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• Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease

  Celiac disease is an autoimmune disorder in which ingestion of dietary gluten triggers an immune reaction in the small intestine leading to destruction of the lining epithelium. Current treatment focusses on lifelong adherence to a gluten-free diet. Gluten-specific CD4+ T cells and cytotoxic intraepithelial CD8+ T cells have been proposed to be central in disease pathogenesis. Here we use unbiased single-cell RNA-sequencing and explore the heterogeneity of CD45+ immune cells in the human small intestine. We show altered myeloid cell transcriptomes present in active celiac lesions. CD4+ and CD8+ T cells transcriptomes show extensive changes and we define a natural intraepithelial lymphocyte population that is reduced in celiac disease. We show that the immune landscape in Celiac patients on a gluten-free diet is only partially restored compared to control samples. Altogether, we provide a single cell transcriptome resource that can inform the immune landscape of the small intestine during Celiac disease.

  Study EGAS00001003751

• Comparison of WGBS, EPIC array, EM-seq, and Nanopore sequencing in assessing DNA methylation marks

  Bisulfite sequencing has long been the default method for analyzing methylation marks due to its single base resolution. However, the associated DNA degradation poses a concern for fragmented samples. Although several methods have been proposed to circumvent this issue, there has yet to be a clear consensus on which method is best suited for detecting methylation. We present an overview of the two mostly used and two alternative approaches: whole-genome bisulfite sequencing (WGBS), Illumina methylation microarray (EPIC), Enzymatic Methyl-sequencing (EM-seq) and third-generation sequencing by Oxford Nanopore Technologies (ONT). We evaluated DNA methylation levels in three human genomes derived from tissue, cell line, and whole blood.

  Study EGAS00001008014

• OMKar

  The whole genome karyotype refers to the sequence of large chromosomal segments that make up an individuals genotype. karyotype analysis, which includes descriptions of aneuploidies and other rearrangements is crucial for understanding genetic risk factors, for diagnosis, treatment decisions, and genetic counseling linked to constitutional disorders. The current karyotyping standard is based on microscopic examination of chromosomes, a complex process that requires high expertise and offers Mb scale resolution. Optical Genome Mapping (OGM) technology can identify large DNA lesions in a cost-effective manner. In this paper, we developed OMKar, a method that uses OGM data to create a virtual karyotype. OMKar processes Structural (SV) and Copy Number (CN) Variants as inputs and encodes them into a compact breakpoint graph. It recomputes copy numbers using Integer Linear Programming to maintain CN balance and then identifies constrained Eulerian paths representing entire donor chromosomes. In tests using 38 whole genome simulations of constitutional disorders, OMKar reconstructed the karyotype with 88% precision and 95% recall on SV concordance and 95% Jaccard score on CN concordance. We applied OMKar to 50 prenatal, 41 postnatal, and 63 parental samples from ten different sites. OMKar reconstructed the correct karyotype in 144 out of 154 samples, covering 25 of 25 aneuploidies, 32 of 32 balanced translocations, and 72 of 82 unbalanced variations. Detected constitutional disorders included Cri-du-chat, Wolf-Hirschhorn, Prader-Willi deletions, Down, and Turner syndromes. Importantly, it identified a plausible genetic mechanism for five cases of constitutional disorder that were not detected by other technologies. Together, these results demonstrate the robustness of OMKar for OGM-based karyotyping.

  Study EGAS00001008245

• Genetic alterations that deregulate RB and PDGFRA signaling pathways drive tumor progression in IDH2-mutant astrocytoma

  In IDH-mutant astrocytomas, IDH2 mutation is quite rare and biological mechanisms underlying tumor progression in IDH2-mutant astrocytoma remain elusive. Here, we report a unique case of IDH2 mutant astrocytoma, CNS WHO grade 3 that developed tumor progression. We performed a comprehensive genomic and epigenomic analysis for primary and recurrent tumors and found that both tumors harbored recurrent IDH2R172K and TP53R248W mutation with CDKN2A/B hemizygous deletion. We also found amplifications of CDK4 and MDM2 with PDGFRA gain in the recurrent tumor and upregulated protein expressions of these genes. We further developed, for the first time, a xenograft mouse model of IDH2R172K mutant astrocytoma from the recurrent tumor, but not from the primary tumor. Consistent with parent recurrent tumor cells, amplifications of CDK4 and MDM2 with PDGFRA gain was found, while CDKN2A/B was identified as homozygous deletion in the xenografts, qualifying for integrated diagnosis of astrocytoma, IDH2-mutant, CNS WHO grade 4. Cell viability assay found that CDK4/6 inhibitor and PDGFR inhibitor potently decreased cell viability in recurrent tumor cells, as compared to primary tumor cells. These findings suggest that gene alterations that activate retinoblastoma (RB) signaling pathways and PDGFR may drive tumor progression and xenograft formation in IDH2-mutant astrocytoma, which is equivalent to progressive IDH1-mutant astrocytoma. Also, our findings suggest that these genomic alterations may represent therapeutic targets in IDH2-mutant astrocytoma.

