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• Congenital_anosmia_1

  Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). To date, only a single recessive gene underlying complete anosmia has been identified. Here we sequenced the exomes of 10 individuals from a single family, including three with complete anosmia, across three generations to identify the genetic basis of congenital anosmia in this family. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001124

• HipSci___RNAseq___Rare_Monogenic Diabetese

  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 perform RNAseq on iPS cells generated from skin biopsies or blood samples from rare disease patients diagnosed with Monogenic Diabetes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001137

• Single-cell RNA-sequencing reveals that glioblastoma recapitulates a normal neurodevetlopmental hierarchy

  We discovered a conserved neural tri- lineage cancer hierarchy centered around glial progenitor-like cells. We also found that this progenitor population contains the majority of the cancer’s cycling cells, and, using RNA velocity, is often the originator of the other cell types. Finally, we show that this hierarchal map can be used to identify therapeutic targets specific to progenitor cancer stem cells. Our analyses show that normal brain development reconciles glioblastoma development, suggests a possible origin for glioblastoma hierarchy, and helps to identify cancer stem cell-specific targets.

  Study EGAS00001004422

• Understand_Paratyphoid_Disease___host_responses_to_human_challenge_with_S__Paratyphi_A

  This project aims to evaluate the transcriptional response to disease measured in whole blood of participants who developed enteric fever after challenge and, importantly, those who were challenged but stayed well throughout the challenge period. This data will provide unique coverage of the transcriptome and will yield invaluable insight after integration with a wealth of clinical data collected during this trial. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001260

• SNP genotyping data in genes related to trace element homeostasis

  In this study we provide data regarding sample charactheristics and genotypes in 150 human samples of European origin for SNPs located around genes related to metal homeostasis. SNPs were genotyped with the Illumina VeraCode technology (192-plex format). The genotyped SNPs were used to identify quantitative trait loci in the same samples. Data referring to the quantification of 18 micronutrients, the expression levels of 90 genes and the protein abundances of 40 proteins related to metal homeostasis in the same samples are directly available as supplementary material in the publication of this study.

  Study EGAS00001001292

• Ultraviolet radiation drives mutations in a subset of mucosal melanomas

  Although identified as the key environmental driver of common cutaneous melanoma, the role of ultraviolet radiation (UVR)-induced DNA damage in mucosal melanoma is poorly defined. We present the largest cohort of mucosal melanomas of conjunctival origin to be analyzed by whole genome sequencing and show a predominance of UVR-associated single base substitution signature 7 (SBS7) in the majority of the samples. Our data shows mucosal melanomas with SBS7 dominance have similar genomic patterns to cutaneous melanomas and therefore this subset could benefit from treatments currently used for common cutaneous melanoma.

  Study EGAS00001004697

• HCA_Female_Reproductive_Adult_WSSS_RNA

  HCA Endometrium_LM The endometrium regenerates monthly and its transformation is executed through dynamic changes in states and interactions of multiple cell types. Using transcriptomics methods we seek to profile changes of the endometrium across the menstrual cycle. Our map will have implications in women’s health and cancer, by enabling the interpretation of GWAS analyses or the studying functional consequences of somatic mutations. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001004727

• Premalignant SOX2 overexpression in the fallopian tubes of ovarian cancer patients: Discovery and validation studies

  To identify early driver mutations in ovarian cancer cells, we used dense whole genome sequencing of micrometastases and microscopic residual disease collected at three time points from a single patient during treatment for high-grade serous ovarian cancer (HGSOC). Laser capture microdissection of tumour islets was performed on samples prior to chemotherapy, after three cycles of chemotherapy and at recurrence. Long frament read whole genome sequencing was performed and mutations were identified. To our knowledge, this is the first longitudinal study that attempts to investigate spatial and temporal micro-heterogeneity in cancer.

  Study EGAS00001001909

• The aim of this study was to identify underlying hub genes and dysregulated pathways associated with the development of HCC using bioinformatics analysis.

