognostic value when expressed (log-rank p-value 0.028, 0.0083, 9e-4, 0.05, respectively). HERVH_Xp22.2c (log-rank p-value 0.032) and HERVH_8q21.3b (only in multivariate models) were associated with better prognosis when expressed. These markers showed a cumulative effect on survival when expressed. Some HERVs were associated with decreased cytotoxic immune cells and most of them correlated with cell cycle pathways. Our findings provide new insights into lmCRC classification and suggest novel prognostic biomarkers and potential therapeutic targets.

  Study EGAS50000000307

• Novel APC Promoter and Exon 1B Deletion and Allelic Silencing in Three Mutation-Negative Classic Familial Adenomatous Polyposis Families

  The ~80% of individuals with classic familial adenomatous polyposis (FAP) have detectable mutations in the coding sequence of the adenomatous polyposis coli (APC) gene. To investigate the 20% of families without detectable causative mutations, we used exome sequencing and second-generation sequencing of the APC locus including non-coding regions. We identified a novel ~11kb deletion 44kb upstream of APC that was present only in affected individuals of three kindreds. SNP analysis showed that this ~11kb deletion was accompanied by silencing of one of the APC alleles in blood-derived RNA of affected individuals.

  Study phs000904

• UTSW KCP DAC

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

  Dac EGAC50000000203

• Exome sequencing Parkinson's disease patients

  In this project we will sequence the exomes of 250 patients with Parkinson's disease

  Dataset EGAD00001000405

• Genetic measurement of memory B-cell recall using antibody repertoire sequencing

  We developed an improved high throughput sequencing approach to measure the quantities and sequences of the repertoire of antibody heavy chain RNA in a blood sample. Using this approach we analyzed the antibody repertoire in response to yearly vaccinations with influenza vaccines TIV and LAIV in healthy adults in two subsequent years. We determined vaccine response patterns specific to LAIV and TIV and found antibody sequences that were shared between two samples of the same individuals following influenza vaccination in subsequent years, thereby providing a genetic measurement of B-cell memory recall.

  Study phs000656

• Clonal evolution of metastatic colorectal cancer under anticancer therapies

  To investigate the clonal evolution of metastatic CRC at the single-cell level, we performed WGS in 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients. This approach enabled detailed phylogenetic reconstruction of individual clones. We discovered the timing and burden of treatment-related mutations as well as the heterogeneous evolution in driver mutations and genomic rearrangements in late-stage clonal evolution under anticancer therapies in metastatic CRC.

  Study EGAS50000001023

• Childhood B-cell acute lymphoblastic leukemia genomic and transcriptomic data

  The aim of the two studies was: 1) to genetically characterise childhood leukemia patients that lacked established cytogenetic abnormalities (termed B-other leukemia) and assess the clinical features of recurrent genetic abnormalities. 2) Assess the accuracy of whole genome sequencing as a diagnostic genetic test in childhood leukemia, relative to other traditional methods (karyotyping, FISH, MLPA) and whole transcriptome sequencing. As a result, this study includes targeted DNA-sequencing, whole genome sequencing and whole transcriptome sequencing data on childhood leukemia patients enrolled on UK clinical trials (UKALL2003 and UKALL2011).

  Study EGAS00001006863

• H3Africa - Collaborative African Genomics Network

  Genomic studies have become one of the potential tools that could aid in the understanding of disease. HIV disease progression and active TB infection have been studied using these genomic methods to interrogate host factors associated with these diseases and their progression. Prior work has focused on adult populations and limited African cohorts. The Collaborative African Genomics Network aims to fill this gap by conducting HIV and TB disease mapping studies in African children to understand how genetic variation impacts disease progression through the use of genomic technologies.

  Study EGAS00001002656

• RNAseq of resident memory T cells from human lung tumor

  This dataset includes the RNA sequencing of 14 samples. Samples are FACS sorted CD8+ T cells expressing or not the integrin CD103. The paired samples (TRM and non-TRM) were sorted from the tumor of 7 lung cancer patients.

