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• METABRIC

  The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (CNVs, SNPs) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, although the landscape was dominated by cis and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP, and MAP2K4. Unsupervised analysis of paired DNA/RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, ER-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration 0152hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 0152CNA-devoid sub-group and a Basal-specific chromosome 5 deletion-driven mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic copy number aberrations on the transcriptome.

  Study EGAS00000000083

• OAC WGS

  Please see our related publication, 'Molecular profiling to predict immunochemotherapy outcomes in esophageal adenocarcinoma'

  Study EGAS00001006470

• Multi-region exome sequencing of lung adenocarcinoma precursors -1

  To characterize the genomic landscape of invasive lung adenocarcinoma and its precursors; to depict the genomic evolution from preneoplasia of lung to invasive lung adenocarcinoma; to decipher mechanism to drive the tumor progression.

  Study EGAS00001003439

• DAC of the 300BCG ATAC-seq data

  To investigate human population variation of trained immunity, we immunized healthy individuals with Bacillus Calmette-Guérin (BCG). This live attenuated vaccine induces not only an adaptive immune response against tuberculosis, but also triggers innate immune activation and memory. We established personal chromatin accessibility maps over a time course of BCG vaccination in 323 individuals using ATAC-seq.

  Dac EGAC50000000056

• Long-read Nanopore data EVOFLUx

  Bam files with all reads covering 976 fCpGs identified in Gabbutt and Duran-Ferrer 2025 to develop the EVOFLUx methodology. These include 10 samples, 6 normal B cells, and 2 CLL patients developing RT.

  Dataset EGAD50000001697

• Distinct immune cell infiltration patterns in pancreatic ductal adenocarcinoma (PDAC) exhibit divergent immune cell selection and immunosuppressive mechanisms

  To elucidate the heterogeneity of tumour immune cell infiltration, we performed single cell RNAseq sequencing on CD45+ cells enriched from matched fresh tumour tissue following surgical resection of 12 treatment-naïve patients and matched PBMCs.

  Dataset EGAD50000001008

• Single-Nuclei RNA-seq of healthy (post-mortem) and temporal lobe epilepsy (biopsy) subjects.

  To identify dysfunctional neuronal subtypes underlying seizure activity in the human brain, we have performed single-nucleus transcriptomics analysis of >110,000 neuronal transcriptomes derived from temporal cortex samples of multiple temporal lobe epilepsy and non-epileptic subjects.

  Dataset EGAD00001006575

• A comprehensive characterisation and analysis of human breast cancers through whole-genome sequencing

  We propose to definitively characterise the somatic genetics of breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing.

  Dataset EGAD00001002740

• Exome_Sequencing_of_Human_myeloid_malignancies (2019-08-28)

  This study involves exome sequencing of blood/bone marrow DNA from patients with myeloid malignancies. Blood DNA samples have been taken from patients at different timepoints of disease phenotype. We hope to elucidate mechanisms of clonal evolution in these patients. . This dataset contains all the data available for this study on 2019-08-28.

  Dataset EGAD00001005299

• Saliva microbiota and STI

  Excess sugar consumption is common among youth and can have adverse health effects. However, the relationship between saliva microbiota and sugar consumption remains sparsely studied. We aimed to explore diversity, composition and functional capacities of saliva microbiota in 11–13-year-old Finnish children with low and high sweet treat consumption.

  Dataset EGAD00001008780

• Single Cell Transcriptomics of peripheral immune cells pre- and post-Immune Checkpoint Blockade

  This is raw sequencing data, analysis of which is presented in the paper "Sensitivity to Immune Checkpoint Blockade and Progression-Free Survival is associated with baseline CD8+ T cell clone size and cytotoxicity", DOI: https://doi.org/10.1101/2020.11.15.383786

  Dataset EGAD00001007942

• WES data of primary tumors and metastasis corresponding to three patients

  Fastq files of WES data. Primary tumor and/or metastasic samples of three chRCC patients. DNA libraries were produced using the SureSelect XT HumanAllExon V5 kit (Agilent Technologies), and sequencing was performed in a HiSeq instrument (Illumina) using a 100-bp paired-end mode.