  In the present study, we identified differentially expressed protein-coding genes from RNA transcriptional profiling performed on 11 paired cancer tissues and adjacent non-cancerous tissues. Then, we conducted GO, KEGG, PPI network and centralities analyses to study and identify changes in pathways and hub genes. The aim of this study was to improve understanding of HCC carcinogenesis by providing information concerning the genetic changes that occur during disease progression and to uncover the expression of biomarkers with potential use for clinical diagnosis, treatment, and monitoring of disease progression.

  Study EGAS00001002526

• Panbody_nanoseq

  Different cell types within the human body are subject to different endogenous and exogenous exposures which may result in distinct patterns of mutagenesis. In non-clonal tissues, it is difficult to assess these mutational patterns, including the rate at which they occur. This study will examine the mutational rates and signatures operating across a wide range of normal tissues using the nanoseq technology to reliably call variants, irrespective of their clonal composition. Each cell type will be enriched for using laser capture microdissection. This will serve as a reference against which future work on benign and malignant disease entities can be compared.

  Study EGAS00001005521

• COVID_19_UK_CIC_Spatial

  Understanding the immune response to SARS-CoV-2 is critical to our ability to control the coronavirus pandemic. Spatial transcriptomics will be performed on COVID-19 post-mortem tissues in collaboration with the UK - Coronavirus Immunology Consortium (UK-CIC). UK-CIC encompasses a concerted effort by the UK's world-leading immunology community to deliver a co-ordinated and agile national research programme to increase our understanding of how the immune system interacts with SARS-CoV-2. UK-CIC is led by Professor Paul Moss (University of Birmingham) and brings together 20 UK immunology centres of excellence, with support from the British Society for Immunology.

  Study EGAS00001005817

• T-cell reconstitution after reduced dose ATLG induction in kidney transplant recipients

  Pre-sensitized kidney transplant recipients have a higher risk for rejection following kidney transplantation and therefore receive a lymphodepletional induction therapy with anti human T-lymphocyte globulin (ATLG). The time course of lymphocyte reconstitution with regards to overall and donor-reactive T-cell receptor (TCR) specificity remains elusive. In this study we aimed to describe the TCR repertoire in a reduced dose ATLG regimen making it possible to evaluate shifts in the shape of the immune repertoire and to detect the reappearance of donor-reactive T-cells following reduced lymphodepletional induction therapy.

  Study EGAS00001005941

• Paediatric_and_adult_nasal_RNAseq___COVID19

  Understanding infectivity, progression and disease severity of COVID-19 in children. Understanding infectivity, progression and disease severity of COVID-19 in children: It has been observed that COVID-19 infection appears to present with reduced clinical severity and prevalence within children (<18 years) compared to adults. This project as part of a national collaborative initiative seeks to answer this question. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001004391

• Pathogenic Neurofibromatosis type 1 (NF1) RNA splicing resolved by targeted RNAseq

  Neurofibromatosis type 1 (NF1) is caused by loss-of-function variants in the NF1 gene. Approximately 10% of these variants affect RNA splicing and are either missed by conventional DNA diagnostics or are misinterpreted by in silico splicing predictions. Therefore, a targeted RNAseq-based approach was designed to detect pathogenic RNA splicing and associated pathogenic DNA variants. an in-house developed tool (QURNAS) was used to calculate the enrichment score (ERS) for each splicing event. RNA enrichment of NF1 and SPRED1 was done using SPET (NUGEN - NF1 only) and using SureSelect (Agilent - NF1 and SPRED1).

  Study EGAS00001005530

• Understanding_hematopoietic_stem_cell_mobilization_and_engraftment_

  This study looks at patients undergoing gene therapy for genetic blood and immune disorders, in particular sickle cell disease. From each patient, single blood HSPC colonies are grown from patient blood mononuclear cells, bone marrow mononuclear cells, or CD34+ at multiple time points: pre gene transduction, post-transduction, and post-infusion (at several time points). Whole-genome sequencing will be performed on DNA from these colonies and somatically-acquired mutations will be called. Using these mutations, a phylogeny of these cells can be inferred and further inferences can be made about the gene therapy transduction and engraftment steps.