  Dataset EGAD00001006812

• A Randomized Multi-Institutional Phase II Trial of Everolimus as Adjuvant Therapy in Patients with Locally Advanced Squamous Cell Cancer of the Head and Neck

  This genomic study was an analysis of DNA samples from subjects enrolled in a randomized, interventional, parallel assignment trial of everolimus versus placebo in advanced Head and Neck Cancer. Next Generation Sequencing was performed on samples obtained from primary tumors before treatment. The purpose was to evaluate potential associations between intervention, mutations and outcomes.

  Study phs002986

• SLAMF7 Regulates Synovial Macrophages in Rheumatoid Arthritis

  The purpose of this study was to characterize the role of SLAMF7 on human macrophages. RNA-sequencing was performed on myeloid populations from blood of healthy controls or rheumatoid arthritis patients, or synovial fluid of rheumatoid arthritis patients, based on high or low expression of SLAMF7. Then, monocyte-derived macrophages from healthy controls were left untreated, or stimulated with anti-SLAMF7 or recombinant SLAMF7 protein, and transcriptional profile was defined after SLAMF7 engagement.

  Study phs002771

• Breast Cancer Family Registry Early-onset Breast Cancer GWAS

  In order to enhance our understanding of the genetic etiology of breast cancer, this study analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 age-matched population control women, all of whom were age 50 or younger at enrollment. Subjects were recruited from the eight sites, some of which oversampled cases with a personal or family history of breast cancer.

  Study phs001589

• Integrated targeted deep sequencing reveals unique tissue-of-origin and donor cell-free DNA signatures in transplant recipients

  We have developed a targeted deep methylation sequencing assay that integrates cell-free DNA (cfDNA) tissue-of-origin analysis with donor-derived cfDNA quantification to non-invasively monitor transplant health. In this study, liver and kidney transplant recipients were assessed in conjunction with healthy controls to characterize the dynamic patterns of cfDNA release and clearance, and to identify distinct tissue injury signatures throughout the transplant journey.

  Study EGAS50000000987

• Genomic landscape of aplastic anemia

  This study investigates the genomic landscape of aplastic anemia using complementary sequencing approaches. Single-cell DNA and protein profiling were performed using the Mission Bio Tapestri platform to characterize clonal structure and immunophenotypic features. Long-read whole-genome sequencing (PacBio) and single-cell whole-genome sequencing (BioSkryb) were also generated to capture structural variants and genome-wide clonal architecture. Together, these datasets aim to elucidate mutational processes and clonal evolution underlying aplastic anemia.

  Study EGAS50000001516

• Multi-omic characterisation of PBMCs in IBD

  We generated 10X, droplet-based Multiome (paired RNA+ATAC) data of PBMCs in 38 IBD patients. Patients are either UC or CD patients. To test the responsiveness of the cells to bacterial stimuli, we stimulated samples with either RPMI, LPS or S. Salmonella (total: 80 samples). Single-nuclei libraries are multiplexed across donors. Genotypes are provided in this dataset to perform genetic demultiplexing, phenotypes providing mapping information to retrace donors / pools / stimulations.

  Study EGAS50000000140

• Whole-exome sequencing of HPV-negative HNSCC to identify pathway alterations

  This study applies whole-exome sequencing (WES) to characterize genomic alterations in HPV-negative head and neck squamous cell carcinoma. Tumors were analyzed to derive pathway-level alteration scores, enabling stratification into Hedgehog-high and Hedgehog-low groups. The genomic data were integrated with imaging, transcriptomic, and functional analyses to investigate tumor-intrinsic Hedgehog signaling. The study aims to identify molecular features associated with biologically distinct tumor subgroups.

  Study EGAS50000001550

• HipSci HumanHT 12 Expression BeadChip analysis - Usher syndrome and congenital eye defects

  The HipSci project brings together diverse constituents in genomics, proteomics, cell biology and clinical genetics to create a UK national iPS cell resource and use it to carry out cellular genetic studies. In this sub-study we performed Expression analysis using the Illumina HumanHT -12 Expression BeadChip on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Usher syndrome and congenital eye defects.

  Study EGAS00001002023

• Mutational analysis of an oligoprogressive sarcomatoid hepatocellular carcinoma treated with an immune checkpoint inhibitor.