  Dataset EGAD00001010173

• Familial Exome Sequencing in Rare Pediatric Phenotypes

  To discover novel candidate genes associated with rare Mendelian phenotypes, we will conduct individual genomic and phenotypic characterization using genome-wide array, pedigree exome sequencing, candidate genotyping, and pertinent clinical testing to define phenotype. Pedigrees included in this submission will have a variety of clinical pathological phenotypes.

  Study phs000553

• Expression profiles of DLL1 positive and negative subpopulations in metastatic colorectal cancer organoids under cetuximab treatment

  Bulk RNA sequencing was performed on metastatic colorectal cancer (mCRC) organoids subjected to cetuximab treatment and FACS-sorted according to DLL1 positivity. This study is part of a larger set of studies focused on investigating cetuximab induced populations in mCRC organoids

  Study EGAS50000001780

• Translational analyses from a phase II study of pembrolizumab and epigenetic modification with azacitidine in platinum-resistant epithelial ovarian cancer

  Epigenetic modulators may sensitize platinum-resistant ovarian cancer (PROC) to immune checkpoint inhibition by reprogramming the tumor microenvironment. We report clinical and translational findings from a phase II non-randomized study of pembrolizumab and oral azacytidine in 34 women with PROC (NCT02900560). The effect of combined epigenetic and immunotherapy was evaluated by transcriptomic analyses of serially biopsied tumors. Differential gene expression analyses revealed an upregulation of inflammatory and cytolytic genes and co-inhibitory checkpoints 6 weeks on-therapy. Upregulation of interferon signaling, antigen presentation and immune cell adhesion and migration gene sets was prominent on-therapy, together with an increased density of CD8+ T -cells. Patients with a CA-125 and/or clinical response showed an enrichment of adaptive and conserved immune response gene sets on-therapy.

  Study EGAS50000001165

• Tobacco exposure and somatic mutations in normal human bronchial epithelium

  That tobacco smoking causes lung cancer is well-established, but we lack quantitative understanding of its effects on genomes of normal bronchial epithelium. We sequenced whole genomes of 632 colonies derived from single bronchial epithelial cells across 16 subjects. Tobacco smoking is the major influence on mutation burden, adding 1000-10,000+ mutations/cell, massively increasing both between-subject and within-subject variance, and generating several distinct signatures of substitutions and indels. A population of cells in subjects with smoking history had mutation burdens equivalent to that expected for never-smokers: these cells lacked tobacco-specific mutational signatures, were four-fold more frequent in ex-smokers than current smokers, and had significantly longer telomeres than their more mutated counterparts. Driver mutations increased in frequency with age, affecting 4-14% of cells in middle-aged never-smokers. In current smokers, ≥25% of cells carried driver mutations and 0-6% cells had 2 or even 3 drivers. Thus, tobacco smoking increases mutation burden, cell-to-cell heterogeneity and driver mutations, but quitting promotes replenishment of bronchial epithelium from mitotically quiescent cells that have avoided tobacco mutagenesis.

  Dataset EGAD00001005193

• Whole exome sequencing of Finnish hereditary breast cancer families

  A remarkable proportion of factors causing genetic predisposition to breast cancer (BC) are unknown in non-BRCA1/2 families. Exome sequencing was performed for 13 high-risk Finnish hereditary breast and/or ovarian cancer (HBOC) families to detect variants contributing to BC susceptibility