  Study EGAS00001004620

• Human Developmental Biology Resource (HDBR) abnormal fetal samples

  The HDBR (www.hdbr.org) is a human embryonic and fetal tissue bank supplying registered researchers with access to these valuable research materials up to 22 weeks post-conception (PMC4640175). All of the samples collected are analysed for chromosomal abnormalities, and all samples with an abnormal phenotype are either analysed by SNP array, or exome sequenced. This dataset is generated from those abnormal samples that have been analysed by exome sequencing. To request access to this dataset, or if any researcher is interested in obtaining tissue from any of the samples HDBR collect, please email enquiries@hdbr.org.

  Study EGAS00001006300

• Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes

  Non-small cell lung cancer (NSCLC) is the leading cause of cancer deaths worldwide. Only a fraction of NSCLC harbour actionable driver mutations and there is an urgent need for patient-derived model systems that will enable the development of new targeted therapies. NSCLC and other cancers display profound proteome remodelling compared to normal tissue that is not predicted by DNA or RNA analyses. We generated NSCLC patient-derived xenografts (PDXs) that recapitulate the histology and molecular features of primary NSCLC. Here, we completed whole exome sequencing on 122 NSCLC PDXs.

  Study EGAS00001006068

• NOTCH-mutations drive immune-escape mechanisms in B cell malignancies

  Here we provide access to MCL expression data that were used for interrogating the molecular functions of NOTCH1 and NOTCH2, which are two of the most commonly mutated genes in CLL and MCL and associated with a poor clinical outcome. The mechanisms underlying how NOTCH1 contributes to disease progression, resistance to treatment and Richter’s transformation remain largely unknown. The main goal of this study is to compare the gene expression profile of primary MCL cells transduced with the intracellular part of NOTCH1 or NOTCH2 lacking of the PEST domain vs cells transduced with an empty vector.

  Study EGAS00001005793

• Discovery and capture of novel dynamic DNA methylation in human sperm with preferential links to altered folate metabolism

  The sperm DNA methylation landscape is unique and critical for offspring health. If gamete-derived DNA methylation escapes reprogramming in early embryos, epigenetic defects in sperm may be transmitted to the next generation. Current techniques to assess sperm DNA methylation show bias towards CpG dense regions and do not target areas of dynamic methylation, those predicted to be environmentally sensitive and tunable regulatory elements. Thus, this study aim to assess variation in human sperm DNA methylation and design a targeted capture panel to interrogate the human sperm methylome.

  Study EGAS00001003617

• scRNA-seq of patient-derived PDAC organoids and matched CAFs

  We established direct three-dimensional (3D) co-cultures of primary PDAC organoids and patient-matched CAFs. Single-cell RNA sequencing was performed for three organoid/CAF pairs in mono- and co-culture to uncover transcriptional changes induced by tumor-stroma interaction. Single-cell RNA sequencing data evidenced induction of a pro-inflammatory phenotype in CAFs in co-cultures. Organoids showed increased expression of genes associated with epithelial-to-mesenchymal transition (EMT) in co-cultures and several potential receptor-ligand interactions related to EMT were identified, supporting a key role of CAF-driven induction of EMT in PDAC chemoresistance.

  Study EGAS00001006661

• Measurement of SARS-CoV-2 variants fraction in infected alveolar cells

  With the continuous emergence of highly transmissible SARS-CoV-2 variants, the comparison of their infectivity has become a critical issue for public health. However, a direct assessment of the viral characteristic has been challenging due to the lack of appropriate experimental models and efficient methods. Here, we conducted full-length transcriptome sequencing of single human alveolar cells infected by multiple SARS-CoV-2 variants, including GR (B.1.1.119), Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (BA.1). Using unique mutations of each VOC, we calculated the fraction of VOCs in infected cells.

  Study EGAS00001006730

• Organ_maturation_in_preparation_for_birth__Peds_RFA__to_develop_a_tissue__resource_and_a_single_cell_atlas_of_organ_development_and_maturation_for__dissemination_among_the_scientific_and_clinical_community__RNA

  Knowledge about abnormal organ development is important to understand pathology and to develop novel treatment approaches for individuals with congenital and acquired disease. Most of our current understanding is based on examination of tissues from the embryo and early foetus, collected from women undergoing termination of pregnancy in the first trimester (third) of pregnancy. There is very little known about normal and abnormal organ development from a developmental perspective during the crucial last two-thirds of pregnancy when much remodelling of foetal tissues occurs. This study will generate a single-cell atlas of late-foetal lungs, blood, heart, bone and immune organs.

