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• MutWP4__CRUK_Grand_Challenge_Mutographs_of_Cancer__Mutagen_treated_organoids

  The Mutographs project aims to advance our understanding of the causes of cancer through studies of mutational signatures. Led by Mike Stratton, together with Paul Brennan, Ludmil Alexandrov, Allan Balmain, David Phillips and Peter Campbell, this large-scale international research endeavour was awarded a Cancer Research UK Grand Challenge. Different patterns of somatic mutation are generated by the different environmental, lifestyle and genetic factors that cause cancer, many of them are still unknown. Within Mutographs, Kings College London will characterise the mutational signatures induced by putative human carcinogens in order to identify the origins of mutational signatures found in human cancers. To achieve this human organoid cell cultures will be exposed to a representative catalogue of known or suspected human carcinogens and mutagens and, using whole genome sequencing, the patterns of mutations induced by them will be determined. Somatic mutational signatures will be subsequently extracted by non-negative matrix factorisation methods and correlated with exposure data. Through an enhanced understanding of cancer aetiology, Mutographs unprecedented effort is anticipated to outline modifiable risk factors, lead to new approaches to prevent cancer, and provide opportunities to empower early detection, refine high-risk groups and contribute to further therapeutic development.

  Study EGAS00001004873

• Study of Melanoma Risk in Australia and the United Kingdom

  The results from a small number of melanoma GWAS have been published. Initial studies identified several pigmentation- and nevus-associated loci that mediate an effect on melanoma risk, however, these studies were somewhat limited in that sample number (hence power) was low, they used first-generation low density SNP arrays, or used pools of DNA samples. Subsequently, additional melanoma GWAS have been completed, including a "Phase 2" study by the International Melanoma Genetics Consortium (GenoMEL), a full GWAS of the Australian sample resource previously used in a pooled-DNA GWAS, and study conducted through the MD Anderson Cancer Center and the Brigham and Women's Hospital. The groups who performed these studies have recently shared data and replicated a number of new melanoma susceptibility loci. Aside from the identification of novel loci, there are two additional notable outcomes of these studies. Firstly, an examination of the observed versus expected test statistics (Q-Q plot) from the Australian study, even after removing data from SNPs within known replicated susceptibility loci, reveals that there remains an excess of positive results. Similarly, the latest GenoMEL study finds almost three times as many SNPs reaching p-values between 10-4 and 10-5 as would be expected by chance. In the light of other studies of complex traits [1], these data suggest that studies based on additional melanoma samples from the same population are likely to identify an even larger "polygenic tail" and should prove invaluable in identifying and characterizing the underlying loci. A second observation, is that the effect size for replicated associations differs very little between GWAS. Given the strong effect of ultraviolet radiation (UVR) on risk of melanoma this might be expected to affect penetrance, particularly in the Australian and English samples, which are ethnically similar, but have very different sun exposures. We hypothesize that those SNPs whose effects are strongly mediated by UVR exposure may have smaller marginal effects on risk and are therefore harder to detect initially, suggesting a whole category of genetic effects that are unexplored.Indeed, most melanoma GWAS performed to date used samples from both European and Australian populations in discovery and or replication, and thus, existing studies have been poorly powered to detect associations with a wide difference in effect between these low- and high-UVR populations. Here, we wish to pursue this hypothesis further and plan to genotype additional cases drawn from the English and Australian populations. This will serve two complementary objectives: firstly, it will greatly increase our collective power to detect additional new melanoma risk alleles; secondly, it will highlight associations that are stronger specifically within the context of either low-UVR or high-UVR exposure environments. We posit that these data will be invaluable, not just for identifying novel melanoma-associated loci, but also for addressing gene-environment interactions. We have available a collection of valuable resources to help fulfill our aims. These include a considerable number of well-characterized and ungenotyped Australian and UK melanoma cases, as well as existing genotype data from sets of Australian and UK cases and population-based controls. We propose the following Specific Aims: To extend our current collective melanoma GWAS by genotyping a large number of additional UK and Australian cases. To jointly analyze these data and identify new melanoma risk loci. To determine whether pre-existing and new melanoma risk alleles show different degrees of association between the English and Australian populations, and assess whether these differences might be due to differences in sunlight exposure.

