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• Spatial transcriptomic data of breast cancer

  Fastq files from spatial transcriptomic of breast cancer coming from 8 Breast cancer sections. Sample preparation: frozen BC samples were chosen based on tissue structure and RNA quality (RIN > 8). The “Visium Spatial Tissue Optimization Slide and Reagent Kit” (10X Genomics; #PN-1000193) was then used to optimize permeabilization conditions for BC tissues. Briefly, sections were fixed, stained and then permeabilized at different time points to capture mRNA, and the reverse transcription was performed to generate fluorescently labeled cDNA. The permeabilization time that resulted in the highest fluorescence signal with the lowest background diffusion was chosen. The best permeabilization time for BC tissue was 18 min. Cryostat sections of 10 μm of thickness were cut and placed on Visium Spatial Gene Expression slides (10X Genomics, PN-1000184). The slide was incubated for 1 min at 37°C, then fixed with methanol for 30 min at -20°C followed by Hematoxylin and Eosin (H&E) staining and images were taken under a high-resolution microscope. After imaging, the coverslip was detached by holding the slide in water and the slide was mounted in a plastic slide cassette. The spatial gene expression process, including tissue permeabilization, second strand synthesis and cDNA amplification, was performed according to the manufacturer’s instructions (10X Genomics; #CG000239). cDNA quality was next assessed using Agilent High sensitivity DNA Kit (Agilent, #5067-4626). The spatial gene libraries were constructed using Visium Spatial Library Construction Kit (10X Genomics, PN-1000184).

  Dataset EGAD50000000322

• Whole-genome variant calling of individuals from the study of allergic diseases in the Canary Islands

  Research study of genetic susceptibility and analyses of polygenic risk scores in allergic diseases. This dataset consists of variant data derived from whole-genome sequencing in reference samples from one of the parental populations (i.e., North Africans). The dataset consist of 15 VCF files (and corresponding index files) with a total of 1.58 million variants called using GATK v4 and following the Broad Variant Calling Best Practices, from a set of unrelated individuals sequenced in paired-read mode 2x150 bp using an Illumina HiSeq 4000 sequencer.

  Dataset EGAD50000000429

• Kids First: Whole Genome Sequencing in Recessive Structural Brain Defects

  Almost 5% of all live births in the US (1:20 births) display an inborn defect, including both structural and functional/metabolic abnormalities. These are among the most common causes of Infant mortality in the developed world and underlie nearly half of hospitalizations in the first 3 years of life. Of the 35 major defects observable at birth from the International Clearinghouse for Birth Defects Surveillance Program (www.icbdsr.org, external link), about half involve the nervous system. Many of these result in lifelong neurodevelopmental disorders. Structural Brain Defects (SBDs) result from errors in development of the central nervous system, including defects in the forebrain, midbrain and hindbrain. Many SBDs arise as the consequence of a single gene bi-allelic mutation, and for this reason, occur more commonly in populations or communities with elevated consanguinity.Our lab has identified dozens of novel SBD genes using WES/WGS in consanguineous SBD families. Importantly, the genes that we and others have identified in these unique families are then used to advance diagnosis in pediatric SBDs around the world. We have built an enormous cohort of SBD families, including newly recruited families not yet studied genetically, and previous families that were negative for cause following WES analysis. Here we propose to collaborate with the Gabriella Miller Kids First Pediatric Research Program (X01) to have sequencing performed in individuals from a total of 200 families with genetically undiagnosed SBDs. The Gleeson Lab team of researchers is dedicated to the field of SBDs, with an outstanding track record of high-impact science, and a collaborative approach to discovery. We have 150 newly recruited families that we propose to study by WES by sequencing blood-derived DNA from two affected patients, or the parents and one affected patient. We also have 50 families in which WES was negative, which we propose to study in a multi-omics approach combining WGS from blood-derived DNA. We anticipate that this study will lead to the identification of many new molecular causes of SBDs, as well as uncover new genotype-phenotype correlations and new disease mechanisms, paving the way for future breakthroughs in detection, treatment and prevention.

