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• Whole exome sequencing of 184 unrelated subjects with 22q11.2 deletion syndrome (DiGeorge syndrome/velo-cardio-facial syndrome)

  Our goal is to find genetic modifiers of major phenotypes in patients with 22q11.2 deletion syndrome, also known as DiGeorge syndrome or velo-cardio-facial syndrome. Whole exome sequencing was performed as part of a contract to the NHLBI, Resequencing and Genotyping Service. We have obtained cardiac phenotype information from the de-identified subjects enrolled in the study, either by echocardiography report or medical doctor report. All of the subjects have a 3 million base pair 22q11.2 deletion flanked by low copy repeats, LCR22, A-D.

  Study phs000987

• Genome Wide Association Study of Subjects with Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS)

  Myalgic encephalomyelitis, also known as chronic fatigue syndrome or ME/CFS, is a complex and heterogeneous disease that severely impacts the health and quality of life of those afflicted. Several lines of evidence support the possibility that ME/CFS development may involve a heritable component. In this pilot study, 42 cases that meet the diagnostic criteria of ME/CFS and 38 healthy controls were consented into this study. The goal of this study was to identify candidate polymorphisms that can be used for a large multi-center screening study.

  Study phs001015

• Deep Sequencing of 3 Cancer Cell Lines on 2 Sequencing Platforms (Illumina HiSeqX and NovaSeq)

  To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we performed whole-genome sequencing of 3 common cancer cell lines (COLO-829, HCC-1143 and HCC-1187) along with their matched normal cell lines to great sequencing depths (up to 278X coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. This dataset can be used for benchmarking purposes by the genomic community and as a reference call set for scientists using these 3 cell lines.

  Study phs001839

• Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

  This observational study was designed to determine the cellular tropism of Influenza A and B Viruses (IAV, IBV) from samples taken from the upper respiratory tract collected during routine nasal washes during the 2017-2018 season. Using single-cell RNA sequencing (scRNA-seq) we sought to determine which cell types could be infected, what the cellular response was to infection in both infected and bystander cells, and to compare the intra/inter-host variability of IAV and IBV during a single season at a single healthcare provider location.

  Study phs002039

• Aerobiology, Immunology, and Mycobacterium Tuberculosis Transmission

  We submit data from the TB Aerobiology, Immunology and Transmission (TBAIT) study examining clinical and transcriptomic characteristics associated with Tuberculosis cough aerosolization. From a prospective longitudinal cohort of 142 participants with previously untreated pulmonary Mycobacterium tuberculosis (Mtb) infection, we assessed presence of culturable Mtb aerosols using a cough aerosol sampling system (CASS), as well as other clinical, microbiologic, and immunologic characteristics. We performed whole blood transcriptional profiling (submitted here) on a convenience subset of 29 cough aerosol culture (CAC) positive participants and 29 CAC negative participants, using Illumina NextSeq RNA Sequencing (RNA-Seq).

  Study phs003727

• FEGA Sweden Helpdesk

  FEGA Sweden is an archive for storing and sharing all kinds of data resulting from biomedical research projects. As a national node of the Federated European Genome-phenome Archive (FEGA), we enable researchers to store their data in Sweden in a way that meets the requirements of the General Data Protection Regulation (GDPR). Any data submitted to the archive is subject to controlled access, meaning access to the data only will be granted after a formal application procedure. Using FEGA Sweden for storing and sharing data is free of charge for academic users affiliated with a Swedish university. However, the university must have a signed Data Processing Agreement (DPA) with Uppsala University. The current list of universities with a signed DPA can be found here: https://fega.nbis.se/submission/complying-with-gdpr.html. FEGA Sweden is hosted by the National Bioinformatics Infrastructure Sweden (NBIS), which legally is part of Uppsala University. NBIS forms the bioinformatics platform at SciLifeLab and constitutes the Swedish node of the European organisation ELIXIR. Contact the FEGA Sweden Helpdesk at fega-sweden@nbis.se for further questions.

  Dac EGAC50000000077

• Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

  Gastric cancer (GC) is a major cause of global cancer mortality with high levels of heterogeneity, and intratumoral heterogeneity (ITH) represents a significant barrier to GC patient outcomes. In this study, we applied GeoMx DSP technology to identify ITH in GC. We found spatially colocalized RNA-based intratumor subgroups within samples, each correlated with distinct spatially oriented TME and immune profiles. The findings broadening our understanding of the spatial and molecular complexity of GC ITH and offering a valuable data resource for future exploration and discovery.

  Study EGAS50000000345

• Synthetic - FEGA Sweden Heilsa synthetic dataset December 2023

  Synthetic - This submission contains a subset of a synthetic dataset derived from the project Heilsa Tryggvedottir - a Nordic collaboration on sharing sensitive human data. Heilsa Tryggvedottir is funded by the Nordic e-Infrastructure Collaboration (NeIC), the ELIXIR nodes of Finland, Norway, and Sweden, Computerome in Denmark, and the Estonian Scientific Computing Infrastructure (ETAIS). In the synthetic data creation process, it was attempted to strike a fine balance between the usability of the datasets (e.g. technical FEGA development, testing, user training, and basic bioinformatics) and compliance with GDPR. File names and file content (e.g. headers in fastq) are anonymized. Moreover, the X, Y, and mitochondrial sequences have been discarded from the original data since these data can be used for maternal, paternal, or ethnic origin tracing. The dataset does not follow natural haplotype distribution (inherent to imputation panels). The only inputs derived from real sequence data are variant distribution density per chromosome and learning sequencing error models. The synthetic dataset consists of two fastq files, a cram file, a vcf file, and two index files.

  Dataset EGAD50000000119

• Genome-wide NanoRCS of cfDNA from plasma of healthy individuals

  Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challenging, as much fewer than 5% of the cell-free DNA in the blood typically originates from the tumor. To detect lowly abundant molecules, extremely sensitive sequencing methods are required. We adapted a new technique, NanoRCS, which is based on Oxford Nanopore sequencing of concatenated copies of a single DNA molecule for genome-wide sequencing, and applied this to plasma of healthy controls.

  Study EGAS50000000695

• Splicing signature analysis of RNU4-2, RNU5A-1 and RNU5B-1

  Pathogenic variants in the snRNA RNU4-2 were recently described as a frequent cause of neurodevelopmental disorders. In our study we further delineate the phenotype associated with RNU4-2 and we also identify pathogenic variants in RNU5A-A and RNU5B-1. Capture-based RNA-Seq were performed to compare splicing pattern between affected and control individuals. A strong signature based on alternative 5' splice site usage was found for RNU4-2 patients, and we suggest an either 5' or 3' signature depending on the variant's localiztion in U5 genes.

  Study EGAS50000000889