  Study phs000519

• Single Cell and Spatial Transcriptomic Profiling of Haemophilus ducreyi Infection

  We investigated the immune response in end-point pustules formed by Haemophilus ducreyi in volunteers using an experimental infection model. Six volunteers were infected in the skin of the upper arm at three sites with 41-85 CFU of H. ducreyi loaded on an allergy testing device; a sham-inoculated (e.g., wound) site was also performed. Five volunteers (4 men and 1 woman; 2 Asians and 3 Whites; aged 27-46 years) formed pustules 6-8 days post infection; 1 volunteer spontaneously resolved all sites. If a volunteer formed pustules, biopsies were performed to collect their pustule and wound sites. Biopsy pairs for all 5 pustule formers were subjected to single cell (sc) RNA-seq. Sequencing libraries were prepared using the 10X Genomics Single-cell 3' RNA-seq kit. Spatial transcriptomics was performed on biopsy pairs from 4 of the 5 pustule formers. Ten micron sections were placed on 10X Genomics Visium slides for fresh-frozen tissue, and libraries were prepared with the 10X Genomics Visium spatial 3' gene expression kit. All samples were sequenced on an Illumina NovaSeq 6000. Count tables were produced with CellRanger and SpaceRanger, respectively, and Seurat was used to analyze the data. We identified 13 major cell types by scRNA-seq; the proportion of some immune cell subsets was increased in pustules compared to wound sites. We also localized the major cell types within the tissue by using the scRNA-seq data to deconvolve the spatial transcriptomic data. The FASTQ files and count tables from CellRanger and SpaceRanger are provided.

  Study phs003754

• Genome-wide Ancestry and Demographic History of African-Descendant Maroon Communities from French Guiana and Surname.

  The transatlantic slave trade (TAST) was the largest forced migration in world history. However, the origins of the enslaved Africans and their admixture dynamics remain unclear. To investigate the demographic history of African-descendant Marron populations, we generated genome-wide SNP data (4.3 million markers) from 107 individuals from three African-descendant populations in South America, as well as 124 individuals from six west African populations to complement underrepresented African data sets. Our study sheds additional light on the demographic consequences of the TAST and illustrates how genetic data can complement historical sources.

  Study EGAS00001002535

• Risk Factors for Asymptomatic Diverticulosis

  Data for this analysis came from a prospective study of colonic diverticulosis at the University of North Carolina Hospital in Chapel Hill, North Carolina (NIH R01DK094738). This is a case-control genetic and transcriptomic study to identify the genetic and cellular determinants underlying colonic diverticulosis and the relationship with other gastrointestinal disorders. The study inclusion and exclusion are described below. DNA and RNA sequencing were performed on colonic tissue from 404 patients with (N=172) and without (N=232) diverticulosis. We assessed variation in the transcriptome associated with diverticulosis and integrated this variation with human intestine single-cell RNA-seq data. We integrated our expression quantitative trait loci with GWAS using Mendelian Randomization. A polygenic risk score analysis examined associations between severity of diverticulosis and other gastrointestinal disorders. We identified 38 genes with differential expression and 17 genes with varied transcript usage linked to diverticulosis. Our results suggest tissue remodeling as a primary mechanism for diverticula formation. The presence of diverticulosis was linked to stromal and epithelial cells in the colon including endothelial cells, myofibroblasts, fibroblasts, goblet, tuft, enterocytes, neurons, and glia. MR highlighted five genes including CCN3, CRISPLD2, ENTPD7, PHGR1, and TNFSF13. In diverticulosis cases, ENTPD7 upregulation was confirmed. A greater burden of diverticula was positively correlated with genetic predisposition to diverticulitis. The data related to the study including total RNA-Seq, SNP array and imputed genotypes will be available through dbGaP.