  Study JGAS000646

• Viral integration analysis of hepatocellular carcinoma using virus capture sequence.

  Hepatitis B viral (HBV) DNA is frequently integrated into the genome of hepatocellular carcinoma (HCC) in patients with chronic HBV infection (chronic HBV, hereafter), whereas it is yet to be clarified in patients after HBV disappearance (prior HBV, hereafter). This study aimed to identify viral integration such as HBV and adeno-associated virus type 2 (AAV2) into the HCC genome as oncogenic event.

  Study JGAS000194

• Y_phylogeny_haplogroupDE

  High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. 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 EGAS00001002674

• EGA account management

  How to manage your EGA account Welcome to the documentation page for creating an EGA user. The European Genome-Phenome Archive (EGA) is a platform for archiving, managing, and sharing human genomic and phenotypic data. To submit, access, and manage requests for the data hosted on the EGA platform, users are required to register for an account. This documentation page provides step-by-step instructions for creating an EGA user account, as well as information on the different types of EGA user accounts and their associated privileges. You can check the EGA data flow for a better understanding. Manage EGA account step-by-step guide Contact Information Public Keys Password Authenticator Federated Identity Sessions Request an EGA account step-by-step guide Fill in this form.You cannot use a generic email account (e.g., Gmail). Make sure you use your institutional email account.Your email is by default your username.The criteria for a strong password is: It should contain between 8 and 32 charactersIt should contain at least one uppercase letterIt should contain at least one numberIt should contain at least one special characterYou will need to wait for the Helpdesk team to check your identity. Please allow two business days for this step.After the Helpdesk validation step, you will receive an email with a link to validate your institutional email.Click the link to verify your email. It will redirect you to the EGA website.As soon as your account has been validated, you will be able to start adding more information to your EGA profile. For that, you first need to log in using your credentials from step 1. Manage EGA account step-by-step guide As a logged-in user, go to your profile by clicking on Welcome > My Profile. To modify it, click the Edit button.You will see the following options: Contact Information In this section, you can modify the personal information of your EGA account. Public Keys Adding a public key is necessary for downloading data via Live Outbox distribution. If you don’t know how to generate your key, you can follow the instructions available on How do I create a key? Password In the Password tab, you can change your password anytime to ensure the security of your account. However, if you receive an email notifying you that your password was modified and you did not initiate the change, it could be a sign that your account has been compromised. In this case, you should immediately contact our Helpdesk team to report the issue and receive assistance in restoring your account security. Authenticator You can set your two-factor authentication (2FA) system for your EGA account as an identity and access management security method that requires two forms of identification to access resources and data. To obtain your code, please follow the instructions below, also available in the Authenticator tab in your profile. Sessions The Sessions tab displays a list of all devices where you are currently logged in as an EGA user. This includes any open sessions you have on your computer, phone, or other devices. By reviewing the list of active sessions, you can monitor the devices that have access to your account and ensure that there are no unauthorised logins. If you notice any suspicious activity, you can close the sessions from this page to immediately terminate access to your account from the unauthorised device.

  Documentation how-to-manage-your-account

• STAMPEED: Northern Finland Birth Cohort 1966 (NFBC1966)