  Study phs002590

• Integration of T Cell Repertoire, CyTOF, genotyping and symptomatology data reveals subphenotypic variability in COVID-19 Patients

  A total of 61 patients (33 mild and 28 severe) with a median age of 51 years who recovered from COVID-19 were included in this study (Table 1). All collected samples were confirmed in diagnosis of COVID-19 by RT-PCR and positive IgG serolog. For the 61 patients, TCR-seq, CyTOF, and genotyping data were generated and analyzed in separate studies, as part of larger cohorts. In total, there are 143 variables, with 129 being quantitative (TCRseq and CyTOF metrics) and 13 being qualitative (symptomatology and genotyping). For more information about cohort characteristics, data adquisition an pre-processing, please visit PMID: 39227859, 36969980 and 37287057.

  Dataset EGAD50000000840

• How to upload Crypt4GH files

  Uploading files Users who hold an ega-box-XXX account can upload files using either INBOX or FTP. Users who have a Submitter role associated with their email will only be able to upload files using INBOX. Before uploading your files, please make sure that any files that will be uploaded to EGA do not use special characters in their naming convention, such as # ? ( ) [ ] / \ = + < > : ; " ' , * ^ | &. This can cause issues with the archiving process, leading to problems for end users. The EGA is a shared, public service with limited storage. To manage the available resources, we enforce a limit of 10TB per submission account at any one time. If you exceed this limit, a “permission denied” message will be displayed. This will prevent you from uploading more files, but connecting to your inbox.For submissions larger than 10TB, please perform uploads in 10TB batches: register all the metadata and then finalise the submission. Upload the next batch of files and repeat the same metadata registration and finalisation process until you have completed the file upload. Further information can be found in the SP documentation. INBOX FTP The INBOX is only compatible with files encrypted using the Crypt4gh tool Before uploading If you are not a registered EGA user, you will first need an EGA user account. Please note that it may take a few days for your account to be activated, as it needs to be vouched for by the EGA Helpdesk. Once your account is validated, you will be able to request a submitter role. [Optional] Meanwhile, you can create and add your public key to your EGA account profile. This option is not available for old submission accounts (e.g., ega-box-NNN). As soon as you have been granted a submitter role, you will be able to connect with your username and password to the EGA inbox using the SFTP protocol. If you have also registered a public key in your profile, you can also connect using this key. To upload files to your account, you can use the graphical user interface (GUI) or the command line. Graphical User Interface (GUI)We recommend using FileZilla, a free, open-source FTP client. However, you can use any other GUI that allows connecting over the SFTP protocol. For FileZilla as your GUI, follow these steps to upload files: Create a new connection in Site Manager (File > Site Manager) and select the following options (Figure 1): Protocol: SFTP - SSH File Transfer ProtocolHost: __EGA_INBOX_DOMAIN__Logon Type: Key fileUser: your EGA usernameKey file: Path/to/your/private_keyFigure 1: Process of establishing a new connection to __EGA_INBOX_DOMAIN__ using a key file as the logon method in FileZilla. The figure showcases the FileZilla version 3.52.2 operating on IOS v11.2.3. By following the depicted steps, users can create a secure and efficient connection to the inbox, ensuring seamless data transfers.Click Connect, and you will log in remotely to your home directory. You can think of this folder as a storage "in the EGA cloud" in which you will add your files for the EGA. The uploading area has three folders:To-encrypt: Files uploaded in this folder will be encrypted automatically on the fly.Encrypted: Files uploaded in this folder must already be encrypted with Crypt4gh. Upload your files here if your connection is unstable or you have problems completing the upload into-encrypt.Etc: This folder contains two files that allow the server to show you your username and group instead of some internal numbers. Please do not upload files here; otherwise, you will obtain a permission denied error. Find the files you want to upload by browsing your local storage (left side of your screen in FileZilla). Select all the files you want to upload, then right-click on them and select Upload (Figure 2). Figure 2: Step-by-step process of manually uploading files to __EGA_INBOX_DOMAIN__ using FileZilla, with FileZilla version 3.52.2 operating on IOS v11.2.3. The figure demonstrates how users can transfer data from their local storage to the "EGA cloud" by following the depicted steps Please note that regardless of which folder you upload your files in, both folders (to-encrypt, encrypted) will point to the same path (/) (Figure 3). Therefore, you will see your files in both folders. Figure 3: Both folders, to-encrypt and encrypted, point to the same path (/)" If your connection is unstable, please encrypt your files first using Crypt4gh. Then upload them to the ‘encrypted’ folder. The example above shows how to connect to __EGA_INBOX_DOMAIN__ using the private key. However, if you prefer to log in using your credentials, you can do so. Please go to the Frequently Asked Questions (FAQs)  for more information. SFTP command line To upload files securely to your private area of the EGA, you can use SFTP(Secure File Transfer Protocol) with your favorite FTP client. Here's what you need to know to get started: Connect to the target host __EGA_INBOX_DOMAIN__. This is the new hostname for the EGA SFTP service. Log in with your EGA username and key files (or password). Upload files to your private EGA inbox to ensure that only you can access the files. By following these steps, you can securely upload your files to the EGA for safe storage and sharing. Using the SFTP command line client in Linux/Unix Open a terminal and type sftp username@hostnameEnter your EGA passwordTo see a list of available SFTP commands, type helpsftp> put – Upload filesftp> get – Download filesftp> cd path – Change remote directory to ‘path’sftp> pwd – Display remote working directorysftp> lcd path – Change the local directory to ‘path’sftp> lpwd – Display local working directorysftp> ls – Display the contents of the remote working directorysftp> lls – Display the contents of the local working directoryType the "put" command to upload files. For example: put *.bamUse the bye command to close the connection (SFTP session). After uploading- Once you have uploaded files to the inbox, please bear in mind that the checksum needs to be calculated, which can take up to two days. You will only be able to link your files to a run/analysis once the encrypted checksum has been calculated.