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• Variables of diversity, clonality, V and J usage and main COVID-19-reactive GLIPH2 frequencies.

  Main results of the T cell repertorie analysis of a cohort of 61 patients. For each patient, repertorie diversity and clonality metrics, V an J alelle frequency and COVID-19-reactive sequencies have been calculated using open.source code. For more information about the study, please visit DOI: 10.1186/s40246-024-00654-0

  Study EGAS50000000587

• Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases

  Single-cell analysis of the transcriptome, T cell immune receptors, and surface proteome (CITE-seq) from peripheral blood mononuclear cells (PBMCs) of COVID-19 patients with pre-existing autoimmune diseases (rheumatoid arthritis n = 5, psoriasis n = 4, or multiple sclerosis n = 3), as well as COVID-19 patients without pre-existing autoimmunity as controls (n = 10) to investigate altered immune responses.

  Dataset EGAD00001007982

• Shedding light over COVID-19 susceptibility and severity

  “One of the most remarkable features of SARS-CoV-2 infection is the variation in consequence ranging from asymptomatic to life-threatening” state the authors of the majestic Nature paper released in accelerated pre-view on July 2021. This variation in consequences represent not only an issue of burning medical relevance, but also a scientific and intellectual challenge for scientists around the globe. Researchers are known to be easily triggered by a challenge, and they recently demonstrated to be even better at double their efforts to focus on an urgent societal need. In this work led and coordinated by the COVID-19 Host Genetics Initiative (COVID-19 HGI), researchers gathered data from 49,562 cases and two million controls from 46 studies performed worldwide. The majority of the data has been deposited at the EGA, where 29 datasets have been collected under the study number EGAS00001005304. Data gathered from diverse sources conferred a huge robustness to the results. Genetic data from different ancestry origin were included in the analyses, even though data from patients with European origin was highly predominant (approx. 75%). Separated analysis of the different ancestries gave rise to relevant differences in the results, highlighting how important it is to take this aspect in consideration for future studies. Data from the individual studies was compiled into three categories according to COVID-19 severity for a meta-analysis: (a) critically ill cases (b) moderate or severe cases (c) all cases. They were paired with non-COVID-19-reported controls. All three analysis resulted in a total of 13 genetic loci associated with COVID-19 severity. Out of those, 9 loci associated specifically with critical illness, while 6 (a few overlapped) associated with moderated illness. Some genomic position matched previous findings. Interestingly, working with such an enormous amount of data allowed the depth to discriminate association with disease susceptibility vs severity, an issue of large medical relevance. Several loci mapped into biological relevant genes, like TYK2, PPP1R15A and FOXP4, previously implicated in immune response and/or lung functions. Researchers participating in the COVID-19 Host Genetics Initiative have worked in an unprecedented time-tight collaboration, prioritizing data sharing and collective results to tackle the pandemic affecting the world. The scientific community won’t miss any of the lessons to learn from this, and the EGA is ready to keep working to enable safe data sharing and fruitful collaborations.

  Blog covid-19-susceptibility-and-severity

• Age-dependent association of clonal hematopoiesis with COVID-19 mortality in patients over 60 years

  Targeted sequencing with the Myeloid Solutions™ Panel (MYS) of SOPHiA Genetics for COVID-19 patientds (n=241 deceased, n=239 survivors).

  Dataset EGAD50000000001

• scRNA-seq of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 to assess dexamethasone response in the lungs

  Single-cell RNA-sequencing of bronchoalveolar lavage (BAL) samples from patients with severe COVID-19 with or without Dexamethasone treatment and for responders and non-responders was performed using 10x Genomics technology.

  Dataset EGAD50000000292

• Elucidation of male-specific genetic regulation through multi-layered omics analysis

  We performed single-cell RNA-sequencing of peripheral blood mononuclear cells from asthma patients and single-cell multiome (RNA+ATAC) profiling from COVID-19 patients.

  Study JGAS000862

• WES CRAM files of HUG-CEL Covid-19 Genomics Study

  Whole Exome Sequencing Dataset (CRAM files) of 415 admixed Brazilians with Covid-19 extreme phenotypes from recovered nonagenarians and centenarians to deceased adults.

  Dataset EGAD00001009652

• ESGI - Whole Genome Sequencing of samples from the INGI-Val Borbera genetic isolate (X10) (2019-08-19)

  Whole genome sequencing of sampels from an isolated population from the Val Borbera valley in Italy. The samples are sequenced using the Illumina HiSeq X Ten system. . This dataset contains all the data available for this study on 2019-08-19.

  Dataset EGAD00001005268

• CONTAGIOUS trial - COVID-19 16S dataset

  16S amplicon data of nasopharyngeal swabs in a COVID-19 cohort recruited at UZ Leuven. The dataset contains a single experiment, comprising 150 runs corresponding to 125 unique samples. Runs comprise paired fastq files (2*250 bases) obtained from an Illumina MiSeq instrument.

  Dataset EGAD00001006864

• COVID Response Study 2 (COVRES-2)

  COVID Response Study 2 (COVRES-2) - is a collaborative effort between researchers at Ulster University and the Western Health and Social Care Trust. The study aims to identify temporal immune responses associated with COVID-19 severity. A total of n=20 individuals (10=Hospitalised/10=Non-hospitalised) were recruited following a positive PCR result for COVID-19. Current studies 1. Distinct Omicron longitudinal memory T cell profile and T cell receptor repertoire associated with COVID-19 hospitalisation At 3 months post-infection T Cell Receptor (TCR) sequencing and RNA Sequencing were preformed to investigate immunopathological signatures associated with clinical outcome and recovery. This dataset contains both TCR-seq and RNA-seq data for all participants that took part in this study.

  Dac EGAC50000000594