  In this study, we describe a patient diagnosed with metastatic sarcomatoid hepatocellular carcinoma that showed a remarkable tumor response to Nivolumab, an immune checkpoint inhibitor, followed by an oligoprogression. Molecular analysis of the primary tumor in addition to a bone and brain metastasis was performed and we were able to identify driver genetic alterations indicating a possible role in the tumorigenesis process besides some alterations that may be associated with metastasis.

  Study EGAS00001005064

• Single-cell RNA and TCR sequencing of CSF cells and PBMCs from individuals with neurological disorders

  We performed single-cell RNA sequencing combined with T-cell receptor sequencing to characterize immune cells from cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) of patients with multiple sclerosis and individuals with other inflammatory neurological diseases used as controls. The aim of this study was to identify and characterize T cells with TCRs shared among people with MS and enriched in the CSF compartment.

  Study EGAS50000001897

• OXEL pilot WES data

  This dataset contains aligned BAM files from whole-exome sequencing of 29 patients from the Oxel pilot study. Alignment to GRCh38 reference genome was performed using the BWA aligner.

  Dataset EGAD50000000327

• HumanMethylation450_NL

  This dataset includes IDAT files from 2,790 blood samples. The samples were profiled using the Illumina Infinium HumanMethylation450 (450k) BeadChip.

  Dataset EGAD00010001938

• RNAseq data of fetal ISCs and iPSCs derived of fetal ISCs

  This dataset includes RNAseq data of the fetal ISCs and iPSCs derived of the fetal ISCs to confirm successful reprogramming

  Dataset EGAD00001008473

• WES data from 5 DGCR8 schwannomas

  This dataset contains the exome sequencing data (BAMs, VCFs and CNVs) from 5 schwannoma tumors from the same patient.

  Dataset EGAD00001008200

• Total RNA-seq of CRPC and NEPC

  This dataset contains total RNA-seq of 10 patient samples: 5 castration resistant prostate cancer (CRPC) and 5 neuroendocrine prostate cancer (NEPC). Total RNA-seq was constructed using ribosomal RNA-depleted random hexamer-primed RNA library preparation kit and sequenced on Illumina at pair-end 150bp. Total RNA-seq allows for circular RNA and mRNA analyses. Each sample was sequenced on two separate lanes, therefore, two pairs of raw fastq files (4 files in total) are provided for each sample.

  Dataset EGAD50000001312

• Semmelweis University - Biophysics Data Access Committee

  This DAC belongs to the dataset entitled: Next generation sequencing on cardiac samples in Hungarian patients of dilated cardiomyopathy.

  Dac EGAC50000000053

• DAC IBMsnRNAseq

  This DAC manages the data access to our snRNA-seq and spatial transcriptomic data set on healthy and inflamed human skeletal muscle.

  Dac EGAC50000000220

• BCG prime DNA methylation data

  This dataset contains the DNA methylation data of 384 samples from individuals with one or more comorbidities

  Dataset EGAD00010002767

• Trained immunity DNA methylation data

  This dataset contains the DNA methylation data of 904 samples from Dutch healthy individuals.

  Dataset EGAD00010002738

• Raw naive B cell AIRR-seq data

  This dataset contains raw bulk adaptive immune receptor repertoire sequencing (AIRR-seq) data targeting the B cell receptor heavy (IGK), kappa light (IGK) and lambda light (IGL) chains in peripheral blood naïve B cells. The dataset contains raw demultiplexed fastq files from a total of 102 subjects with celiac disease and 102 controls, split into 15 sequencing libraries. The dataset also contains an accompanying metadata file (csv). Peripheral blood mononuclear cells were obtained from study participants, and naïve B cells were FACS-sorted for RNA extraction and library preparation. Libraries were generated using a 5' RACE strategy incorporating unique molecular identifiers. Separate IGH, IGK and IGL libraries from each individual were constructed using combinatorial dual indexes, and pooled before sequencing. Pooled libraries were sequenced on an Illumina MiSeq platform using 300 bp paired-end reads.