- When linking your files to the 'Run' or 'Analysis', ensure that the file name matches the file path '/name' in the INBOX folder.- Please delete the files from your SFTP INBOX after all the runs/analyses have been registered and files are ingested (SP > Files > Files ingested). This will clear your inbox space an allow you to upload more files. This will also prevent the files from reappearing in your Submitter Portal inbox. Frequently Asked Questions Specific to the inbox What username should I use to log in to my inbox? The authentication process for logging in to the EGA website, as well as accessing your inbox and outbox, requires the use of your username.  If you have forgotten your registered username, please contact our Helpdesk team for assistance. How are checksums calculated in your inbox? If you encrypt the file beforehand and upload it to the "encrypted" folder, the unencrypted checksum will not be calculated until the file is ingested (i.e., until it is used in a run/analysis). If the file is uploaded to the "to-encrypt" folder, then both checksums are calculated.Please bear in mind that after files have been uploaded to the inbox, the checksum must be calculated, which can take from a few hours to two days.  Specific to using keys to authenticate Can I access one EGA account from different devices? Yes, you can access your account from different devices by linking several public keys to your EGA account. Each device can generate a unique public-private key pair, and the corresponding public keys can be linked to the same account. This way, you can use different public keys on different devices and still have access to the same account and data. I have several keys and I don't remember which one is which When generating SSH keys, it's a good practice to add a comment using the -C flag. This will allow you to add a descriptive tag to your key, making it easier to identify later on. Here's an example command that generates an SSH key with a comment: ssh-keygen -t ed25519 -C work-pass In this example, we're generating an ed25519 SSH key with the comment work-pass. Once you have multiple keys with different comments, you can use the comments to easily identify each key. To view the comments for your existing SSH keys, you can use the following command: ssh-keygen -l -f /path/to/key This will display the key fingerprint and the associated comment. By checking the comments, you should be able to identify which key is which. What if I can't find my SSH keys for uploading files with a key file, and how can I use new keys? If you can't find your SSH keys, don't worry - you can make new ones. To do this, open your terminal or command prompt and type a command to make a new SSH key. You can pick a name for the key, and choose a password to keep it safe. After making the key, you can add the new key to your account or server where you want to upload files using the key file. This usually involves copying and pasting the key's "public" (e.g. file.pub) part to the right place. If you lose track of the key again, just make a new one and add it again. Keep in mind that SSH keys belong to you and your computer, so if you switch computers or accounts, you'll need to make new keys. I don't want to type the passphrase every time I use the key. What can I do? You can use an ssh-agent to avoid typing the passphrase every time you use the key. An ssh-agent is a program that stores your private keys in memory and provides them to ssh when needed. You can add your key to the ssh-agent using the command ssh-add followed by the path to your key file.Here's an example of the steps to follow: Open a terminal window.Start the ssh-agent by typing the command eval $(ssh-agent).Add your key to the ssh-agent by typing the command ssh-add [key filepath]. For instance, if your key file is located in the home directory with the name mykey, the command will look like this: ssh-add ~/mykey After adding your, key to the ssh-agent, you should be able to use ssh without having to enter your passphrase every time. Can I use my password for authentication (without my private key)? If you prefer to use your username and password for authentication instead of your private key, you can still do so. When using a Graphical User Interface (GUI) such as FileZilla, you can select Ask for password as your Logon Type (Figure 3). This option will prompt you to enter your password when you click Connect, instead of using your private key. Figure 3: This option will prompt you to enter your password when you click "Connect", instead of using your private key. Figure 3: Process of establishing a new connection to __EGA_INBOX_DOMAIN__ using your password as the logon method in FileZilla. The figure showcases the FileZilla version 3.52.2 operating on IOS v11.2.3. By following the depicted steps, users can create a secure and efficient connection to the inbox, ensuring seamless data transfers. It's worth noting that using a password for authentication can be less secure than using an SSH key, as passwords can be more easily compromised through various means. However, if you choose to use your password for authentication, selecting "Ask for password" as your Logon Type is a good way to do so securely via a GUI. Why is it better to use my key and not my password? SSH keys for authentication is generally considered to be more secure and convenient than using passwords. SSH keys are more difficult to crack than passwords, and they can be restricted to specific users and machines, giving you more control over access. Once you set up your SSH keys, you can use them to authenticate quickly and easily, without having to enter a password every time. This makes automation of tasks, such as uploading encrypted files, much simpler. Additionally, SSH keys provide better logging, allowing you to keep track of who is accessing your systems and when. All in all, using SSH keys is a good practice for improving security and convenience in your authentication process.

