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• WGS - germline - oral squamous cell carcinoma

  We conducted a retrospective, single-center Canadian cohort study of patients who underwent primary surgery for OSCC between 2010 and 2024. Nucleic acid quality was assessed using the 4150 TapeStation System (Agilent) prior to library preparation. WGS was performed on germline DNA, following Genome Analysis Toolkit’s (GATK) Best Practices and procedures, with a target of 30X deduplicated coverage per sample, using an Illumina NovaSeq 6000 instrument.

  Dataset EGAD50000002608

• Lymphoma_primary_patient_drug_perturbed_RNASeq_samples

  3'-end low-depth RNA sequencing data from 108 patients with chronic lymphocytic leukemia and 8 patients with lymphoma. Each primary patient sample was treated in vitro with DMSO as a control and with up to ten small-molecule inhibitors (ibrutinib, duvelisib, everolimus, trametinib, nutlin-3a, I-BET-762, MK2206, selinexor, compound 26, and a combination of ibrutinib and compound 26). Sequencing was performed on the Illumina HiSeq4000. The dataset contains FASTQ files.

  Dac EGAC50000000578

• Association studies using the Metabochip array - Samples analysed by the WTCCC (1958 British Birth Cohort (58BC), Hypertension cohort (HT), Type 2 Diabetes Cohort (T2D) and Coronary Artery Disease (CAD) cohort)

  Genomewide association studies (GWAS) have proven a powerful hypothesis-free method to identify common disease-associated variants. Even quite large GWAS, however, have only at best identified moderate proportions of the genetic variants contributing to disease heritability. To provide cost-effective genotyping of common and rare variants to map the remaining heritability and to fine-map established loci, the Metabochip Consortium has developed a 200,000 SNP chip that has been produced in very large numbers for a fraction of the cost of GWAS chips. This chip provides a powerful tool for genetic studies of metabolic, cardiovascular and anthropometric traits (Voight et al., in press PLoS Genetics).

  Study EGAS00000000115

• New set of services for all users unveiled at the EGA

  The European Genome-phenome Archive (EGA) releases today a brand-new website as well as a set of improved services for users, comprising a revamped Submitter Portal with an improved API and data brokering functionality for submitters, as well as a new DAC Portal for Data Access Committee members to easily manage data access requests. The EGA team has been working hard over the past months on these improvements that will provide a better experience for the users. Discover them below! Visit our new EGA website and check the new functionalities and updated guides Our new website is live, with a fresh look and updated features to discover all the novelties. The homepage now includes three pathways to guide our users, depending on whether they want to deposit, download or manage data within the Archive. One of the most outstanding developments is the introduction of a streamlined process for requesting access to data: EGA Users can now directly request access to their preferred datasets through the website using their EGA accounts. Additionally, users can customise their profile, oversee active sessions, and manage the public keys, essential for our latest array of services, alongside a range of other features. Another major change is our new Help Desk contact method: a built-in website form tailored for user inquiries. This system, called "Need Help?", can be easily located on the top right-hand side of the website. It will encompass both EGA and Federated EGA node users' requests. We will detail its use soon, so stay tuned. Register your metadata to the EGA easily with our new Submitter Portal The new Submitter Portal makes the submission process quicker and more intuitive. The process is currently divided into sections that the user will know beforehand by taking the tour that the EGA team has created to guide users through the Portal before starting the first submission. Do not complete your data submissions alone! Our Submitter Portal now includes a collaboration mode so that every submission can be completed by authorised collaborators with an EGA Profile. There are a lot more features that we will be detailing from now on in incoming posts. A new platform for Data Access Committee Members The new DAC Portal brings novelties for individuals engaged in governance, legal, technical, operational roles, or those acting as data stewards. DAC members will be able to easily manage DACs, policies, and data access requests with the new Portal. Take the tour now to check them out! Help us improve the services completing the EGA Survey As part of our ongoing journey to improve your experience, we have created an EGA User Survey. This questionnaire covers a wide range of aspects such as user experience, support and data accessibility, among others. Participate now and take the opportunity to suggest your own improvements. Help us enhance your experience in this new era for the EGA. Subscribe to the EGA Mailing List and stay tuned In the next weeks we will share more information about the possibilities of the new services. You can easily join the EGA Mailing List to receive all the updates.