  Study EGAS00001001835

• Experimental and Clinical Studies of Presbycusis

  This study aimed to investigate genes and variants associated with adult-onset progressive hearing loss, a common and complex disease with a strong genetic component.Participants enrolled in an ongoing longitudinal study of age-related hearing loss at the Medical University of South Carolina (MUSC), dating from 1987. Pure tone thresholds at 0.25, 0.5, 1.0, 2.0, 3.0, 4.0, 6.0 and 8.0 kHz were obtained for each ear of each person, along with questionnaire responses concerning noise exposure history. Based on the audiometry, participants were classified into 5 groups as "Older-Normal", "Metabolic", "Sensory", "Unclassified" and "Unselected" by their hearing loss.Exome sequencing was carried out using the Agilent SureSelect X2 Target Enrichment System (version 5) and the Agilent SureSelect Human All Exon V5 kit, which included 5' and 3' UTRs. DNA was sheared using the Covaris S220 focused ultrasonicator. Libraries were sequenced on the Illumina HiSeq 2500. Variant loads per gene were calculated and compared between groups. Individual variants affecting hearing thresholds were also identified. Analyses were followed up in a second cohort. Several genes and variants were identified as novel candidates associated with both better and worse hearing. Data available through dbGaP include whole exome sequencing (WES) files and audiometric phenotyping.

  Study phs003327

• Whole exome sequence in EGFR-TKI resistant non-small cell lung cancer

  Whole exome analysis to clear molecular basis and mutation spectrum in EGFR-TKI resistant non-small cell lung cancer

  Study JGAS000102

• Genetic analysis in an inherited cardiac arrhythmia

  To identify a causative gene for an inherited cardiac arrhythmia, exome sequence analysis was conducted in 6 patients and 5 controls.

  Study JGAS000041

• Genomic data from analysis of the human placenta, part of the Pregnancy Outcome Prediction study (POPs)

  The Pregnancy Outcome Prediction (POP) study is a prospective cohort study of nulliparous women attending the Rosie Hospital (Cambridge, UK) for their dating ultrasound scan. The study included 4512 women with a viable singleton pregnancy; study participants provided written informed consent and were recruited between January 2008 and July 2012. The POP study aimed both at evaluating performance of known biomarkers and serial ultrasonography in assessing maternal and fetal well-being, as well as identifying novel biomarkers. The study is sufficiently large to be powered for relatively uncommon adverse pregnancy outcomes. Women attended four study visits scheduled every 8 weeks, starting with the first trimester. Participants had blood taken during the dating/recruitment visit (at approximately 12 weeks gestation (wkGA)), as well as at three subsequent visits (at ∼20wkGA, ∼28wkGA and ∼36wkGA). For more detail, please visit: https://www.obgyn.cam.ac.uk/research/pops-2/.

  Study EGAS00001002205

• OAC RNASeq

  Please see our related publication, 'Molecular profiling to predict immunochemotherapy outcomes in esophageal adenocarcinoma'

  Study EGAS00001006468

• Genome Sequencing of Circulating Tumor Cells for Minimally Invasive Molecular Characterization of Multiple Myeloma Pathology

  ​​Multiple Myeloma (MM) develops from well-defined precursor stages known as Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering MM (SMM); however, invasive bone marrow (BM) biopsy limits screening and monitoring strategies for patients. In this study, we enumerated circulating tumor cells (CTCs) from patients with precursor and overt diseases, and developed a novel approach, MinimuMM-seq, which enables detection of translocations and copy number abnormalities through whole-genome sequencing of highly pure CTCs. In a cohort of 51 patients, 24 with paired BM, we applied our method MinimuMM-seq and detected 100% of clinically reported BM biopsy events. The next-generation sequencing (NGS) assay could replace molecular cytogenetics by Fluorescence In Situ Hybridization (FISH) for diagnostic yield and risk classification. In 8 patients we could apply MinimuMM-seq on serially collected samples to track and monitor major clones in peripheral blood. We describe clonal evolution and shifting dynamics of subclones over time, as well as in between blood and marrow compartments. All whole-genome sequencing (WGS) data generated in this study will be made accessible through dbGaP.