  Documentation submission/data/uploading-files/inbox

• A Genome-Wide Association Study of Fuchs' Endothelial Corneal Dystrophy (FECD)

  Fuchs&#39; Endothelial Corneal Dystrophy (FECD) is a common disease that results in loss of vision associated with progressive corneal edema and loss of corneal transparency. In the initial stages of the disease, excrescences on Descemet&#39;s membrane with the appearance of an abnormal posterior collagenous layer, result in the clinical and pathologic appearance of guttae. Corneal edema ensues as endothelial function is compromised that may result in stromal edema, epithelial edema, and painful bullous keratopathy. Penetrating or endothelial keratoplasty is the only definitive treatment, with palliative care the only option prior to surgery. The pathophysiology underlying FECD, particularly in the common cases that affect older individuals, remains unknown, with a genetic predisposition being reported as the single best predictor of disease. Three independent groups funded by the National Eye Institute (NEI), with well-established programs in the genetics of FECD, conducted a genome-wide association study of FECD. The collaboration comprised investigators from Case Western University (CWRU), Duke University (DUEC), and Johns Hopkins University (JHU). CWRU and DUEC contributed samples that were genotyped at CIDR for the GWAS. Johns Hopkins University (JHU) provided samples for the replication phase of the study, where their data are not listed in dbGaP. Cohorts of FECD cases and controls were assembled. Synchronization of clinical and coded data was performed to unify the information across centers. The family history, clinical, demographic information, and genome-wide genotype data for samples from CWRU and DUEC were deposited in dbGaP.

  Study phs000421

• CTN - 0051: Extended-Release Naltrexone vs. Buprenorphine for Opioid Treatment (X:BOT)

