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Analyses de base

The BQC19 performs a series of core analyses on its samples.

These analyses provide researchers with multi-omics experimental data that are generated on a large set of samples, all using the same protocols. This approach fosters cutting-edge research on the biological determinants of COVID-19. In addition, this approach slows down any rapid depletion of collected biological samples by avoiding redundancy of baseline analyses. The results of these baseline analyses can be obtained by filing a BQC19 data access request.

The core analyses include the following:

  • Two types of proteomics;

  • Metabolomics;

  • Immuno-serology;

  • Transcriptomics;

  • Genomics;

  • Clinical laboratory analyses performed on the ROCHE platform.

 

Sample selection

 

Sample selection is based on the following criteria, corresponding to a wide range of severity and clinical presentation:

  1. Hospitalized SARS-CoV-2-positive participants with critical illness.

  2. Hospitalized SARS-CoV-2 positive participants with moderate to severe disease.

  3. SARS-CoV-2-positive participants with asymptomatic or mild disease (with or without persistent symptoms).

  4. Controls (SARS-CoV-2 negative participant).

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Analyses are performed on clinical specimens that were collected in the following situations:

  • Approximately 1400 samples, including from COVID positive and COVID negative participants, were collected during hospitalization, in the acute phase of the infection.

  • An additional 400 samples from hospitalized participants were collected following hospitalization, i.e., approximately 90 days after the infection date.

  • Finally, approximately 200 samples were analyzed from COVID negative and COVID positive participants who were not hospitalized, approximately 90 days after the infection date with and without persistent symptoms. 

BQC19 analyses

 
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Genome-wide sequencing and genotyping (GWAS)

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These analyses are performed on genomic DNA extracted from snap-frozen whole blood aliquots. They include identification of all genetic variants in the host genome and genetic variations such as changes in copy number of certain genes (genome-wide sequencing), as well as common genetic variations across the genome (GWAS genotyping).

 
 

Proteomics

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SomaScan® platform

Simultaneous measurement of nearly 5,000 proteins in collected blood plasma using aptamer-based technology. This technology was chosen for the large number of proteins it can measure in a single sample.

 
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Immuno-inflammatory markers

This approach, complementary to SomaScan® above, will allow for the measurement of established markers of immuno-inflammation on plasma samples, using a very specific and sensitive technique (antibodies specific to each analyte).

Standardized Core Laboratory

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These baseline assays will provide standardized baseline blood tests from the Roche Diagnostics panel for all visits. This includes baseline values for liver, heart and kidney disorders, as well as standard inflammation parameters measured on plasma samples

 

Metabolomics

This large-scale metabolomics analysis (Metabolon platform) will use ultra-high-performance liquid chromatography/tandem mass spectrometry (UHPLC/MS/MS) methods. This extensive small molecule profiling includes 12 000 metabolites.

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Immunoserology

The generation and maintenance of virus-specific antibody responses are likely key for protective immunity against SARS-CoV-2. Andrés Finzi (CRCHUM) is carrying out the following two serological tests on BQC19 plasma samples: i) ELISA (receptor binding domain, RBD): total antibodies, IgM, IgA, IgG; ii) Cell-based ELISA (CBE) measuring antibody binding to the full-length S glycoprotein.

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The National Microbiology Laboratory (NML) will provide plaque reduction neutralizing antibody testing on plasma samples. The plaque reduction neutralization test will quantify the titer of neutralizing antibody in 2,000 BQC19 samples by measuring the number of plaques formed in host cells following mixture of a viral suspension with the plasma samples. These data will provide important information on the immune response of BQ19 participants to COVID-19.

Transcriptomics

Many studies in human viral diseases, including COVID-19, have shown associations between molecular signatures in peripheral blood cells and disease outcome. RNA is extracted from the PAXgene RNA tube collected at the same study visit as the plasma sample analyzed by the other assays and standard short-read RNA sequencing on poly-A RNAs performed on a fraction of the RNA extracted. Initial quality control will be performed at the sequencing facility.

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