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• whole-genome sequencing of gastric cancer

  Gastric cancer is one of the most common cancers. Genome-wide analysis of genomic signatures might reveal novel mechanisms for gastric cancer tumorigenesis. Here, we analyzed structural variations and mutational signatures via whole-genome sequencing of 168 gastric cancer samples. Our data demonstrates diverse models of complex structural variations operative in GC, which lead to high-level amplification of oncogenes.

  Study EGAS00001003512

• Chronic myelomonocytic leukemia

  Chronic myelomonocytic leukemia is an aggressive hematological malignancy with dismal outcomes, with the pCMML subtype in particular having median OS of <2 years and high rates of AML transformation (Patnaik et al., 2014). Given limited therapeutic options for affected patients, we carried out this study to define the genetic and epigenetic landscape of pCMML and identify therapies that could modify disease biology.

  Study EGAS00001005107

• Targeted sequencing of paired tumour/blood of 78 Ta stage bladder cancer patients

  In continuation of our whole-exome and targeted sequencing study on non-muscle-invasive bladder cancer, we carried out this targeted paired tumour/blood sequencing study including 78 Ta stage bladder cancer patients. Agilent’s SureDesign tool was used to design a 1.133 Mb SureSelect custom capture for all coding exons of the 140 selected candidate genes.

  Study EGAS00001005766

• Finding structural variation and functional consequences from the primary leukemia cells (CLL) at the single-cell level

  In this study, we aimed to identify somatic structural variation of chronic lymphocytic leukemia (CLL) at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of primary leukemia samples from 63-year-old female patient.

  Study EGAS00001004925

• Genomic and epigenomic study of Japanese renal cell carcinoma including WGS, RNA-seq, ATAC-seq, and methyl-seq

  We performed whole-genomic and transcriptomic sequencing of more than 100 Japanese renal cell carcinoma (RCC) cases, including clear cell RCC, papillary RCC, chromophobe RCC, and TFE3-translocated RCC. In addition, we conducted epigenome sequencing analyses: the assay for transposase-accessible chromatin sequencing (ATAC-seq) and enzymatic methyl sequencing.

  Study EGAS00001006919

• Targeted_sequencing_of_blood_DNA_from_Human_twins (2019-05-31)

  The goals of this study is to investigate the prevalence and heritability of age-related clonal haemopoeisis (ARCH) in healthy elderly individuals.We will use a bespoke bait set to pull down DNA regions of interest in whole blood samples combined with HiSeq at a deep level . By correlating findings from each individual to their respective twin we hope to elucidate whether heritable traits influence the development of ARCH. a. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ . This dataset contains all the data available for this study on 2019-05-31.

  Dataset EGAD00001005055

• Single cell RNA sequencing data in "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2"

  This dataset includes a total of 5 single cell RNA sequencing (scRNAseq) data of SARS-CoV-2 infected human alveolar stem cell culture models. Two scRNAseq data were obtained from SARS-CoV-2 infection with MOI of 1.0 (1 for control and 1 for infected case) and the other three were obtained from SARS-CoV-2 infection with MOI of 0.1 in the study entitled "Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2". The 10x Chromium Single Cell 3' Reagent kits were used to generate libraries.

  Dataset EGAD00001006242

• TS and WGS data

  The dataset contains the targeted sequencing (TS) and the whole genome low pass (WGS) BAM files of the study. For the TS: Samples: TS_XXX There are normal and tumor DNA samples. Each DNA strand has been sequenced independently (PoolA and PoolB). A TruSeq Custom Amplicon panel of 20 genes frequently mutated in ILC and/or ER-positive BC in general was designed using DesignStudio from Illumina: AKT1, ARID1A, CDH1, ERBB2, ERBB3, ESR1, FOXA1, GATA3, IGF1R, JAK2, MAP2K4, MAP3K1, NF1, PIK3CA, PTEN, RB1, RUNX1, STAT3, TBX3, and, TP53. For the WGS: Samples: WGS_XXX There are normal and tumor DNA samples. Samples were sequenced to an average target coverage of 0.5X.