  Study phs003084

• CLL_targeted_exome_sequencing

  Aim to characterise cancer gene landscape in CLL, particularly in cases with mutated POT1 gene. Treatment-naïve CLL cases will be interrogated by targeted exome sequencing using a cancer gene panel.

  Study EGAS00001001963

• CXCR4 induces memory formation over exhaustion in CAR-T cells to achieve durable leukemia targeting

  This project focuses on acute myeloid leukemia and the development of chimeric antigen receptor (CAR) T cell therapy. We investigated how enforced expression of the chemokine receptor CXCR4 promotes memory acquisition and long-term persistence of CAR-T cells, thereby enhancing their therapeutic efficacy and durability against leukemia.

  Study JGAS000848

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

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

  Dataset EGAD50000002012

• Transcriptome and Exome from longitudinal samples of human glioblastoma

  We obtained paired longitudinal specimens from a total of 38 glioblastoma (GBM) patients (34 primary and 4 secondary GBM patients). Treatment-naive initial tumors were available for 35 cases; for the other 3 cases, we used the first available recurrent tumors in lieu of initial tumors. Tumor specimens were subjected to whole-exome sequencing (27 of 38 cases, with the matched normal/blood for 22 of the 27 cases) and transcriptome sequencing (30 of 38 cases).

  Dataset EGAD00001001424

• Single-cell TCR sequencing of DQ2.5-hor-3-specific T cells

  In order to characterize the T cell receptor (TCR) repertoire of DQ2.5-hor-3-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.5:DQ2.5-hor-3- tetramer binding CD4+ T cells isolated from biopsies of celiac disease patients. We also sequenced the TCR of the T-cell clones (TCCs) that were generated by cloning by limited dilution and antigen-free expansion of HLA-DQ2.5:DQ2.5-hor-3-tetramer binding CD4+ T cells from biopsies of celiac disease patients.

  Dataset EGAD00001005048

• HGSC WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

  HGSC cases in the OvCaRe and CRCHUM Tumour Banks were selected according to the following criteria: (i) were administered platinum taxane based therapy; (ii) relapsed within 12 months (365 days) or had at least longer than 4.5 years (1642.5 days) follow-up data; (iii) had at least 50% tumour content by H&E staining and expert pathology review. All cases were re-reviewed by expert pathologists to confirm the diagnosis of HGSC. Germline BRCA1 and BRCA2 was determined for all patients through hereditary cancer screening programs. The design of cases selection as a discovery cohort was engineered to amplify biological differences by selecting cases from the extremes of the outcome distribution. All HGSC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

  Dataset EGAD00001003268

• The scRNA dataset for TIGIT in MCL with CART

  We collected longitudinal samples from 15 patients with MCL at various clinical time points before and after CAT-T therapy brexucabtagene autoleucel (BA) infusion. The patients were grouped into three categories based on their clinical responses after BA treatment: 1) responsive (n = 9), 2) relapsed (n = 5), and 3) refractory (n = 1). All patients in category #1 and #2 had initially attained a complete response (CR) after BA therapy. The responsive group maintained CR with no relapse at the time of last follow up, while the relapsed group achieved initial CR but eventually relapsed. The 10x Chromium™ Single-Cell 5′ Reagent Kit v2 (PN-1000190, 10x GENOMICS) and Chromium Single-Cell Human TCR amplification Kit (PN-1000252, 10x GENOMICS) were used to perform single-cell separation, cDNA amplification, and library construction for gene expression and TCR repertoire following the manufacturer’s guidelines. Thirty-nine samples passed quality control and underwent single-cell transcriptome profiling with simultaneous single-cell T-cell receptor (TCR) repertoire analysis.