  The overarching goal of CTN-0051 is to foster adoption of new relapse-prevention pharmacotherapies in community-based treatment programs (CTPs) where these could have a substantial public health impact. To this end CTN-0051 will assess the comparative effectiveness of extended-release injectable naltrexone (XR-NTX, Vivitrol&#174;), an opioid antagonist recently approved and indicated for the prevention of relapse to opioid dependence, versus buprenorphine-naloxone (BUP-NX, Suboxone&#174;), a high affinity partial agonist indicated for maintenance treatment of opioid dependence, as pharmacotherapeutic aids to recovery. The study is conducted in 8 CTN-affiliated CTPs that provide or partner with detoxification services (inpatient/residential) which have the capacity to maintain participants opioid-free for approximately 3-7 days, have the capacity to provide medication-assisted therapy, and can provide a minimum of one group or individual counseling session per week during the 24-week treatment period. Up to 600 eligible participants will be randomized to treatment with XR-NTX or BUP-NX for 24 weeks (sufficient to include 350 participants who are randomized more than 72 hours after their last opioid). To maximize generalizability, the point of randomization is flexible, from shortly after program admission until just prior to program discharge. The primary goal of the study is to estimate the difference, if one exists, between XR-NTX and BUP-NX in the distribution of the time to relapse (i.e., loss of persistent abstinence) during the 6-month trial. The primary outcome measure is the time to the event, with the event called relapse. Secondary objectives are to: (1) compare outcome on XR-NTX versus BUP-NX across a range of clinical safety and secondary efficacy domains, (2) explore demographic, clinical, and genetic predictors of successful treatment and moderators of differential effectiveness (i.e., what variables may help clinicians choose which of these treatments is best for a given patient), and (3) collect a limited dataset to permit analyses of economic costs and benefits of the two treatments.

  Study phs002876

• Security Overview

  Security Overview The European Genome-phenome Archive (EGA) houses consented human data under controlled access. Access decisions are handled by the relevant Data Access Committee (DAC), which autonomously manages requests through the DAC Portal. This document provides an overview of EGA’s practices in ensuring the security of data stored at EGA. As security is a prime concern of the EGA, the EGA is a member of the Global Alliance for Genomics and Health (GA4GH) Data Security work stream. The EGA contributes and helps develop the recommendations outlined the GA4GH Security Technology Infrastructure document, which defines guidelines, best practices, and standards for building and operating an infrastructure that promotes responsible data sharing in accordance with the GA4GH Privacy and Security Policy. Explore the EGA dataflow to gain deeper insights! Accessing data in the EGA involves several steps. First, users need to create an EGA account. Once logged in, they can request access to data controlled by a DAC through the EGA website (see documentation). The DAC oversees these requests through the DAC Portal, and if approved, grants the necessary permissions to the user's EGA account, allowing them to access and download all relevant data and metadata for the requested dataset(s). The key points of EGA security strategy are: 1 Regular Risk Assessment The EGA regularly identifies and assesses risk related to the following: Breach of confidentiality,Breach of privacy or autonomy,Malicious or accidental corruption or destruction of data archived at EGA,Disruption of services provided by the EGA. 2 Risk mitigation The EGA implements and maintains safeguards to minimise the risks identified above in accordance with the 6 control objectives listed in Appendix 1 and outlined in the GA4GH Security and Infrastructure document.If a breach is discovered, the EGA applies a defined protocol to minimise damage. 3 Identity and authorisation management The EGA authenticates the identity of individuals or software accessing controlled access data held at the EGA.The EGA ensures an appropriate level of assurance (LoA) is applied to the identity consistent with the risk associated with that individual, such as multi-factor authentication for DACs.The EGA provides the minimum access rights and privileges consistent with the user’s identity, allowing access consistent with the GA4GH Privacy and Security Policy, as determined by the appropriate DAC. 4 Audit Logs The EGA maintains a set of logs recording: Changes to user access rights,Data access requests,Resource usage. 5 Cryptography, communication security, and data integrity The EGA ensures data transmission integrity using a hash function.All data transmitted to or from the EGA is end-to-end encrypted.All data at EGA is stored using strong encryption.Encryption keys are not stored in the same system as the encrypted data.All data archived at EGA must be accompanied by a signed submission statement ensuring appropriate consent or ethical approval has been obtained, and is in accordance with all applicable laws and regulations. The EGA has a defined protocol defining the response in the event of a security breach, and is continuing to work with the GA4GH Data Security Work Stream to help define best practice and associated standards for breach responses. Appendix 1 GA4GH Control Objectives Control Objective 1: Implement technology safeguards to minimise the risk of unauthorised access, use, or disclosure of confidential and private data.Control Objective 2: Implement technology safeguards to minimise the risk of discovery, access, and use of individuals’ clinical and genomic data, and individual identities, other than as authorised by applicable jurisdictional law, institutional policy, and individual consents.Control Objective 3: Implement technology safeguards to minimise the risk of accidental or malicious corruption or destruction of data.Control Objective 4: Implement technology safeguards to minimise the risk of disruption, degradation, and interruption of services enabling access to data.Control Objective 5: Implement technology safeguards to minimise the risk of potential security attacks and misuse of authorised accesses and privileges.Control Objective 6: Implement technology safeguards to promptly detect the failure to attain the above control objectives and to respond with proper countermeasures.Appendix 2Refer to the document below to learn more about EGA long-term data preservation policy and procedures at EMBL-EBI.Long-term data preservation