  Study EGAS00001008256

• Targeted myeloid panel DNA-Sequencing Mutations Matrix Validation Cohort

  Profiling of co-mutations was done by targeted resequencing using the TruSight Myeloid assay (Illumina, Chesterford, UK) covering 54 genes recurrently mutated in AML: BCOR, BCORL1, CDKN2A, CEBPA, CUX1, DNMT3A, ETV6, EZH2, IKZF1, KDM6A, PHF6, RAD21, RUNX1, STAG2, ZRSR2, ABL1, ASXL1, ATRX, BRAF, CALR, CBL, CBLB, CBLC, CDKN2A, CSF3R, FBXW7, FLT3, GATA1, GATA2, GNAS, HRAS, IDH1, IDH2, JAK2, JAK3, KIT, KRAS, MLL, MPL, MYD88, NOTCH1, NPM1, NRAS, PDGFRA, PTEN, PTPN11, SETBP1, SF3B1, SMC1A, SMC3, SRSF2, TET2, TP53, U2AF1 and WT1. For each reaction, 50 ng of genomic DNA was used. Library preparation was done as recommended by the manufacturer (TruSight Myeloid Sequencing Panel Reference Guide 15054779 v02, Illumina). Samples were sequenced paired-end (150 bp PE) on NextSeq- (Illumina) or (300 bp PE) MiSeq-NGS platforms, with a median coverage of 3076 reads (range 824–30565). Sequence data alignment of demultiplexed FastQ files, variant calling and filtering was done using the Sequence Pilot software package (JSI medical systems GmbH, Ettenheim, Germany) with default settings and a 5% variant allele frequency (VAF) mutation calling cut-off. Human genome build HG19 was used as reference genome for mapping algorithms.

  Dataset EGAD00001008506

• Dataset for the Pearl study

  Biomarkers to identify patients without benefit from adding everolimus to endocrine treatment in metastatic breast cancer (MBC) are needed. We report the results of the Pearl trial conducted in five Belgian centers assessing 18F-FDG-PET/CT non-response (n=45) and ctDNA detection (n=46) after 14 days of exemestane-everolimus (EXE-EVE) to identify MBC patients who will not benefit. Metabolic non-response rate was 66.6%. Median PFS in non-responding patients (using as cut-off 25% for SUVmax decrease) was 3.1 months compared to 6.0 months in those showing response (HR: 0.77, 95% CI: 0.40-1.50, p=0.44). Difference was significant when using a “post-hoc” cut-off of 15% (PFS 2.2 months vs 6.4 months). ctDNA detection at D14 was associated with PFS: 2.1 months vs 5.0 months (HR-2.5, 95% CI: 1.3-5.0, p=0.012). Detection of ctDNA and/or the absence of 18F-FDG-PET/CT response after 14 days of EXE-EVE identifies patients with a low probability of benefiting from treatment. Independent validation is needed.

  Dataset EGAD00001007979

• Upper cortical layer-driven network impairment in schizophrenia - 10x genomics v3 snRNA-seq and Visium spatial transcriptomics datasets

  This dataset contains 10x Genomics v3 3’ single nuclei RNA sequencing (24 human schizophrenia and control samples) and 10x Genomics Visium spatial transcriptomics (14 human schizophrenia and control samples) datasets. Files are in .bam format, output of the cellranger v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.1/using/count) for snRNA-seq and spaceranger v1.1.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/1.1/using/count) for Visium samples. Reads were mapped against Release 97 of human genome from Ensembl (http://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz http://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz). More details on sample processing are available in the biorXiv pre-print (https://doi.org/10.1101/2020.11.17.386458) and upcoming publication in Science Advances. BAM files can be converted to fastq files using bamtofastq tool (https://support.10xgenomics.com/docs/bamtofastq) with downstream remapping using tools and genomes of choice.

  Dataset EGAD00001009173