  Dataset EGAD00001006393

• Longitudinal Studies of Brain Structure and Function in MPS Disorders

  Mucopolysaccharidosis (MPS) types I, II, IV, VI and VII, are inherited diseases that result from the bodies inability to break down large sugar molecules that are by-products of metabolism. MPS affects most organs of the body and causes abnormalities in the liver, spleen, bones, and brain. We are studying the central nervous system (primarily the brain) so we can better understand the nature of the problems individuals with MPS I, II, IV, VI and VII have so we can find ways of better treating these problems. We would like to find out about the changes in the brain of individuals with MPS I, II, IV, VI and VII using data from MRI and neuropsychological tests. This is a longitudinal study so patients who enroll will need to be seen 3 times over 5 years. The longitudinal nature of the study allows us to make conclusions about how changes in some structures of the brain and changes in cognitive ability are related. The research objectives are: To identify abnormalities of brain (and central nervous system) structure and function in patients with MPS I, II, IV, VI and VII, regardless of how they are being treated or have been treated in the past; and to track disease progression over time. To examine the degree to which independent variables (e.g., age at first treatment, severity of disease, types of medical abnormalities, mutation, medical events, and sensory abnormalities) have an impact on both functional and structural outcomes as well as on quality-of-life. To identify, through longitudinal study, those measures that most accurately reflect the current disease state. This is a longitudinal study of 75-100 individuals with either MPS I, II, IV, VI and VII. Those participating in the study will be evaluated 3 times over 5 years. The primary site for this study is the University of Minnesota but there are an additional 6 centers in the United States and Canada that are also participating and will provide data for analysis. You will need to be able to travel to Minnesota or one of the participating centers in order to be a part of this study.

  Study phs001328

• Angelman, Rett, Prader-Willi Syndromes Consortium (ARP) Angelman Syndrome Natural History Protocol

  This study is a longitudinal multidisciplinary investigation on the natural history, morbidity and mortality of Angelman Syndrome (AS). We will collect detailed longitudinal data on a cohort of AS individuals to gain a better understanding of the disease progression, and to follow the natural history of the clinical features of this cohort including assessment of quality of life and longevity. The participants to be recruited for the study will include 1) patients who have a documented molecular diagnosis of AS and 2) patients with a clear clinical diagnosis of Angelman Syndrome as determined by the Principal Investigator (PI) and the Co-investigators in this study but who do not have a known molecular defect. One of the goals of the natural history study will be to characterize the phenotypic differences between patients with Class I deletions and those with Class II deletions, particularly with respect to the issue of autism. A blood sample may be collected on the participants in order to create a DNA repository, and in some cases, to establish cell lines if further material is required for molecular studies. Alternatively, DNA may be obtained by buccal mucosa swabs/brushing. In those AS patients with known deletions involving the 15q11-q13 regions, a blood sample will be collected to perform comparative genome hybridization (CGH) microarray studies to characterize the extent of the deletion. No drugs or treatments will be administered through this protocol. In rare instances, a skin biopsy to establish a fibroblast cell line may be requested (using separate consent).

  Study phs000576

• A Single Cell Transcriptomic Analysis of Human Neocortical Development

  Defining the number, proportion, or lineage of distinct cell types in the developing human brain is an important goal of modern brain research. We produced single cell transcriptomic profiles for 40,000 cells at mid-gestation to define deep expression profiles corresponding to all known major cell types at this developmental period and compare this with bulk tissue profiles. We identified multiple transcription factors (TFs) and co-factors expressed in specific cell types, including multiple new cell-type-specific relationships, providing an unprecedented resource for understanding human neocortical development and evolution. This includes the first single-cell characterization of human subplate neurons and subtypes of developing glutamatergic and GABAergic neurons. We also used these data to deconvolute single cell regulatory networks that connect regulatory elements and transcriptional drivers to single cell gene expression programs in the developing CNS. We characterized major developmental trajectories that tie cell cycle progression with early cell fate decisions during early neurogenesis. Remarkably, we found that differentiation occurs on a transcriptomic continuum, so that differentiating cells not only express the few key TFs that drive cell fates, but express broad, mixed cell-type transcriptomes prior to telophase. Finally, we mapped neuropsychiatric disease genes to specific cell types, implicating dysregulation of specific cell types in ASD, ID, and epilepsy, as the mechanistic underpinnings of several neurodevelopmental disorders. Together these results provide an extensive catalog of cell types in human neocortex and extend our understanding of early cortical development, human brain evolution and the cellular basis of neuropsychiatric disease.