  Study phs003556

• Chordoma_Sequencing_Project_RNAseq

  This is a continuation of the Chordoma Sequencing Project. All cancers arise due to somatically acquired abnormalities in DNA sequence. Systematic sequencing of cancer genomes allows acquisition of complete catalogues of all classes of somatic mutation present in cancer. These mutation catalogues will allow identification of the somatically mutated cancer genes that are operative and characterise patterns of somatic mutation that may reflect previous exogenous and endogenous mutagenic exposures. In this application, we aim to perform whole genome sequencing on 10 chordoma matched genome pairs. RNA Sequencing/Methylation and SNP6 and an additional sequencing of three cancer cell lines will be added to this work.

  Study EGAS00001000410

• Disease and phenotype relevant genetic variants identified from histone acetylomes in human hearts

  Identifying genetic markers for heterogeneous complex diseases such as heart failure has been challenging, and may require prohibitively large cohort sizes in genome-wide association studies (GWAS) in order to demonstrate statistical significance1. On the other hand, chromatin quantitative trait loci (QTL), elucidated by direct epigenetic profiling of specific human tissues, may contribute towards prioritising variants for disease-association. Here, we captured non-coding genetic variants by performing enhancer H3K27ac ChIP-seq in 70 human control and end-stage failing hearts, mapping out a comprehensive catalogue of 47,321 putative human heart enhancers. 3,897 differential acetylation peaks (FDR < 0.05) pointed to recognizable pathways altered in heart failure (HF). To identify cardiac histone acetylation QTLs (haQTLs), we regressed out confounding factors including HF disease status, and employed the G-SCI test2 to call out 1,680 haQTLs (FDR < 0.1). A subset of these showed significant association to gene expression, either in cis (180), or through long range interactions (81), identified by Hi-C and Hi-ChIP performed on a subset of hearts. Furthermore, a concordant relationship was found between the gain or disruption of specific transcription factor (TF) binding motifs, inferred from alternative alleles at the haQTLs, associated with altered H3K27ac peak heights. Finally, colocalisation of our haQTLs with heart-related GWAS datasets allowed us to identify 62 unique loci. Disease-association for these new loci may indeed be mediated through modification of H3K27-acetylation enrichment and their corresponding gene expression differences.

  Study EGAS00001003586

• Therapeutic Targeting of ATR Yields Durable Regressions in High Replication Stress Tumors

  Patients with relapsed or recurrent small cell lung cancer or extra-pulmonary small cell cancers were enrolled on an investigator-initiated, single-arm, phase 2 trial (NCT02487095) combining an ATR inhibitor M6620 (VX-970, berzosertib) administered at 210 mg/m2 intravenously over 60 minutes on day 2 and day 5, and topotecan 1.25 mg/m2 intravenously over 30 minutes every 23 hours on days 1 through 5, with a support of pegfilgrastim 6mg subcutaneously on day 6 in 21-day cycles. Tumor samples were collected either just before starting the treatment or before starting treatment prior to be enrolled in the trial. Whole exome and RNA were sequenced to evaluate genomic and transcriptomic characteristics associated with the response to the combination treatment.