  Dataset EGAD00001010180

• Clonal dynamics after allogeneic haematopoietic cell transplantation using genome-wide somatic mutations - WGS

  Allogeneic haematopoietic cell transplantation (HCT) replaces the stem cells responsible for blood production with those harvested from a donor, and is received by 40,000 patients worldwide each year. To quantify dynamics of long-term stem cell engraftment, we sequenced whole genomes of 2,824 single-cell-derived haematopoietic colonies from blood samples of 10 donor-recipient pairs taken 9-31 years after HLA-matched sibling HCT. With younger donors, 10,000-50,000 stem cells had engrafted and were still contributing to haematopoiesis at time of sampling, but estimates were 10-fold lower with older donors. Engrafted stem cells made multilineage contributions to myeloid, B-lymphoid and T-lymphoid populations, although individual clones often showed biases towards one or other mature cell type. Recipients had lower clonal diversity than matched donors, equivalent to ~10-15 years of additional ageing, arising from up to 25-fold greater expansion of stem cell clones. An HCT-related population bottleneck alone could not explain these differences: instead, phylogenetic trees evinced two distinct modes of HCT-specific selection. In 'pruning selection', cell divisions underpinning recipient-enriched clonal expansions had occurred in the donor, preceding transplant - their selective advantage derived from preferential mobilisation, harvest, survival ex vivo or initial homing. In 'growth selection', cell divisions underpinning clonal expansion occurred through proliferative advantage in the recipient's marrow after homing - clones with multiple driver mutations especially demonstrated this pattern. Uprooting stem cells from their native environment and transplanting them to foreign soil exaggerates selective pressures, distorting and accelerating the loss of clonal diversity compared to the unperturbed haematopoiesis of donors.

  Dataset EGAD00001010872

• Single cell transcriptional characterization of human megakaryocyte lineage commitment and maturation

  Single cell RNA-sequencing of sternal bone marrow reciding Hematopoietic Stem Cells (HSCs) and Megakaryocytes (MKs) from individuals undergoing elective open heart valve replacement. HSCs were defined as Lineage-, CD34+, CD38-, CD45RA-, CD90+, CD49f+ cells. MKs where CD41a+, CD42b+ and ploidy was determined with Hoechst. A sternal bone marrow scraping was taken directly following median sternotomy using a Volkmann’s spoon. The sample was collected into an EDTA Vacutainer tube containing 1.8mg/ml EDTA. 4mL of Dulbecco’s phosphate buffered saline (PBS, Sigma) containing 10% human serum albumin (HSA, Gemini Bio Products) was added and the whole volume was resuspended by pipetting 2-3 times. The sample was then put on metallic thermal beads (ThermoFisher Scientific) at a temperature between 0-4°C and transported to the University of Cambridge for further processing. For HSC isolation the cells were stained with the following antibody cocktail: PECy5 conjugated anti-lineage specific antibodies: CD2 (BD), CD3 (BD), CD10 (BD), CD11b (BD), CD11c (BD), CD19 (BD), CD20 (BD), CD56 (BD), biotinylated CD42b (Pab5, NHS Blood and Transplant, International Blood Group Reference Laboratory [IBGRL]), biotinylated GP6 (Pab5, NHS Blood and Transplant, International Blood Group Reference Laboratory [IBGRL]) used in combination with PECy5 conjugated streptavidin (Biolegend). Alexa Fluor 700 conjugated anti-CD34 (BD), PerCP-Cy5.5 conjugated anti-CD38 (BD), Pacific Blue conjugated anti-CD45RA (Invitrogen), PECy7 conjugated anti-CD90 (BD),PE conjugated anti-CD49f (BD). After staining cells were kept at 4°C before sorting using a FACS Aria Fusion flow sorter (BD). Single HSCs defined as Lineage-, CD34+, CD38-, CD45RA-, CD90+, CD49f+ cells were sorted by FACS directly into individual wells of a 96-well plate. Index sort data was collected for each single cell. For MK isolation the cells were stained for surface MK markers with mouse anti-human CD41a APC conjugated antibody (BD) and mouse anti-human CD42b PE conjugated antibody (BD) and for ploidy analysis with 1ug/ml Hoechst 33342 (Invitrogen). After incubation at 37°C for 30 minutes, the cells were kept at 4°C before sorting using a FACS Aria Fusion flow sorter (BD). Single cells and MK pools of 20 cells were sorted by FACS according to ploidy level using a 100uM nozzle directly into individual wells of a 96-well plate. cDNA synthesis and poly(A) enrichment was performed following the G&T-seq protocol (Macaulay et al. 2015), a variation of the Smart-seq2 protocol1. ERCC spike-in RNA (Ambion) was added to the lysis buffer in a dilution of 1:4,000,000.