  Dataset EGAD50000002732

• KRT17High/CXCL8+ Tumor Cells Display Both Classical and Basal Features and Regulate Myeloid Infiltration in the Pancreatic Cancer Microenvironment

  Recent studies have uncovered the co-existence of basal and classical subtypes within pancreatic ductal adenocarcinoma (PDAC). We sought to characterize these intermediary cells using single-cell RNA sequencing of PDAC. We performed subtyping on 18 single-cell RNA sequencing human PDAC samples to identify multiple intermediary subtypes. We compared single-cell profiling of patient-matched blood and tumor samples to measure changes in the local and systemic immune microenvironments in CXCL8-high tumors vs. CXCL8-low tumors. Finally, we leveraged longitudinally patient-matched blood over the course of chemotherapy. In our studies we identified a cluster of KRT17high intermediary cancer cells that uniquely express high levels of CXCL8 and other cytokines which in turn influence the myeloid compartment both locally and systemically. We utilized sequencing data from dbGaP study accession phs002070. In addition to that, we included sequencing from new specimens which are deposited to this submission, consisting of one additional tumor specimen and 5 PBMC samples, sequenced after chemotherapy (longitudinally matched to PBMC samples in phs002071.v1.p1). FASTQ files of these sequencing runs are available through this dbGaP submission.

  Study phs003436

• tFL with a PMBL GE signature

  We investigated the clinicopathologic features of 5 follicular lymphomas (FL) that transformed to morphologic diffuse large B-cell lymphomas (DLBCL) and had a primary mediastinal large B-cell lymphoma (PMBL)-like gene expression profile. None of the transformed FL (tFL) arose in the mediastinum, all cases tested had a germinal center B-cell immunophenotype, 20% were CD30+, 60% CD23+, 80% MAL+, 20% CD200+, and 0% CD273/PDL2+. Whole exome sequencing detected alterations in genes associated with both FL/DLBCL (CREBBP, KMT2C, KMT2D, ARID1A, HIST1 members, and TNFRSF14) and PMBL (JAK-STAT pathway genes, B2M, and CD58). Copy number (CN) analysis detected gains/amplification of REL in 60% and STAT6 in 40%, gains of chromosome 16, including IL4R, in 40%, and both deletions and gains of 11q in 20%. This cohort, although limited in size, supports a subset of tFL that has blended features between FL/DLBCL and PMBL. Despite having some features that are less common in DLBCL (MAL and CD23 expression, JAK-STAT activation), these cases lack the most characteristic CN alteration seen in PMBL (9p24.1 gain/amplification). This cohort expands the biologic heterogeneity of tFL, illustrating a subset with blended FL/DLBCL and PMBL features, with potential treatment implications that include the use of novel PMBL-targeted therapies.

  Study EGAS00001005870

• scWGS profile, paediatric acute lymphoblastic leukemia ALL40

  Single cell sequencing using the direct nuclear tagmentation and RNA sequencing (DNTR-seq) method was performed on the diagnostic bone marrow sample (ALL40). This dataset consists of the DNA (scWGS) profile from 384 cells. Two fastq files are associated with each cell identifier.

  Dataset EGAD50000001774

• LBC1921 gvcfs

  297 members of the LBC1921 were sequenced using the Illumina HiSeq X platform. This dataset contains the gvcfs.

  Dataset EGAD00001006416

• NIHR BioResource Common Disease Patients 2016

  NIHR BioResource Common Disease Patients 2016. The dataset includes 13489 samples from blood donors, they were not screened for any particular disease, and therefore they are representative of the general population. Genomic data includes 845487 snps collected using the UK BioBank V1 Affymetrix array. Phenotypic data includes gender, age, ethnicity and disease. According to our internal quality check there are 81 duplicates in this dataset.

  Dataset EGAD00010002059

• Mosaic Chromosomal Aneuploidies Detection in Clinical Samples

  Mosaic chromosomal aneuploidy occurs when only a subset of cells carries an abnormal number of chromosomes. Mosaic aneuploidy has been reported in multiple types of diseases. Here we have developed a new sequencing-based approach to identify, characterize and quantify mosaic aneuploidy events in human tissue samples. This ongoing study has begun with results from sequencing data from two clinical patients, one with autism spectrum disorder (ASD) and the other with hemihyperplasia (OMIM 235000). We captured ~100,000 common SNPs from the samples to identify the nature of the mosaic aneuploidy events in each of the samples.