  Study phs002327

• EGA submission account terms

  Submission account terms Each EGA submission account has a dedicated submission box. To ensure continued service to all submitters EGA submission boxes should not exceed 8Tb in size, and cannot exceed 12Tb. Those that are near to or exceeding this value will be monitored on a weekly basis by the helpdesk team and the submitter will be contacted and guidance provided accordingly on completing their metadata registration. You will be able to register your metadata associated with the files in your submission account via EGA Submitter Portal, Webin or the EGA REST API. EGA also requests that metadata is submitted within 60 days of upload data to a submission box. When we detect files that are over 60 days old in a submission box we will notify the submitter requesting that metadata be submitted or the files removed from the submission box. It is important to note that data is not archived at the EGA until the metadata describing the files has been associated and the archival process has completed. It is only when associated metadata has been submitted that the archival process into EGA is fully triggered. EGA removes files from the submission box once they have been successfully archived, so no action is required by a submitter to remove successfully archived files. Files over 90 days old will be deleted from the submission box unless EGA Helpdesk has been contacted and confirmed an exemption with the submitter.

  Documentation submission/terms

• NHLBI TOPMed: Defining the Time-Dependent Genetic and Transcriptomic Responses to Cardiac Injury Among Patients with Arrhythmias

  The UMMS miRhythm Study is an ongoing study of adult patients undergoing an elective electrophysiology study or arrhythmia ablation procedure for a supraventricular or ventricular arrhythmia, including atrial fibrillation (AF). Atrial fibrillation is a major clinical and public health problem that is related to atrial pathologic remodeling. Few tools are available to quantify the activity or extent of this remodeling, rendering it difficult to identify individuals at risk for AF. Previous studies have suggested an important role for miRNA in cardiovascular disease through gene expression regulation, making this a promising avenue for studying AF mechanisms. The aim of the study is to determine the time-dependent changes to key circulating miRNAs in a model of planned atrial injury and remodeling via ablation. Such knowledge might provide additional insight into the biology and activity of the acute atrial injury response, and furthermore, inform new targets for development of preventative interventions or allow for better AF risk stratification. To assess pathways regulating atrial pathological remodeling, patient blood samples are collected prior to their ablation procedures and also at a regularly scheduled 1-month follow-up appointment. Plasma expression of miRNA is measured using high-throughput quantitative reverse transcriptase polymerase chain reaction (RT-qPCR), providing novel insights into the regulatory processes underlying AF, as well as acute atrial injury in vivo. Additionally, data collected from whole-genome sequencing (WGS) is used to supplement miRNA analyses and further explore new relations between genes and abnormal heart rhythm.

  Study phs001434

• Effective screening strategy for deafness using a new-genetation sequencing platform: a consecutive analysis

  The diagnosis of the genetic etiology of deafness contributes to the clinical management of patients. We performed the following four genetic tests in three stages for 52 consecutive deafness subjects in one facility. We used the Invade assay and Sanger sequencing for the GJB2 gene or SLC26A4 gene in the first stage test, TaqMan genotyping assay in second stage test, and targeted exon sequencing using the massively parallel DNA sequencing in third stage test. Overall, we identified the genetic cause in 40% (21/52) of patients. The diagnostic rates of the first-, second- and third-stage genetic testing were 17%(9/52), 9%(4/43) and 21% (8/39), respectively. The combination approach using these genetic tests appears to be useful as a diagnostic tool for deafness patients. We recommended that genetic testing for the screening of common mutations in deafness genes using the Invader assay or TaqMan genotyping assay be performed as the initial evaluation. For the remaining undiagnosed cases, targeted exon sequencing using MPS is clinically and economically beneficial. This data set was MPS reads data (fastq) for 39 sensorineural hearing loss patients.

  Study JGAS000032

• Hematopoietic Cell Transplant for Sickle Cell Disease (HCT for SCD)