  Study phs001836

• Decoding Human Heart Morphogenesis through Single-cell Multi-modal Analyses

  The heart, which is the first organ to develop, is highly dependent on its form to function. However, how diverse cardiac cell types spatially coordinate to create complex morphological structures critical for heart function remains to be elucidated. Here, we show that integration of single cell RNA-sequencing with high-resolution multiplexed error-robust fluorescent in situ hybridization (MERFISH) not only resolves the identity of cardiac cell types developing the human heart but also provides a spatial mapping of individual cells that enables illumination of their organization into cellular communities forming distinct cardiac structures. We discovered that many of these cardiac cell types further specified into subpopulations exclusive to specific communities, supporting their specialization according to cellular ecosystem and anatomic region. In particular, ventricular cardiomyocyte subpopulations displayed an unexpected complex laminar organization across the ventricular wall and formed, with other cell subpopulations, several cellular communities. Interrogating cell-cell interactions within these communities revealed signaling pathways orchestrating the spatial organization of cardiac cell subpopulations during ventricular wall morphogenesis. In vivo conditional genetic mouse models and in vitro human pluripotent stem cell studies confirmed an intricate multicellular PLXN-SEMA crosstalk among specific ventricular cardiomyocyte, fibroblast and endothelial cell subpopulations that directs the compaction of the ventricular wall layers. Thus, these detailed findings into the cellular social interactions and specialization of cardiac cell types constructing and remodeling the human heart offer new insights into structural heart diseases as well as engineering complex multi-cellular tissues for human heart repair. Reprinted from Farah et al. (In press), with permission from Nature.

  Study phs002031

• UK10K_NEURO_MUIR

  In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches.The sample selection consists of subjects with schizophrenia (SZ), autism, or other psychoses all with mental retardation (learning disability). The samples were initially collected under the leadership of Walter J Muir (deceased), now with Prof. Blackwood, Dr McKechanie and Prof McIntosh as custodians. These subjects represent the intersection of severe forms of neurodevelopmental disorders, appear to have a higher rate of familiality of SZ than typical, and are likely to have more serious and penetrant forms of mutations.For further information on this cohort please contact Andrew McIntosh (andrew.mcintosh@ed.ac.uk).

  Study EGAS00001000122

• Establishing stable brain tumor stem cell lines and translational research for new treatments

  Choroid plexus carcinomas (CPCs) have dismal prognoses with limited clinical options. A lack of characterized cell lines has hindered the development of new treatment strategies. Here, we perform whole genome sequencing analyses of two cell lines established from CPCs. Whole genome sequencing (WGS),was performed in CCHE-45 and NGT131 cell lines. Both cell lines harbored pathogenic TP53 point mutations; CCHE-45 additionally displayed TP53 loss. Furthermore, alterations of the NOTCH and WNT pathways were also detected in both cell lines. Two protein-coding gene fusions, BZW2-URGCP, and CTTNBP2-ERBB4, mutations of two oncodrivers, GBP-4 and KRTAP-12-2, and several copy number alterations were observed in CCHE-45, but not NGT131. The discovered difference's importance and implications highlight the possible diversity of choroid plexus carcinoma and call for additional research to fully understand disease pathogenesis. Whole genome sequencing revealed that the two choroid plexus carcinoma cell lines shared TP53 mutations and other common pathway alterations and activation of NOTCH and WNT pathways. Noticeable differences were also observed. These cell lines can serve as valuable models to propose new treatments in these rare but deadly brain tumors.

  Study JGAS000657

• Investigation of molecular diagnosis by molecular biological analysis using next-generation sequencer for actionable endocrine diseases (including neoplastic diseases)

  Fructose-1,6-bisphosphatase (FBPase) deficiency, caused by an FBP1 mutation, is an autosomal recessive disorder characterized by hypoglycemic lactic acidosis. Due to the rarity of FBPase deficiency, the mechanism by which the mutations cause enzyme activity loss still remains unclear. Here we identify compound heterozygous missense mutations of FBP1, c.491G>A (p.G164D) and c.581T>C (p.F194S), in an adult patient with hypoglycemic lactic acidosis. The G164D and F194S FBP1 mutants exhibit decreased FBP1 protein expression and a loss of FBPase enzyme activity. The biochemical phenotypes of all previously reported FBP1 missense mutations in addition to G164D and F194S are classified into three functional categories. Type 1 mutations are located at pivotal residues in enzyme activity motifs and have no effects on protein expression. Type 2 mutations structurally cluster around the substrate binding pocket and are associated with decreased protein expression due to protein misfolding. Type 3 mutations are likely nonpathogenic. These findings demonstrate a key role of protein misfolding in mediating the pathogenesis of FBPase deficiency, particularly for Type 2 mutations. This study provides important insights that certain patients with Type 2 mutations may respond to chaperone molecules.