  Study phs001557

• Singapore Gastric Cancer Consortium GeoMx DSP tissue microarray (SGCC TMA) cohort

  Gastric cancer (GC) remains a significant global health challenge due to its high heterogeneity, with intratumoral heterogeneity (ITH) posing a major obstacle to effective patient outcomes. In this study, utilizing GeoMx Digital Spatial Profiler (DSP) technology, we specifically investigated ITH within GC patients by comparing tumor core regions to tumor edge regions. Our findings indicate that tumor edge regions exhibit more advanced tumor activity, akin to the G2-like progressed state, compared to tumor core regions. The findings confirm the spatial locations of G2 RNA-ITH subregions and support the conclusions drawn from the discovery cohort.

  Study EGAS50000000640

• The Haplotype Reference Consortium

  The Haplotype Reference Consortium (HRC) will create a large reference panel of human haplotypes by combining together sequencing data from multiple cohorts. By combining together multiple cohorts, the reference panels produced by the project will be as large as possible in terms of both number of haplotypes, and numbers of variants. This will increase the accuracy of the genotype imputation, especially at low-frequency variants, and the number of imputable variants, thus increasing the power of GWAS.

  Study EGAS00001001710

• Pan Prostate Cancer Group DK BAM files

  This dataset contains the BAM files from 32 Danish patients with prostate cancer, both germline and tumor tissues. These samples are part of the Pan Prostate Cancer Genome project.

  Dataset EGAD50000002318

• Dataset of Clonal Evolution of PPM1D Mutations in the Spectrum of Myeloid Disorders

  This dataset contains genomic profiles of 7 PPM1D-mutated patients across the spectrum of myeloid disorders using single-cell analyses (Tapestri technology) on diagnostic and longitudinal samples.

  Dataset EGAD50000001229

• WES bam files associated with 119 breast cancer patients associated with the Liberate Tracer Study

  This dataset contains WES bam/bai files associated with 119 breast cancer patients as part of with the Liberate Tracer Study

  Dataset EGAD50000001133

• Whole-genome sequencing (Illumina HiSeq X-Ten) of tumor-stage mycosis fungoides

  This dataset contains whole-genome sequencing data of tumors from 9 patients with mycosis fungoides. The data was generated using the Illumina HiSeq X-Ten platform.

  Dataset EGAD00001003982

• RNA-sequencing (Illumina HiSeq 4000) of tumor-stage mycosis fungoides

  This dataset contains RNA-sequencing data of tumors from 8 patients with mycosis fungoides. The data was generated using the Illumina HiSeq 4000 platform.

  Dataset EGAD00001003983

• Kuusamo whole exome sequencing

  Whole exome sequencing of samples selected from the Finrisk sample collection. The samples sequenced in this study have all been collected in Kuusamo, Finland.

  Dataset EGAD00001000299

• Fragmentomics profiling and quantification of plasma Epstein-Barr virus DNA enhance prediction of future nasopharyngeal carcinoma.

  This dataset included human plasma EBV DNA target-capture sequencing data. The capture probes were designed to cover the entire EBV genome and selected human autosomal regions. After enrichment, the products were sequenced on the NextSeq500 System (Illumina) and aligned to the EBV genome (AJ507799.2) and the human genome (hg19) in BAM format.

  Dataset EGAD50000000580

• smRNA-seq of human post-mortem brain data from the frontal lobe (goettingen part)

  This dataset contains smRNA-seq data from human post-mortem brain tissue of the frontal lobe of patients with FTD and healthy controls. These samples depict the data generated at the DZNE Göttingen and should be used together with the data generated at the DZNE Tübingen.

  Dataset EGAD00001006845

• Tissue DNA, WBC DNA and cfDNA (deep-)sequencing of mCRC patients treated with doublet chemotherapy and anti-EGFR in the CAIRO5 study

  This study assessed whether ctDNA based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC) derived DNA. In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 metastatic colorectal cancer patients participating in the prospective phase III CAIRO5 clinical trial (NCT02162563) were analyzed using the PGDx elio plasma resolve assay.

