HostSeq Studies

HostSeq Studies

The following Study Partners are currently enrolled in the HostSeq initiative. This list will be updated as additional studies are on-boarded as part of the HostSeq initiative.

Study Title: COVID genMARK study
Principal Investigator: Upton Allen
Affiliation: The Hospital for Sick Children
Study Summary/Research Question: The study intends to understand why some people get severe while others get mild illness. This will be done through a study of the genetic and immune profile among individuals.
Study Design: Any individual who has a positive COVID diagnosis or has symptoms of COVID-19 or has household contact with a COVID-19 patient can participate in the study. Individuals will be required to answer a questionnaire, provide blood for genetic and immune testing and do a nasal brush test. Altogether 2000 individuals will be studied.
Genetic assays planned: WGS
Other assays planned: Immune profiling – cellular as well as humoral responses, including antibody testing. Immune responses will also be measured in respiratory epithelial cells.
Related research: The genMARK study has affiliated projects including a targeted focus on susceptibility among North American and Caribbean Black populations.
Website: www.covidgenmark.ca

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Study Title: Implementation of serological and molecular tools to inform COVID-19 patient management (GENCOV)
Principal Investigators: Jordan Lerner-Ellis, Jennifer Taher
Affiliation: Sinai Health
Study Title: Implementation of serological and molecular tools to inform COVID-19 patient management (GENCOV)
Study Summary/Research Question: There is considerable variability in symptom severity and outcomes among patients infected by SARS-CoV-2. Linking genome and viral sequencing information to antibody (immune) response and other biological information (sex, age, ancestry, symptom severity, comorbidities and outcome), may identify characteristics of patients that are associated with poor and favorable outcomes. This study will address three aims. Aim 1: Identify the characteristics of the antibody response that result in maintained immune response and better patient outcomes. Aim 2: Determine impact of genetic differences on COVID-19 infection severity and immune response. Aim 3: Determine impact of different viral strains on antibody response and patient outcomes. Evidence from this study will determine if immune response, viral strain and genome sequencing are effective for the diagnosis, prognosis and management of patients with COVID-19.
Study Design: Patients with COVID-19 will be recruited from six hospitals in Ontario. This is a prospective observational cohort study with a study size of 1500 patients, 18 years and above. The target population includes patients seen in the emergency department and COVID assessment centres with mild symptoms as well as hospital in-patients with severe symptoms. Samples will be obtained at baseline and at 1 month, 6 months and 1 year post COVID-19 diagnosis. Immunity will be assessed by measuring antibody response (isotype, titer, antigen target, and viral neutralization) and T/B Cell receptor sequencing. Genetic variation assessed by sequencing patient and viral genomes and physiological response characterized by biochemical laboratory parameters as well as from patient characteristics obtained from patient charts. Statistical analysis will be used to test for associations between antibody levels, genetic variation, viral genome variation, and patient characteristics including age, sex, ethnicity, comorbidities, outcome, treatment, and symptom severity. This study will link serological, genomic and patient characteristics to provide a comprehensive understanding of factors that contribute to variability in clinical symptoms and outcomes among COVID-19 patients.
Genetic assays planned: Host Genome Sequencing, Viral Genome Sequencing, T/B Cell Receptor Sequencing
Other assays planned: Immune profiling, Antibody characterization (ELISA assay), Biochemistry panel testing

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Study Title: The Genetics of Mortality in critical care (GenOMICC)
Principal Investigator: David Maslove
Affiliation: Queens University
Study Summary/Research Question: GENOMICC is an international COVID study with collaborations in UK and Canada. Susceptibility to COVID-19 is almost certainly, in part, genetically determined. The GenOMICC study focuses on trying to find the genetic determinants of severe, life-threatening COVID-19 infections. All patients with confirmed COVID-19 admitted to intensive care units are eligible. By identifying genetic features that are associated with severe COVID-19, we will identify new targets for prevention and treatment, in order to respond to the global crisis.
Study Design: Patients with severe COVID-19 requiring ICU admission will be recruited. A single sample of whole blood will be collected and used for whole genome sequencing. The initial comparison group will be healthy controls, with comparisons to milder disease carried out according to data availability. The target enrollment for is 1,000 patients in Canada.
Genetic assays planned: WGS
Other assays planned: Analysis of clonal hematopoiesis and its association with COVID-19

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Study Title: COVID 19 surveillance collaboration
Principal Investigator: Bruce Ritchie
Affiliation: University of Alberta
Study Summary/Research Question: The team aims to study the biology of Covid-19 infection in humans, develop and improve tests for Covid-19, develop vaccines to prevent covid-19 and find better ways to treat Covid-19 and other infections in the future
Study Design: The study will recruit COVID positive individuals from University of Alberta Hospital in Edmonton, AB; Royal Alexandra Hospital in Edmonton, AB; Misericordia Hospital in Edmonton, AB; Hospital in Grand Prairie, AB and affiliated nursing homes. COVID negative individuals will be included as controls. Ths goal is   to recruit 200 Covid-19 positive patients and 200 Covid-19 negative controls.  The team is collecting serial samples of saliva, urine, plasma (EDTA & Lithium Heparin), peripheral blood monocytes, platelets and neutrophils.
Genetic assays planned: WGS, RNA sequencing
Other assays planned:  Immune profiling, viral sequencing, methylation and glycemic marker testing, extensive metabalomics, Lipidomics, glycomics program, as well as plans to study platelets, neutrophils, & lymphocytes, blood coagulation factors, and lipids from plasma, platelets and neutrophils.

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More coming soon…