  The Center for International Blood and Marrow Transplant Research (CIBMTR) is a hematopoietic cell transplant registry that was established in 1972 at the Medical College of Wisconsin. The overarching goal of the registry is to study trends in transplantations and to advance the understanding and application of allogeneic hematopoietic cell transplantation for malignant and non-malignant diseases. Included in this dataset are children, adolescents and young adults with severe sickle cell disease who received an allogeneic hematopoietic cell transplant in the United States and provided written informed consent for research.Hematopoietic cell transplant for sickle cell disease is curative. Offering this treatment for patients with severe disease is challenging as only about 20-25% of patients expected to benefit have an HLA-matched sibling. Consequently, several transplantations have utilized an HLA-matched or mismatched unrelated adult donor and HLA-mismatched relative. Transplantation strategies have also evolved over time that has included transplant conditioning regimens of varying intensity, grafts other than bone marrow and novel approaches to overcome the donor-recipient histocompatibility barrier and limit graft-versus-host disease. The data that is available for sickle cell disease transplants have been utilized to report on outcomes after transplantation and compare outcomes after transplantation of grafts HLA-matched related, HLA-mismatched related, HLA-matched and HLA-mismatched unrelated donors. Collectively, these data have advanced our knowledge and understanding of hematopoietic cell transplant for this disease. These data can also serve as "contemporaneous controls" for comparison with other more recent curative treatments like gene therapy and gene editing.Data available for request include allogeneic hematopoietic cell transplants for sickle cell disease (Hb SS and Hb Sβ thalassemia) in the United States from 1991 to 2019. Follow-up data through December 2020 are available.Instructions for requesting individual-level data are available on BioData Catalyst at https://biodatacatalyst.nhlbi.nih.gov/resources/data/. Apply for data access in dbGaP. Upon approval, users may begin accessing requested data in BioData Catalyst. For questions about availability, you may contact the BioData Catalyst team at https://biodatacatalyst.nhlbi.nih.gov/contact.

  Study phs002385

• Cognitively Affected DMD Patients have Unique Methylation Signatures Compared to Cognitively Normal DMD Patients

  The overarching goal of this project was to identify changes in methylation patterns in Duchenne muscular dystrophy (DMD) patients with discordant symptoms using whole genome bisulfite sequencing (WGBS) from genomic DNA isolated from whole serum. DMD siblings (biological brothers) had the same genetic mutation in the dystrophin gene but with discordance in symptoms such as ambulation, cardiopulmonary function, and cognition. Trios (DMD sibling brothers and biological mother or father) and quartets (DMD sibling brothers and biological mother and father) were recruited for this study for intra- and inter-familial comparisons of the methylation of gene bodies.

  Study phs003118

• Initial leukemic epigenomic state determines hypomethylating agent response

  Hypomethylating agents (HMAs) are a mainstay of therapy for myeloid cancers, but genetic biomarkers do not predict who will respond to treatment. Using a variety of single-cell sequencing approaches to define the epigenomic state of responder and nonresponder leukemic cells, we aim to demonstrate that leukemic stem cells (LSC) exist in at least two different epigenomic states: a hematopoietic stem cell (HSC)-or multipotent progenitor (MPP)-like state that is sensitive to HMAs, independent of genetic mutations, or a lymphoid-primed MPP (LMPP)-like nonresponder state. Additionally, we aim to demonstrate that hypomethylation and chromatin accessibility at ZNF143- and CTCF-binding sites result in activation of HOXB4, which defines the HSC/MPP-like state and HMA-sensitivity. Our study aims to provide evidence that the epigenomic state of the LSC is a major determinant of response to HMAs, and demonstrates that a routine clinical assay can identify patients who will respond.