  Study EGAS00001006695

• Differential Mutations in Matched Primary and Metastatic Colorectal Cancers

  This study compares DNA mutations detected in matched primary and metastatic colorectal cancer samples from 18 individuals across 1,321 genes. We found many more mutations were shared between tumor pairs (avg. 33.3 mutations/tumor) than were discordant (avg. 2.3 mutations / tumor). Nearly all tumors showed at least one discordance, and these were observed in genes known to be involved in colorectal cancer progression. Therefore, although primary and metastatic colorectal tumors are highly genetically concordant, evidence exists for discordance, which has clinical implications especially in situations of chemotherapy resistance or insensitivity.

  Study phs001084

• WES data from 165 tumor/germline samples with muscle invasive bladder cancer.

  In this study, a total of 300 patients with MIBC receiving chemotherapy were included; 62 received NAC before cystectomy and 245 received first-line chemotherapy upon detection of locally-advanced (T4b) or metastatic disease. Treatment response, defined as pathological downstaging (< pTa,CIS,N0) after NAC or complete or partial response after first-line treatment (RECIST criteria). WES was performed using DNA from 165 tumors (76x median coverage) and associated germline DNA (46x median coverage). Data provided here consist of 5,828 fastq files for WES.

  Study EGAS00001004507

• SARS-CoV2 mRNA-vaccination-induced Immunological Memory in Human Non-Lymphoid and Lymphoid Tissues

  This dataset includes combined single-cell RNA-Seq and T cell receptor profiling data for SARS-CoV-2 spike protein-reactive CD4+ T cells and NK cells from blood, liver, lungs, and bone marrow of human donors.

  Dataset EGAD50000000062

• Bulk RNAseq dataset for "Longitudinal Multi-Omics Study Reveals Molecular Drivers and Tumor Microenvironment in Extramedullary Multiple Myeloma"

  This dataset contains 84 paired fastq files of Bulk RNAseq collected from 14 patients with Extramedullary multiple myeloma, 14 patients with newly diagnosed multiple myeloma and 14 patients with Relapsed/refractory multiple myeloma

  Dataset EGAD50000000051

• Tam-seq of germline samples for HGSOC copy-number signatures study

  This dataset contains targeted amplicon sequencing of Germline DNA extracted from 56 blood samples. They were sequenced on Illumina HiSeq 2500 and aligned to human genome assembly GRCh37 (hg19)to produce 127 bam files (2-3 technical replicates per sample).

  Dataset EGAD00001004172

• Whole-exome sequencing and microRNA profiling predicted relapse risk of stage I lung adenocarcinomas

  This dataset contains BAM files for whole exome-sequencing of stage I lung adenocarcinomas from Asian patients. In total, there are 113 patients and 262 samples, including 113 tumor samples, 113 adjacent normal samples and 36 buffy coat samples.

  Dataset EGAD00001006188

• Whole Genome Bisulfite sequencing data for Oncogenic 3D genome conformations identify novel therapeutic targets in ependymoma

  This dataset contains Whole Genome Bisulfite sequencing data from seven samples (six tumor samples and on tumor derived cell line). Sequencing was performed Illumina HiSeq 2000 machine resulting in 14 FASTQ files.

  Dataset EGAD00001008805

• Neuroblastoma hybrid capture sequencing panel

  Patient neuroblastoma hybrid capture sequencing panel. 5 samples from 2 donors (BAM files). For each donor, we obtained neuroblastoma tumor samples and neuroblastoma ALKi resistant samples. This dataset was used to study ALKi resistance in neuroblastoma.

  Dataset EGAD00001008343

• CBD-RAW-SC-VDJ-T: 10X Single-Cell VDJ TCR

  Raw Illumina sequencing data. For further information regarding this dataset, please contact Benjamin Fairfax and Rachael Bashford-Rogers at contact@combat.ox.ac.uk.