  The Northern Finland Birth Cohorts program (NFBC) was initiated in the 1960s in the two northernmost provinces of Finland to study risk factors involved in pre-term birth and intrauterine growth retardation, and the consequences of these early adverse events on subsequent morbidity and mortality. The uniqueness of NBFCs is that the data of the cohorts were obtained from early fetal life (including maternal health during pregnancy) to adulthood. The NFBC1966 includes 12,058 live births to mothers in the two northern-most provinces of Finland. Two decades later, a second cohort of 9432 births was obtained (NFBC1986). In NFBC1966 pregnancies were followed prospectively from the first antenatal contact (10-16th week). After birth, the offspring were examined and then again underwent clinical evaluation at ages 1y, 7y, 14-16y and 31y. At each visit, a wide range of phenotypic, lifestyle and demographic data were gathered by questionnaires and clinical examinations. For the most part, NFBC1986 has undergone similar evaluations to NFBC1966. Linkage to national registries includes hospitalization, deaths, education, medication, pensions, and provides up-to-date demographic and clinical information for members of both cohorts. DNA samples were obtained from 5,923 subjects from NFBC1966 and 6688 subjects from NFBC1986. Data coverage, 96% of all births in 1966 and 99% in 1986, is highly representative for the whole population. The NFBC program comprises more than 20 different projects coordinated by the Center of Lifecourse Disease studies in Northern Finland (COLD) at Oulu University. The prospective data collected from the NFBCs form a unique resource, allowing the study of disease emergence, and of the importance of genetic, biological, social and behavioral risk factors. The genome-wide association (GWA) study sponsored through the STAMPEED program of NHLBI employed genomic DNA samples previously collected by the NFBC1966 study and stored in the DNA repository of the National Institute for Health and Welfare, Finland. This NHLBI sponsored RO1 project aimed to identify genetic variants contributing to metabolic and cardiovascular diseases (CVD). In addition to de-identified genome wide genotypic data, a selected list of phenotypic data related to CVD including weight, height, BMI, HDL, LDL, total cholesterol, triglyceride, glucose, insulin and fasting status, are also available in dbGaP. A summary of the GWAS for the NFBC1966 cardiovascular risk traits can be found in Sabatti et al., Nature Genetics 41: 35-46, 2009, PMID: 19060910. The version 2 release of this study contains sequence data from seventeen loci associated with levels of triglyceride, HDL-C, LDL-C, total cholesterol, fasting plasma glucose, and fasting plasma insulin (Kathiresan et al. 2008, Willer et al. 2008, Sabatti et al. 2009, Dupuis et al. 2010, Teslovich et al. 2010). At each locus, protein-coding regions and 5' and 3' untranslated regions of genes nearest to single nucleotide polymorphisms showing genome-wide significant association with metabolic syndrome-related traits, were sequenced. Targeted Illumina sequencing of 78 genes (~270kb) using 150bp probes was performed on 4943 subjects of the Northern Finland Birth Cohort 1966 (NFBC1966). Whole exome sequencing on the Illumina platform was carried out on 586 of those participants. The sequencing study is part of a larger project that is funded by the National Human Genome Research Institute's Allelic Spectrum in Common Disease Initiative, and comprises sequence data from more than 7000 individuals in two Finnish cohorts: NFBC1966 and the Finland-United States Investigation of NIDDM Genetics (FUSION) study.

  Study phs000276

• Noninvasive prenatal molecular karyotyping from maternal plasma

  Fetal DNA is present in the plasma of pregnant women. Massively parallel sequencing of maternal plasma DNA has been used to detect fetal trisomies 21, 18, 13 and selected sex chromosomal aneuploidies noninvasively. Case reports describing the detection of fetal microdeletions from maternal plasma using massively parallel sequencing have been reported. However, these previous reports were either polymorphism-dependent or used statistical analyses which were confined to one or a small number of selected parts of the genome. In this report, we reported a procedure for performing noninvasive prenatal karyotyping at 3 Mb resolution across the whole genome through the massively parallel sequencing of maternal plasma DNA. This method has been used to analyze the plasma obtained from 6 cases. In 5 cases, fetal microduplications or microdeletions have been detected successfully from maternal plasma. The two cases with fetal microduplications represented the first noninvasive prenatal detection of such changes from maternal plasma. In the remaining case, the plasma DNA sequencing result was consistent with the pregnant mother being a carrier of a microduplication. Simulation analyses were performed for determining the number of plasma DNA molecules that would need to be sequenced and aligned for enhancing the diagnostic resolution of noninvasive prenatal karyotyping to 2 Mb and 1 Mb. In conclusion, noninvasive prenatal molecular karyotyping from maternal plasma by massively parallel sequencing is feasible and would enhance the diagnostic spectrum of noninvasive prenatal testing.

  Study EGAS00001000439

• Sequence-Based Analysis of Human Breast Tumors

  The goal of this study is to study gene expression patterns in tumors, normal tissues, and cell lines.

  Study phs000676