  Study JGAS000625

• Patient-derived organoids as predictive models for drug testing and repurposing in glioblastoma therapy

  Glioblastoma multiforme (GBM) remains a highly aggressive brain tumor with limited treatment options and poor prognosis. Temozolomide (TMZ) is the only approved first-line therapy, but frequent resistance limits its efficacy, highlighting the urgent need for alternative treatments. Patient-derived glioblastoma organoids (GBOs) offer a promising preclinical model for personalized drug testing and therapy development.

  Study EGAS50000001221

• RNA004 DRS METTL5 variant of patient sample

  This dataset contains RNA004 DRS data for a single patient sample with heterozygous inactivating SNPs for the methyltransferase METTL5. We provide 1) all reads in a GRCh38 aligned bam file + unaligned reads and 2) filtered reads just for the relevant part of chrR. Both bam files have been called with dorado 0.7.2 to contain the neccessary m6A methylation information. Companion datasets are 1) EGAS50000001201 for DRS of a healthy control with intact METTL5 and 2) PRJEB74238 for IVT 18S rRNA vector data as unmodified control. Please note, that both the companion datasets contain pod5 data, to faciliate re-basecalling.

  Dataset EGAD50000001882

• Capture-based Methods for Transcriptomic Profiling of FFPE material

  This dataset includes all FASTQ files for 11 samples where different capture-based methods for transcriptome profiling have been tested. Specifically, we have the 'traditional' RNA-seq experiment with fresh frozen (FF) material, and 3 different capture methods for the matching formalin-fixed paraffin-embedded samples: Agilent (AGI), IDT, and Twist Biosciences (TBS). In total, there are 43 samples with paired-end FASTQ files (1 sample did not have sufficient material to test all methods). Samples are identified by the R01-R11 IDs with a suffix that indicates the capture method used (or FF for fresh frozen).

  Dataset EGAD00001007655

• Regulatory and Effector T cells in Oral Immunotherapy for Food Allergy

  This study consisted of a clinical trial for peanut oral immunotherapy (OIT) and a follow-up project (see below). Patients were included from 2013-2015, and samples from the last timepoints were collected in 2017. The study focused on peanut-specific CD4+ T cell responses before, during, and after OIT with peanut protein. We analyzed T cell gene expression, cytokine production, and T cell receptor β (TCRβ) and TCRα clonotypes, both in bulk T cell populations and single cells, and sought to correlate these data with differences in clinical sensitivity between peanut-allergic patients before OIT, and with differences in clinical outcome after OIT. The goal was to better understand the role of peanut-specific effector and regulatory T cells in peanut allergy and tolerance, which may inform more effective therapies (e.g., OIT combined with biologicals, probiotics, or adjuvants) in the future. Tolerance Following Peanut Oral Immunotherapy (PNOIT2, NCT01750879): The unifying objective of this project is to determine whether peanut oral immunotherapy (PNOIT)-induced clinical tolerance in the context of food allergy is significantly associated with the expansion of a specific regulatory T cell subset (CD45RA-, CD25++, FoxP3+ +) that is thought to be inducible in the gut-associated lymphoid compartment and associated with immunological tolerance. The hypothesis of the study is that the induction of Treg cells will be associated with clinical tolerance. The investigators will measure the change from baseline of induced Treg cells as a frequency of total CD4+ T cells during active treatment and compare that between participants who achieve significant clinical tolerance and those who do not. High Threshold Peanut Challenge Study (PAID-UP, NCT02698033): This protocol was designed to better characterize a sub-population of peanut-sensitized individuals who may be non-allergic, despite significant sensitization, or who may be allergic, but at high threshold doses. By specifically targeting participants who met the initial screening criteria of an earlier study, NCT01750879, but failed to react during the pre-treatment 443 mg challenge to peanut, the investigators anticipate that they will identify individuals who have become spontaneously tolerant, despite persistent sensitization. The investigators might also find that clinical sensitivity persists but only with higher thresholds, or that sensitivity has increased (or is variable) since the previous allergen exposure. By repeating food challenges through to a full serving dose (7.4 gram), the investigators will distinguish participants who react only at higher doses from those who were not truly peanut-allergic, address whether their sensitivity has changed, and have the opportunity to further investigate their immune response to peanut allergen. Methods: Peripheral blood mononuclear cells were isolated from patient blood samples, and stimulated with peanut protein. Peanut-activated CD4+ T cells were sorted based on the activation marker CD154. For a more recent study, the activation marker CD137 was used as well. Total RNA from peanut-activated CD154+ and resting CD154- CD69- T cells was used for cDNA synthesis and amplification (SMARTer ultra low input RNA kit for sequencing - v3; Clontech Laboratories). Libraries were prepared and sequenced on the Illumina HiSeq platform, at a read depth of approximately 30 million reads per sample. Genomic DNA from CD154+ and CD154- CD69- T cells was used to amplify and sequence the TCRβ CDR3 regions (immunoSEQ assay; Adaptive Biotechnologies). The immunoSEQ approach generates an 87 base-pair fragment capable of identifying the VDJ region spanning each unique CDR3. Amplicons were sequenced using the Illumina NextSeq platform. Using a baseline developed from a suite of synthetic templates, primer concentrations and computational corrections were used to correct for the primer bias common to multiplex PCR reactions. Raw sequence data were filtered on the basis of TCRβ V, D, and J gene definitions provided by the IMGT database (www.imgt.org) and binned using a modified nearest-neighbor algorithm to merge closely related sequences and remove both PCR and sequencing errors. For single-cell analysis, we aimed to recover TCR variable sequences from high-throughput single-cell libraries generated by popular platforms such as SeqWell and DropSeq. We paired TCR information with T cell single-cell RNA sequencing results from patients undergoing peanut OIT to show clonal expansion-related T cell phenotypes.