  Blog new-set-of-services-at-EGA

• Single-cell RNA sequence analysis of iPS cell-derived cardiomyocytes treated with S-RBD-sfGFP or GFP

  To determine the transcriptional response in human cardiomyocytes treated with SARS-CoV-2 spike receptor-binding domain (S-RBD-sfGFP), human cardiomyocytes differentiated from induced pluripotent stem cells (iPSC-CMs) were replated on day 21 after differentiation and treated with S-RBD-sfGFP or control-GFP for 48 hours on day 26-28. iPSC-CMs were dissociated and the single cell suspension was analyzed by single cell RNA-sequence.

  Study JGAS000620

• Circulating cell-free DNA analysis in Small Cell Lung Cancer

  Small cell lung cancer (SCLC) accounts for ~250,000 deaths worldwide each year. Acquisition of adequate tumour biopsies is challenging and liquid biopsies present the best option for patient stratification and response monitoring. We present genome-wide and targeted plasma DNA sequencing data that identifies tumour related changes in 91% of limited (LS-SCLC) and 100% of extensive stage (ES-SCLC) patients. Parallel analysis of circulating tumour cells (CTCs, by CellSearch) based on ≥ 1 CTC/7.5ml blood increased tumour detection frequencies to 98% patients (95% for LS-SCLC) where CTC count and plasma DNA readouts correlated with disease stage and overall survival (OS). Targeted plasma DNA sequencing identified potential therapeutic targets in >50% of patients. This approach will support trials of targeted therapies where improved patients outcomes are urgently required.

  Study EGAS00001003110

• Synthetic data - Genome in a Bottle

  In May, the National Institute of Standards and Technology (NIST) released its first genome in a bottle, a reference sample of DNA for validating human genome sequences. This so-called truth sequence comes from a decades-old sample donated by a Utah woman for (other) research purposes (NA12878 cell line), which, over the years, has been one of the most studied, and hence best-characterized, human samples. Seeing genomic medicine moving toward mainstream healthcare, researchers at NIST recognized the need for a reference human genome and assembled a private-public consortium in 2012 to create one. As detailed in a 2014 Nature Biotechnology paper (Nat. Biotechnol.32, 246–251, 2014), the group integrated and arbitrated among sequences from 14 data sets, five sequencing technologies, seven read mappers and three variant callers.

  Study EGAS00001005591

• Exome-sequencing of human B cell lymphoma cell lines

  26 cell lines derived from human Diffuse Large B Cell lymphomas (DLBCL) or Burkit Lymphomas (BL) were subjected to whole exome sequencing. Exome capture was carried out using the SeqCap EZ Exome Library 2.0 kit (Roche/Nimblegen) and 100 bp single-read sequencing was performed on a HiSeq2500 (Illumina). 82% of the coding region was covered at least 30x.

  Dataset EGAD00001002262

• WES in muscle-invasive bladder cancer (MIBC) treated with durvalumab plus olaparib in the neoadjuvant setting: NEODURVARIB trial

  This submission contains the metadata derived from the whole exome sequencing of 70 samples from 26 patients who developed advanced urothelial carcinomas. The patients were enrolled in the Neodurvarib clinical trial, which compares the molecular profiles at diagnosis and after neoadjuvant treatment with Durvalumab and Olaparib. In this regard, the analyzed samples include: normal tissue and tumoral tissue obtained from the transurethral resection of the bladder (TURBT, a procedure performed prior to neoadjuvant therapy) from the 26 patients (52 samples), as well as tissue obtained from the radical cystectomy (a procedure performed after treatment with the aforementioned drugs; 18 samples).

  Study EGAS50000000791

• SPECTA__NGS_Screening_Program_for_Efficient_Clinical_Trial_Access

  SPECTA comprises a network of participating European clinical sites and NGS screening platforms that can screen individual patients for multiple molecular targets and potentially allow the design of trials that will match the specific biology of the diseases affecting specific patients with cancer.

  Study EGAS00001000728