  Study EGAS50000000936

• The Primary Open-Angle Glaucoma Genes and Environment (GLAUGEN) Study

  Background Information: Primary open-angle glaucoma (POAG) is an age-related, intraocular pressure (IOP)-dependent progressive optic neuropathy that ultimately leads to irreversible blindness. Vision loss from POAG is a condition of public health significance. Current evidence suggests that POAG is a polygenetic disease modified by environmental influences. Despite the fact that a positive family history of disease is an important risk factor for POAG, conventional linkage and candidate gene approaches have revealed less than 5% of the genetic component of the disease. Furthermore, there is no consensus on environment risk factors for POAG. Elevated IOP is the only modifiable risk factor for POAG; yet, lowering IOP slows, but does not halt the disease process. Study Objectives: The overall goal of our research is to elucidate the pathogenesis of POAG so that cost-effective disease detection and primary prevention strategies can be implemented. The primary aim of the Glaucoma Gene Environment Initiative (GLAUGEN), funded by the Human Genome Research Institute (NHGRI), is to discover genetic loci associated with POAG. The secondary aim of GLAUGEN, funded by NHGRI and the National Eye Institute, is to discover gene environment interactions in POAG. Methods and study populations: For this study, we have assembled cases and controls from three studies: the Nurses' Health Study (NHS), the Health Professionals Follow-up Study (HPFS) and the Genetic Etiologies of POAG (GEP) project based at Massachusetts Eye and Ear Infirmary (MEEI). This case-control group includes 1057 unrelated cases and 1272 controls. Members of the NHS and HPFS also have repeated environmental exposure data collected prior to a diagnosis of POAG. NHS - The Nurses Health Study started in 1976 under the direction of Dr. Frank E. Speizer. With funding from the NIH, registered nurses from 11 US states were invited to complete a detailed questionnaire regarding lifestyle and health biennially. Initially, 121,000 women responded to the baseline questionnaire. Currently, Dr. Susan Hankinson serves as the program director for the NHS. HPFS - The Health Professionals Follow-up Study began in 1986 under the direction of Drs. Walter Willett and Meir Stampfer. Under the auspices of the NIH, they enlisted 51,529 male health professionals from throughout the US to complete similarly designed biennial questionnaires. Beginning in 1990, questions regarding ocular health were added to biennial questionaires completed by health professionals participating in the NHS and HPFS. This allowed us to formulate (PI: S. Hankinson; NEI) and maintain (PI: L. Pasquale; NEI) a cohort at risk for POAG derived from the respective general cohorts who were under ophthalmic care. We then developed a definition of POAG that allowed us to identify cases from a population that was geographically dispersed. The centerpiece of this definition is the presence of reproducible visual field loss consistent with nerve fiber layer (NFL) dropout (the NFL contains the axons that comprise the optic nerve) on reliable tests. Reproducible visual field loss occurred in the context of anterior segment findings that did not suggest a secondary cause of elevated IOP and posterior segment findings that did not suggest a secondary cause of visual field loss. We selected controls from the cohort at risk for POAG on the basis of age, gender and time period when cases were identified. GEP - The Genetic Etiologies of POAG was initiated in 1996 with funding from the National Eye Institute under the direction of Dr. Janey Wiggs. The purpose of this work was to discover novel genetic loci associated with POAG. In the GEP, cases were derived predominantly from the Glaucoma Service at MEEI. The majority of cases had an examination by a glaucoma specialist and met the definition for POAG used in NHS and HPFS. Cases with only one reliable visual field consistent with NFL dropout were included if there was a cup-disc ratio of 0.7 or more. The majority of controls were patients who presented to the MEEI comprehensive ophthalmology service for routine eye examination or from spouses of MEEI patients with secondary forms of glaucoma. Other controls were identified from regional glaucoma screenings held throughout Massachusetts. Members of GEP have detailed ocular phenotype data but limited information on environmental exposures. This study is part of the Gene Environment Association Studies initiative (GENEVA, http://www.genevastudy.org) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to primary open-angle glaucoma through large-scale genome-wide association studies of three well-characterized cohorts of cases and controls, some in matched pairs. Genotyping was performed at the Broad Institute of MIT and Harvard, a GENEVA genotyping center. Data cleaning and harmonization were performed at the GEI-funded GENEVA Coordinating Center at the University of Washington.