  Study phs001897

• A Phenotypic and Genomics Approach in a Multi-Ethnic Cohort to Subtype Systemic Lupus Erythematosus

  Systemic lupus erythematosus (SLE) is a complex autoimmune disease that affects multiple organ systems and varies in severity across different populations. To examine the clinical heterogeneity of SLE, we sought to identify different lupus subtypes within our multi-ethnic cohort using a clustering approach. Additionally, with genome-wide methylation and genotype data generated for our cohort, we applied integrative methods to investigate genetic and epigenetic risk factors. This integrative and computational approach revealed molecular differences associated with phenotypic clusters.

  Study phs001850

• L1 Retrotransposon Sequencing in Schizophrenia - Study 1

  Schizophrenia (SZ) is a devastating psychiatric disorder with substantial global clinical and economic implications. While SZ is marked by high heritability, discovery of common variants associated with even moderate risk for SZ has proven difficult. We used Restriction Enzyme Based Enriched L1 sequencing (REBELseq) to amplify L1 retrotransposons in gDNA isolated from dorsolateral prefrontal cortex NeuN+ neuronal nuclei from 63 SZ cases and 63 controls. Amplified libraries were sequenced on the Illumina HiSeq 4000 platform, and sequencing data was analyzed with the REBELseq bioinformatics pipeline.

  Study phs001968

• Studies of L1-mediated Pseudogene Formation in Human HeLa Cells

  Alu elements mobilize from one genomic location to another by a "copy-and-paste" mechanism known as retrotransposition, which requires the human Long INterspersed Element-1 (LINE-1 or L1) ORF2-encoded protein (ORF2p); however, little is known about other cellular factors required for Alu retrotransposition. Isolates of HeLa cells differ in their ability to support Alu retrotransposition. Here, we generated Illumina whole genome sequencing data derived from four HeLa isolates: HeLa-H1, HeLa-CCL2, HeLa-HA, and HeLa-JVM.

  Study phs003397

• Targeted sequencing of genomic regions of interest in depression and obesity

  This study aimed to further explore the genetic relationship between MD and obesity taking advantage of targeted sequencing strategy. Specifically, we searched for genetic risk variants across the entire frequency spectrum in flanking genomic regions and genes previously associated with MD and obesity, assessed the contribution of those variants to the pathophysiology of comorbid MD and obesity, and provided a general overview of the cellular and molecular pathways mapped by those variants when these complex diseases co-occur.

  Study EGAS50000000330

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001895

• DEPArray-based sorting of pure carcinoma and stromal populations from formalin-fixed paraffin-embedded (FFPE) tissues followed by shallow whole genome sequencing

  To overcome the challenges of low DNA yields, degraded DNA by formalin fixation and diluted signal of genomic aberrations by non-carcinoma components in the heterogeneous FFPE samples, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from 9 primary and metastatic breast cancer and 3 primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole genome sequencing (WGS) for copy number landscape profiling for 10 samples. Seven out of 10 samples (even some with low tumour content or of old age) produced good quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations.

  Dataset EGAD50000001894