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: The Canadian COVID-19 Prospective Cohort Study (CanCOV)
Principal Investigators: Angela Cheung and Margaret Herridge
Affiliation: University Health Network
Summary: The Canadian COVID-19 Prospective Cohort Study (CANCOV) is the first Canadian study to provide a comprehensive evaluation of early to 1-year outcomes in patients with COVID-19 and their family caregivers. Built on the GEMINI and RECOVER networks, this study is a multi-centre one-year follow-up of COVID-19 patients across the spectrum of illness severity (non-hospitalized, hospitalized non-ICU and hospitalized ICU) in Ontario, Quebec, Alberta, and British Columbia. We are a consortium of interdisciplinary investigators and clinicians leading multiple COVID19 studies across Canada. Our research ranges from genomics and multi-omics, antibody testing and immune analyses, to physical and mental health outcomes. Our overall objectives are to better understand both short and long-term outcomes in patients and their caregivers, and the predictors of those outcomes. We aim to fully characterize their genetic and clinical risk factors, functional and neuropsychological status, return to work and pattern and cost of healthcare utilization.
Research focus: Disease outcomes, Disease risk factors
Study Design: CANCOV is a prospective observational study of 1000 hospitalized patients (general wards + ICU) and their caregivers as well as 1000 non-hospitalized patients with COVID-19. Inclusion criteria includes positive COVID-19 test and older than 16 years of age. Exclusion criterial includes anticipated death or withdrawal of life sustaining treatment within 48 hours, catastrophic neurological injury, patients unlikely to comply with follow-up or lives greater than 300 km from centre, physician refusal, or no next of kin or SDM available (if patient unable to provide consent).
Genetic Analysis Planned: host whole genome sequencing, genome-wide association studies, epigenomic/transcriptomic profiling including analysis of changes in DNA methylation. T/B cell receptor sequencing and viral genome sequencing.

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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: Immunopathology of post-acute COVID-19 syndrome
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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Study Title: Host Genetic Factors Underlying Severe COVID-19
Principal Investigator: Catherine Biggs and Stuart Turvey 
Affiliation: University of British Columbia, BC Children’s Hospital Research Institute
Study Summary/Research Question: SARS-CoV2 causes a wide range of symptoms–some individuals are asymptomatic, while others experience severe or fatal disease. Our study will determine which components of the immune system are critical for defending against SARS-CoV2. We will do so by looking for genetic changes affecting immune function in otherwise healthy patients who develop severe or unusual SARS-CoV2 complications. This work is part of an international initiative entitled the COVID human genetic effort (COVID-HGE), led by immunologists and geneticists from over 75 participating countries. Our goal is to recruit all patients from across BC who are eligible to participate, supported by Genome Canada’s CANCoGEN initiative to perform whole genome sequencing on Canadians affected by COVID-19. Understanding the host factors underlying susceptibility to severe or unusual COVID-19 complications is a critical step in identifying treatments for those affected. The urgency of this work has been further magnified by the identification of an emerging multisystem inflammatory syndrome in children (MIS-C) recently infected with SARS-CoV2. As clinical immunologists, we have a track record of success in identifying targeted therapies for patients based on the underlying molecular defect predisposing them to infection and immune dysregulation, and this study is crucial for applying this expertise to COVID-19.
Study Design: This translational research program will enrol previously healthy individuals in British Columbia who develop severe COVID-19. Severe disease is defined as any of the following: requiring ICU admission, cardiorespiratory support such as non-invasive or mechanical ventilation, extracorporeal membrane oxygenation, or unusual complications such as multisystem inflammatory syndrome in children (MIS-C) associated with COVID-19, encephalitis, other inflammatory complications. Whole genome sequencing of the study participants will be sponsored by the federally funded CanCOGeN (Canadian COVID Genomics Network) HostSeq project. Genetic sequencing data will be stored in the HostSeq COVID-19 databank and analyzed at our institution and in collaboration with the COVID human genetic effort. Candidate variants will undergo functional characterization, and precision medicine-based testing for treatments specific to the particular immune pathway affected by the individual’s underlying genetic variant.
Genetic assays planned: Whole genome sequencing
Other assays planned: Candidate variants will undergo functional characterization, and precision medicine-based testing for treatments specific to the particular immune pathway affected by the individual’s underlying genetic variant.