  Documentation about/security

• Emirati Genome Project subset of 43,608 WGS samples for population-scale variant discovery and allele frequency mapping.

  Here, we present a comprehensive genomic characterization of a cohort of 43,608 Emirati genomes sequenced as part of the Emirati Genome Program (EGP). This study identified more than 421 million single nucleotide variants and indels and more than 600 million copy number- and structural variants. Small variants had 756 million molecular effects annotated. Of the identified variants, 69.04% were observed with more than one allele. Of 7.7 million polymorphic variants having an allele frequency (AF) of more than 5% in EGP, 1,348 have a predicted deleterious effect on a protein. Characterization of global variation reveals that EGP represents a genetic continuum encompassing the range of African, Asian, and European populations. It is best described by two Arabian, an Eurasian, and an African component, with the predominant Arabian component linked to mitochondrial haplogroups J and T, which are commonly attributed to the Middle East. Various aneuploidies of sex chromosomes were detected in 93 individuals overall and of chromosome 21 in 41 individuals. The median inbreeding coefficient and cumulative runs of homozygosity (ROHs) lengths were increased due to extensive consanguinity, being largest in the groups with Arabian main ancestry components and higher than reported for Qatar. Families were identified based on genetic relatedness and classified into 264 families with unrelated parents and 247 families with third- and fourth-degree consanguineous parents. Representative consanguineous pedigrees of families in EGP were outlined. Cumulative ROHs were affected by the main ancestry component and significantly increased in offspring of consanguineous parents, with a pronounced difference between 3rd and 4th-degree relatedness. Investigation of cumulative AFs of variants causing Mendelian diseases highlighted genes related to alpha- and beta-thalassemia (HBB, HBA2). It showed a high burden of variants causing severe recessive diseases, metabolic and retinal disorders, and hearing loss. In summary, EGP represents a landmark effort in characterizing the genetic diversity of the Emirati population, leveraging the largest Middle Eastern cohort reported to date.

  Study EGAS50000001071

• Local In Time Statistics for processual research

  Background: Functional genomics in a processual analysis cover the time-dependent changes in transcriptomics and epigenetics before diagnosis of a disease, reflecting the changes in both life style and disease processes. The aim of this paper is to explore the dynamic, time-dependent mechanisms of the metastatic processes, using blood transcriptomics and including time in a continuous manner. For achieving this goal we develop new statistical methods based on statistics that are local in time. Methods: The new statistical method, Local In Time Statistics (LITS), is based on calculating statistics in moving windows and randomization. The method has been tested for the analysis of a dataset that collectively provides information on the blood transcriptome up to eight years before breast cancer diagnosis. The dataset from the NOWAC Post-genome Cohort consists of 467 case-control pairs matched on birth year and time of blood sampling. The data for a pair is the difference in log2 gene expression between the case and control. The stratified analyses are based on important biological differences like metastatic versus non-metastatic cancer, and the mode of cancer detection, i.e. screening detected versus clinically detected cancers. The dataset was used for examining whether the gene expression profile varies between cases and controls, with time, or between cases with and without metastases. Results: The null hypotheses of no differences between cases and controls, no time-dependent changes, and no differences between different strata were all rejected. For screening detected cancers the probability of correct prediction of metastasis status was best in year 1 before diagnosis compared to year 3 and 4 before diagnosis for clinically detected cancers. The predictor was not very sensitive to the number of genes included.Conclusions: Using a new statistical method, LITS, we have demonstrated time-dependent changes of the blood transcriptome up to eight years before breast cancer diagnosis.

  Study EGAS00001002520