  Study phs000308

• NHLBI TOPMed: Trans-Omics Analysis for Congestive Heart Failure (TOPCHeF)

  Heart failure (HF) is a serious, common, morbid condition that has a huge public health impact. In 2012 alone, there were >1M hospital discharges and >1.7M outpatient visits where HF was the principal diagnosis. HF is the most common hospital discharge diagnosis of the elderly and led to costs in excess of $30B in 2012. Unfortunately, HF therapies have not impacted the 50% 5-year mortality over the past two decades. Our laboratory focuses on cardiomyopathies (CMs) and HF. Dilated cardiomyopathy (DCM) has been a main focus of our laboratory and is the first and third most frequent cause of heart transplantation and HF, respectively. Attention is shifting from the mere identification and cataloging of CM/HF genes and mutations to understanding the molecular and functional cellular processes that drive HF. In this study, we will utilize whole genome sequencing (WGS) and transcriptome analysis of left ventricle samples from adult and pediatric samples from heart banks at the University of Colorado Anschutz Medical Campus and the Children's Hospital Colorado to develop a complete understanding of left ventricular biology and a partial understanding of HF inferred through the lens of a single-chamber perspective.

  Study phs002038

• Beacon v2

  Beacon v2: a tool for data discovery Motivation In the era of data-driven health research and personalised medicine, human genomic data has become extremely valuable. These are also identifiable data, as they carry information pointing to a specific individual as well as their own family; and as such, they must be protected. This makes data discovery particularly challenging: this is where "Beacon" comes in. A "Beacon" is an API aiming to enable the search of genomic variants and associated information without jeopardising the privacy of the dataset. Here, we refer to its current version, namely version 2 (v2). Definition Beacon v2 is a term that can refer to different aspects. The EGA is playing a central role in the following aspects: The Beacon v2 protocol is a Global Alliance for Health and Genomics standard. The Beacon v2 Reference Implementation (B2RI) is an "out-of-the-box" Beacon instance developed with ELIXIR, which facilitates Beacon deployment. The EGA Beacon(s) are Beacons following the v2 standard and using the B2RI, deployed on top of data hosted at the EGA and allowing for their discovery. Resources Depending on whether you are visiting us a stakeholder (you need more general information about Beacon), a deployer /implementer (you want to have your own Beacon instance), or an EGA user (you want to query Beacon and start browsing data), you will be interested in the following resources: Your role Beacon aspect Documentation type Stakeholder Beacon v2 protocol Beacon website Beacon page on the GA4GH website Deployer/Implementer Beacon v2 protocol Read the docs: Beacon v2 standard technical description GitHub repository Beacon v2 standard Beacon v2 Reference Implementation Read the docs: B2RI technical description GitHub repository B2RI Guide to deploy Beacon using B2RI EGA user EGA Beacon EGA AF Browser

  Documentation about/projects-and-funders/beacon

• Autopsy-Confirmed Parkinson Disease GWAS Consortium (APDGC)

  The APDGC was formed to conduct a genome-wide association study in individuals with neuropathologically confirmed Parkinson Disease (PD) and neuropathologically normal controls. The rationale for the study is that including only cases and controls with neuropathologically confirmed disease status will reduce diagnostic misclassification and increase power to detect novel genetic associations.

  Study phs000394

• ATAC-seq of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  ATAC-seq data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001764

• WGS of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  WGS data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001765

• RNA-seq of iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimicking MPNST progression

  RNA-seq data used in the paper "iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities" by Uriarte-Arrazola, 2026. The uploaded data was used to explore and validate the cellular model as an MPNST progression model.