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Study Title: Genomic determinants of COVID-19: Integration of host and viral genomic data to understand the COVID-19 epidemiologic triangle.
Principal InvestigatorDr. Stuart Turvey
Study Summary/Research Question: COVID-19, caused by the SARS-CoV-2 virus, is a global pandemic and a public health emergency worldwide. While majority of cases present with mild or no symptoms at all, some progress to severe pneumonia, end-stage pulmonary disease and multi-organ failure. Mechanisms underlying susceptibility to disease and variability of health outcomes are unclear. As with any infectious disease, COVID-19 is a complex interaction between the pathogen (SARS-CoV-2), the host (human) and the environment (e.g., lifestyle). Integration and study of large-scale human and viral genomic data with the variable clinical outcomes and other epidemiological data is crucial for understanding the COVID-19 “infectious disease triangle” and to inform public health response. Leveraging federal support through the Canadian COVID-19 Genomic Network (CanCOGeN) and public health efforts at the British Columbia Centre for Disease Control (BCCDC), this study will test the hypothesis that underlying host and viral genomic factors, at least in part, contribute to COVID-19 disease susceptibility and variable health outcomes of infection and are likely influenced by environmental factors such as lifestyle and built environment.
Study Design: This is a genomic epidemiologic study to explore the genomic determinants of COVID-19 and how they contribute to disease susceptibility and health outcomes. The study will generate an integrated data set with viral and host genomic data linked with clinical and epidemiological data to investigate how host and viral genetic constitution contributes to the host immune response. Using public health generated data at the BCCDC, potential study participants (individuals of all ages with documented COVID-19 infection in BC) will be identified and invited to participate in the study. Following recruitment, individual consent and sample collection, we will perform host WGS on all study participants (HostSeq) and with explicit patient consent, link the host genomic data to the existing viral genomic data as well as other clinical, epidemiological data available through the BCC19C and other health authorities and research institutes. The integrated data set will be analysed to identify common and rare germline variants associated with host susceptibility and immune response in COVID-19 using case-case and nested case-control study designs.
Genetic assays planned: Whole genome sequencing

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Study Title: COVID-19 and Aging Adults (CLSA-COVID19 studies)
Principal Investigator: Parminder Raina
Affiliation: McMaster University
Study Summary/Research Question: The CLSA is a large, national, long-term study of more than 50,000 individuals who were between the ages of 45 and 85 when recruited. These participants are being followed until 2033 or death. The aim of the CLSA is to find ways to help people live long and live well and understand why some people age in healthy fashion, while others do not. Participants of CLSA have been invited to participate in a few different COVID-19 studies. For participants who have tested +ve (diagnosis or antibody testing) for COVID-19  CLSA is partnering with HostSeq to gather whole genome sequencing information. The CLSA COVID-19 studies aim to better understand how widespread SARS-CoV-2 infection is among adults over age 50.
Study Design: The CLSA COVID-19 Antibody Study collects and analyzes blood samples from more than 19,000 CLSA participants in 10 provinces. Study participants also complete a questionnaire, either by phone, or online, that collects information about symptoms, risk factors, health- care use and the psychosocial and economic impacts of COVID-19.
Genetic assays planned: WGS
Other assays planned: serological testing, immunoprofiling
COVID related research category: Aging, immunity, antibody

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Study Title: Jewish General Hospital Site of The Biobanque Quebec COVID-19
Principal Investigator: Juthaporn Cowan
Affiliation: The Ottawa Hospital Research Institute
Study Summary/Research QuestionA significant proportion of COVID-19 patients has persistent symptoms, which affect their quality of life. We aim to study immunopathogenesis of persistent symptoms.
Study Design: Cohort study
Genetic assays planned:TBC
Other assays planned: Immune profiling – exhaustion, tolerance, metabolism

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More coming soon…