  Dataset EGAD00001006677

• Organoid drug profiling identifies methotrexate as a therapy for SCCOHT, a rare pediatric cancer

  Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and lethal tumor in adolescent and young adult patients. Currently, there is no standard-of-care treatment for these patients. Reliable models that represent this disease and can be used for translational research are scarce. To model SCCOHTs, we have established eight patient-derived tumoroid lines from tumor lesions of three patients with SCCOHT. The tumoroids recapitulate genomic and transcriptomic characteristics of the corresponding patient tumors and capture intrapatient tumor heterogeneity. Organoid drug profiling using a library of 153 clinical compounds identified methotrexate as an effective and selective drug against SCCOHTs with a clinically relevant IC50 of 35 nmol/L. RNA sequencing demonstrated that methotrexate induced TP53 pathway activation and apoptosis. These data underscore that organoid technology can support the design of therapeutic strategies for rare cancers.

  Study EGAS00001007911

• The Research Institute at Nationwide Children's Hospital Genetics of Congenital Heart Disease (CHD)

  Congenital heart disease (CHD) is the most common type of birth defect, but the cause for the majority of cardiac birth defects remains unknown. Numerous epidemiologic studies have demonstrated evidence that genetic factors likely play a contributory, if not causative, role in CHD. A few genes have been identified by us and other investigators using traditional genetic approaches, but these genes only account for a small portion of the non-syndromic CHDs. Therefore, we are now utilizing whole exome sequencing (WES) and whole genome sequencing (WGS), with the addition of more traditional genetic techniques such as chromosomal microarray or traditional linkage analysis, to identify genetic causes of familial and isolated CHD. With WES/WGS, we are able to sequence all of the genes of an individual and apply different data analysis techniques based on whether we are analyzing a multiplex family or a cohort of trios (mother, father and child with CHD) with a specific isolated CHD. Therefore, WES/WGS is a robust method for identification of novel genetic causes of CHD, which will have important diagnostic and therapeutic consequences for these children. Subjects provided blood samples, skin biopsy, or saliva samples for DNA extraction and creation of cell lines. Tissue remaining after surgical procedures was also collected. Medical records were searched for detailed phenotype data and subjects were followed longitudinally for outcome.

  Study phs002010

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

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

  Dataset EGAD50000001836

• RRBS of 58 pleural mesothelioma samples (Paired-end)

  The dataset contains RRBS data (bam files) for 58 pleural mesothelioma samples. The samples were sequenced on NovaSeq6000 (Illumina, San Diego, CA) in paired-end 150bp mode. RRBS raw reads were trimmed for adaptor sequences using trim galore (v. 0.6.5) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and filtered for low-quality sequences using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High quality trimmed reads were mapped to the Human reference genome (UCSC genome assembly GRCh38/hg38) using Bismark (v. 0.22.3) with default parameters.