  Study EGAS50000001766

• Mutational signatures of aflatoxin

  Aflatoxin B1 (AFB1) is a mutagen and IARC (International Agency for Research on Cancer) Group 1 carcinogen that causes hepatocellular carcinoma (HCC). Here we present the first whole genome data on the mutational signatures of AFB1 exposure from a total of > 40,000 mutations in four experimental systems: two different human cell lines, and in liver tumors in wild-type mice and in mice that carried a hepatitis B surface antigen transgene – this to model the multiplicative effects of aflatoxin exposure and hepatitis B in causing HCC. AFB1 mutational signatures from all four experimental systems were remarkably similar. We integrated the experimental mutational signatures with data from newly-sequenced HCCs from Qidong County, China, a region of well-studied aflatoxin exposure. This indicated that COSMIC mutational signature 24, previously hypothesized to stem from aflatoxin exposure, indeed likely represents AFB1 exposure, possibly combined with other exposures. Among published somatic mutation data, we found evidence of AFB1 exposure in 0.7% of HCCs treated in North America, 1% of HCCs from Japan, but 16% of HCCs from Hong Kong. Thus, aflatoxin exposure apparently remains a substantial public health issue in some areas. This aspect of our study exemplifies the promise of future widespread resequencing of tumor genomes in providing new insights into the contribution of mutagenic exposures to cancer incidence.

  Study EGAS00001002490

• Whole-genome sequencing of rare disease patients in a national healthcare system

  Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and mediating genes for more than half such disorders remain to be discovered. We implemented whole-genome sequencing (WGS) in a national healthcare system to streamline diagnosis and to discover unknown aetiological variants, in the coding and non-coding regions of the genome. In a pilot study for the 100,000 Genomes Project, we generated WGS data for 13,037 participants, of whom 9,802 had a rare disease, and provided a genetic diagnosis to 1,138 of the 7,065 patients with detailed phenotypic data. We identified 95 Mendelian associations between genes and rare diseases, of which 11 have been discovered since 2015 and at least 79 are confirmed aetiological. Using WGS of UK Biobank1, we showed that rare alleles can explain the presence of some individuals in the tails of a quantitative red blood cell (RBC) trait. Finally, we reported 4 novel non-coding variants which cause disease through the disruption of transcription of ARPC1B, GATA1, LRBA and MPL. Our study demonstrates a synergy by using WGS for diagnosis and aetiological discovery in routine healthcare.

  Dataset EGAD00001006065

• Genome-wide Association Study of Adiposity in Samoans

  The research goal of this study is to identify genetic variation that increases susceptibility to obesity and cardiometabolic phenotypes among adult Samoans using genome-wide association (GWAS) methods. DNA from peripheral blood and phenotypic information were collected from 3,119 adult Samoans, 23 to 70 years of age. The participants reside throughout the independent nation of Samoa, which is experiencing economic development and the nutrition transition. Genotyping was performed with the Affymetrix Genome-Wide Human SNP 6.0 Array using a panel of approximately 900,000 SNPs. Anthropometric, fasting blood biomarkers and detailed dietary, physical activity, health and socio-demographic variables were collected. We are replicating the GWAS findings in an independent sample of 2,500 Samoans from earlier studies. After replication of genomic regions and informative SNPs in those regions, we will determine sequences of the important genes, and determine the specific genetic variants in the sequenced genes that are associated with adiposity and related cardiometabolic conditions. We will also identify gene by environment interactions, focusing on dietary intake patterns and nutrients.

  Study phs000914

• Massachusetts General Hospital (MGH) Atrial Fibrillation Study

  The Massachusetts General Hospital (MGH) Atrial Fibrillation Study was initiated in 2001. The study has enrolled serial probands, unaffected and affected family members with atrial fibrillation. At enrollment participants undergo a structured interview to systematically capture their past medical history, AF treatments, and family history. An electrocardiogram is performed; the results of an echocardiogram are obtained; and blood samples are obtained. The Massachusetts General Hospital (MGH) Atrial Fibrillation Study is utilized in the following dbGaP substudies. To view genotypes, analysis, other molecular data, and derived variables collected in these substudies, please click on the following substudies below or in the "Substudies" box located on the right hand side of this top-level study page phs001001 Massachusetts General Hospital (MGH) Atrial Fibrillation Study. phs001116 MGH AF CHARGE-S phs001117 MGH AF Exome Sequencing phs001118 MGH AF Medical Resequencing

  Study phs001001