  Dataset EGAD00001007965

• NIH Division of Intramural Research Multiomic Monogenic Disease Study

  This cross-sectional, observational study utilized high-dimensional approaches, including transcriptomic analysis, serum protein profiling, and peripheral blood frequency assessments, to compare 228 adult and pediatric patients diagnosed with 22 monogenic immune-mediated conditions impacting various key immunological pathways, with 42 age- and sex-matched healthy controls. Participants were enrolled in clinical protocols at the National Institutes of Health in Bethesda, Maryland, USA. The primary objectives of the study were twofold: first, to identify disease-specific and shared "pan-disease" signatures using the collected data, and second, to develop a Random Forest classifier integrating these datasets to differentiate between age- and sex-matched healthy individuals and monogenic patients. This classifier produced a metric known as the "Immune Health Metric" (IHM). Subsequent analysis demonstrated that the IHM effectively distinguished healthy subjects from individuals with multiple polygenic autoimmune and inflammatory diseases in independent datasets. Moreover, it exhibited correlations with healthy aging and tracked disease activities and treatment responses across both immunological and non-immunological conditions. Additionally, the IHM accurately predicted age-dependent antibody responses to various vaccines, including influenza, Hepatitis A/B, Yellow Fever, Varicella Zoster, and Meningococcal vaccines.The microarray-based transcriptomic data, aptamer-based serum protein concentrations (Somalogic platform), peripheral blood frequency data, and clinical information will be made accessible through the database of Genotypes and Phenotypes (dbGaP).

  Study phs002732

• The British Autozygosity Populations BioResource

  This data set contains whole exome sequences of individuals with self-stated parental relatedness from the East London Genes & Health cohort. Rare frequency functional variants in these healthy individuals will be studied with respect to the genetic health of the participants and loss-of-function analysis of human genes.

  Dataset EGAD00001003215

• Enhancing OSCC Prediction: The Prognostic Power of WPOI and Tumor Budding, and the Limited Impact of Molecular Resection Margins

  This dataset contains sequences with results of mutations observed in patients with oral squamous cell carcinoma. Mutations were detected by NGS in tumor tissue, tumor margins, and peripheral blood as a healthy control. Study was using a panel of 88 cancer-related genes, which were selected based on a literature search.

  Study EGAS50000000074

• Myelodysplastic Syndrome (MDS) in Humanized Mice

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

  Study phs001778

• Genomic characterization of a patient with AGS and CdLS transcriptomic comparison of his monocytes against healthy and disease control samples

  In this study, we describe an extreme genetic phenotype of two simultaneous genetic lesions, leading to broad alterations in immunophenotype and transcriptome. Whole Exome Sequencing and RNA-Sequencing of CD14+ monocytes was performed on the case patient, and RNA-sequencing was also performed on disease (Systemic Lupus Erythematosus) and healthy controls.

  Study EGAS00001007829

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• Single-cell genotype-to-phenotype (scG2P) data of single nuclei from cell line mixing experiment and six donors

  We developed Single-cell genotype-to-phenotype (scG2P) to profile mutations in driver gene hotspots and capture mRNA targets of interest, validating this assay in a cell line mixing experiment of KYSE-270, KYSE-410, and HCT-116, and applied the assay to esophageal biopsy samples from six donors.

  Study EGAS50000001429

• Immunoreactive_p53_areas_in_human_skin_2

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

  Study EGAS00001004463

• ChIP-seq analysis of clear cell renal cell carcinoma

  In order to understand the epigenetic basis on ccRCC, we performed ChIP-seq on 3 ccRCC cell lines (786-O, A498, UMRC-2), and 1 normal kidney epithelium cell line (HK-2), cultured under normoxic (20% O2) and hypoxic (0.05% O2) conditions. This study analysed data from H3k4me1, H3K4me3, H3K27ac, H3k27me3, H3k36me3, CTCF, and HIF1A

  Study EGAS50000001322

• RNAseq_Pulldown_

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

  Study EGAS00001000230

• Triple_Negative_Breast_Cancer_Whole_Genome_Validations

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

  Study EGAS00001000426

• scRNA-seq to study interactions between HSPCs, BMSCs and immune microenvironment

  Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

  Study EGAS00001008181

• Targeted Germline Sequencing of the Leeds Melanoma Cohort

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

  Dataset EGAD00001007520

• Single-Cell Genomic Analysis of Gastrointestinal Cancer

  Our study aimed to define the heterogeneity of gastrointestinal cancers at a single-cell resolution. We subjected single-cell suspensions derived from surgical resections of gastrointestinal cancer tissue, paired normal tissue, peripheral blood mononuclear cells (PBMCs) or their ex vivo cultures to high-throughput microfluidics based single-cell RNA and DNA sequencing. We analyzed the features of the tumor microenvironment including fibroblasts, endothelial cells, macrophages and lymphocytes to determine their contribution to tumor growth and progression. We also characterized the mechanisms of immunosuppression in these tumors. This analysis led to novel insights into the biology of the microenvironment and also enabled the identification of new treatment targets.

  Study phs001818

• Investigating immunopathological signatures associated with COVID-19 severity post Omicron

  The aim of this study was to investigate the type and duration of protective immunity alongside immunopathological signatures associated with COVID-19 severity. RNA sequencing was performed using the Illumina Stranded mRNA Prep Ligation kit to investigate the protein coding transcriptome of PBMC cells. T cell receptor (TCR) repertoire profiling was performed with the TakaraBio SMART-Seq Human TCR (with UMIs) on PBMC cells to investigate the depth and persistence of SARS-CoV-2 targeting TCRs. The cohort (n=20) consisted of 10 non-hospitalised and 10 Hospitalised individuals with samples analysed 3 months post positive SARS-CoV-2 PCR.

  Study EGAS50000000926

• A prognostic human brain network for diffuse midline glioma

  Diffuse midline glioma (DMG) are near-universally lethal tumours of the paediatric central nervous system. In animal models, DMG form brain-wide, integrated networks through neuron-to-glioma synapses and glioma-to-glioma gap junctional coupling. This extensive connectivity robustly promotes the growth and invasion of DMG and other glial malignancies through paracrine mechanisms and direct neuron-to-glioma synapses. The organisation and clinical implications of these connections in the living human brain, however, remain to be elucidated. Here, we develop tumour network mapping to compute the brain-wide connectivity profile of DMG: defining a conserved brain network across pontine and thalamic DMG associated with patient short-term survival (DMG network). Tumour functional connectivity with the DMG network was independently predictive of patient overall survival across two external validation cohorts. Tumour growth mapped to DMG network-specific trajectories and peak, in-network neurometabolic changes across development spatiotemporally aligned with the peak age incidence of DMG. Single-nucleus RNA-sequencing confirmed diverse synaptic gene enrichment in high-connectivity DMG. Strikingly, incidental surgical resection of high-connectivity thalamic DMG tissue conferred a significant survival advantage. Collectively, these data define a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMG exploit otherwise healthy brain circuits to promote tumour growth.

  Study EGAS50000001752

• The Genetic Landscape of Metastasis and Recurrence in Head and Neck Squamous Cell Carcinoma

  Recurrence and/or metastasis occur in more than half of patients with head and neck squamous cell carcinoma (HNSCC) and pose the greatest threats to long-term survival. The genetic alterations underlying recurrent/metastatic HNSCC are unknown. This study represents the first whole exome sequencing (WES) cohort study of patient-matched tumor pairs in recurrent or metastatic HNSCC. Synchronous lymph node metastases are genetically more similar to their paired index primary tumors than metachronous recurrent tumors are. Newly arisen mutations in recurrent or metastatic tumors, may have therapeutic implications. Several genes were found to be mutated in multiple metastatic or recurrent tumors, but not in their respective primaries, including C17orf104, ITPR3, and DDR2. DDR2 mutations have been shown to confer enhanced sensitivity to Src-family kinase (SFK) inhibitors in other malignancies. Similarly, we found HNSCC cell lines harboring endogenous and engineered DDR2 mutations to be more sensitive to the SFK inhibitor dasatinib, than those with WT DDR2. This study outlines the first compendium of somatic mutations in primary, metastatic and/or recurrent HNSCC cancers that arise in individual patients; and demonstrates how such data can be used to interrogate potential predictive/prognostic biomarkers to inform and guide personalized therapy.

  Study phs001007