  Dataset EGAD50000002129

• IBD dataset

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

  Dataset EGAD50000000198

• Mapping genetic variants underlying gene regulation in intestinal cell types to identify novel IBD drug targets

  Biopsies from the terminal ileum and rectum of healthy individuals and terminal ileum and blood from Crohns disease patients are collected and processed single cells and processed for single-cell RNA-sequencing using 10X Genomics 3 v3 and v3.1 and Illumina sequencing. 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 EGAD00001016069

• OAC scRNASeq

  Please see our related publication, 'Molecular profiling to predict immunochemotherapy outcomes in esophageal adenocarcinoma'

  Study EGAS00001006469

• Characterization of patient-derived xenograft models of myxoid liposarcoma either sentitive or resistant to trabectedin

  Two patient-derived xenograft model of myxoid liposarcoma one sensitive and one resistant to trabectedin. The aim of the study was to study the resistance to the drug.

  Study EGAS00001003715

• National Cancer Institute (NCI) Primary Human Melanocyte QTL Study

  In order to create a melanocyte-specific QTL resource, we obtained primary human melanocyte cultures isolated from foreskin of 106 healthy newborn males predominantly of European descent. Melanocytes were cultured in lot-matched culture medium in randomized batches to minimize variability that could be introduced by culturing conditions. RNA sequencing and direct SNP genotyping of these samples produced an average of ~87.9 million reads (paired-end, stranded, 126bps), and ~713,000 SNP genotypes, respectively. Illumina 450K methylation array covered over 485,000 CpGs distributed genome wide.

  Study phs001500

• Methylation profiling of osteoblastomas and their mimics

  Here, we set out to comprehensively characterize a series of 77 osteoblastomas by immunohistochemistry, fluorescence in-situ hybridization as well as copy number and methylation profiling and compared our findings to histologic mimics.

  Study EGAS00001005932

• ABIS_1_MeDIP-seq

  We investigated changes in whole genome DNA-methylation in a group of 48 healthy five-year-old children differentiated by their hair cortisol levels. By combining this novel biomarker for chronic stress with methylated DNA immunoprecipitation sequencing (MeDIP-seq), we found that high cortisol were associated with a genome-wide decrease in DNA-methylation targeted to specific zinc finger transcription factor binding sites, repetitive elements and genes important for neurodevelopment and calcium transport. Large scale hypomethylation of repetitive regions, as well as a deficient calcium transport, have been reported in many stress related diseases, as well as in many cancers and biological aging. Thus our findings may aid in our understanding of how susceptibility to these diseases develops.

  Study EGAS00001001099

• Searching for variants associated with endometriosis

  We explored regulatory mechanism of a SNP on chromosome 9p21 associated with endometriosis by leveraging “allele-specific” functional genomic approaches. By re-sequencing 1.29 Mb of 9p21 region and scrutinizing DNase-seq data from the ENCODE project, we prioritized rs17761446 as a candidate functional variant that was in perfect linkage disequilibrium with the original GWAS SNP (rs10965235) and located on DNase I hypersensitive site. Chromosome conformation capture followed by high-throughput sequencing revealed that the protective G allele of rs17761446 exerted stronger chromatin interaction with ANRIL promoter. We demonstrated that the protective allele exhibited preferential binding affinities to TCF7L2 and EP300 by bioinformatics and chromatin immunoprecipitation (ChIP) analyses. ChIP assays for histone H3 lysine 27 acetylation and RNA polymerase II reinforced the enhancer activity of the SNP site. The allele specific expression analysis for eutopic endometrial tissues and endometrial carcinoma cell lines showed that rs17761446 was a cis-regulatory variant where G allele was associated with increased ANRIL expression.

  Study EGAS00001001741

• UK renal cancer samples genotyped on Illumina OmniExpress BeadChip

  Renal cell carcinoma (RCC) cases comprised adult patients with histologically proven RCC were collected through two sources within the UK. First, 856 cases from SORCE, a MRC collection of surgically treated RCC cases ascertained through UK clinical oncology centres. Second, 189 RCC cases collected through the ICR and Royal Marsden NHS Hospitals Trust. Cases included 590 clear cell carcinomas (CCCs), 42 papillary carcinomas (PCs), 33 chromophobe carcinomas (CCs) and 19 mixed or other histological subtypes. DNA was extracted from EDTA-venous blood samples using the conventional methods and quantified using PicoGreen (Invitrogen). Cases were genotyped using the Human OmniExpress-12 BeadChip according to the manufacturer's recommendations (Illumina Inc, San Diego, CA, USA). After strict QC, 944 cases were retained. Data provided in plink format. Controls used were data from the Wellcome Trust Case Control Consortium 2 (WTCCC2) 1958 birth cohort and the UK Blood Service Control Group (available as EGAS00000000028).

  Study EGAS00001002336

• Pheno-Seq, linking 3D phenotypes of clonal tumor spheroids to gene expression

  3D-culture systems have advanced cancer modeling by reflecting physiological characteristics of in-vivo tissues, but our understanding of functional intratumor heterogeneity including visual phenotypes and underlying gene expression is still limited. Transcriptional heterogeneity can be dissected by single-cell RNA-sequencing, but these technologies suffer from low RNA-input and fail to directly correlate gene expression with contextual cellular phenotypes. Here we present pheno-seq for integrated high-throughput imaging and transcriptomic profiling of clonal tumor spheroids derived from 3D models of breast and colorectal cancer. Specifically, we identify characteristic expression signatures that are associated with heterogeneous invasive and proliferative behavior including a rare cell subtype. Furthermore, we identify functionally relevant transcriptional regulators missed by single-cell RNA-seq, link visual phenotypes defined by heterogenous expression to inhibitor response and infer single-cell regulatory states by deconvolution. We anticipate that directly linking molecular features with patho-phenotypes of cancer cells will improve the understanding of intratumor heterogeneity and consequently prove to be useful for translational research.

  Study EGAS00001002999

• Genome-wide study of resistance to severe malaria in eleven worldwide populations

  A genome-wide study of resistance to severe malaria in 18,000 samples from eleven worldwide populations, including eight populations sub-Saharan Africa.

  Study EGAS00001001311

• Multi-modal single-cell analysis of salivary glands from patients with Sjogren's syndrome

  Sjogren's syndrome (SS) is an autoimmune disease that causes salivary gland dysfunction due to immune-mediated destruction. In this study, we apply multi-modal single-cell technologies - single-cell RNA sequencing and T-cell receptor sequencing - to salivary gland lesions, aiming to uncover transcriptional signatures and TCR sequence linked to autoantibody profiles.

  Study JGAS000808

• Tracking the genomic evolution of esophageal adenocarcinoma through neoadjuvant chemotherapy

  Esophageal adenocarcinomas (EACs) are associated with dismal prognosis. Deciphering the evolutionary histories of this disease may shed light on therapeutically tractable targets and reveal changing mutational processes during the disease course and following neoadjuvant chemotherapy (NAC). We exome sequenced 40 tumor regions from 8 patients with operable EACs both before and after platinum-containing NAC. This revealed the evolutionary genomic landscape of EACs with the presence of heterogeneous driver mutations, parallel evolution, early genome doubling events and an association between high intratumor heterogeneity and poor response to NAC. Multi-region sequencing demonstrated a significant reduction in T>G mutations within a CTT context when comparing early and late mutational processes and the presence of a platinum signature with enrichment of C>A mutations within a CpC context following NAC. EACs are characterized by the presence of amplifications containing targetable oncogenes present before and after chemotherapy that may provide a rationale for future therapeutic approaches.

  Study EGAS00001001254

• Whole exome sequencing of patients with esophageal squamous cell carcinoma receiving chemoradiotherapy

  We performed multi-region whole exome sequencing (WES) of pre-treatment and recurrent esophageal cancer receiving chemoradiotherapy in order to characterize clonal evolution of treatment resistant clones. Furthermore, additional solitary pre-treatment tumor samples were subjected to WES to detect biomarkers predicting clinical outcome.

  Study JGAS000227