University of Toronto, SickKids

Position ID:University of Toronto-SickKids-POSTDOC [#17667]
Position Title: Postdoctoral position in COVID-19 host genetics
Position Type:Postdoctoral
Position Location:Toronto, Ontario M5G 1X8, Canada [map]
Subject Areas: Statistics / Life Science
Epidemiology / molecular or genetic epidemiology
Computational Biology
Genetics / Statistical
Appl Deadline:2021/05/27 11:59PMhelp popup (posted 2020/11/27)
Position Description:    

About The Canadian COVID Genomics Network

On April 23, 2020, the Federal Government committed $40 million ( to support Genome Canada’s launch of the newly formed Canadian COVID Genomics Network (CanCOGeN). As Canada’s national facility for genome sequencing and analysis, CGEn will lead a nation-wide Host Genome Sequencing Initiative within this framework to sequence genomes of 10,000 Canadians to help understand the genomic architecture of the host response to SARS-Cov-2. CGEn is mandated to develop regional, national, and international linkages to ensure that this investment has maximal impact for the health of all Canadians.

Area of Research 

The Genetic Epidemiology Committee of the CGen HostSeq project ( is now looking to build a team of talented data scientists to work together to identify genetic variation that contributes to SARS-Cov-2 infection, susceptibility, and COVID-19 disease severity by supporting ongoing investigations and by addressing independent research questions. Successful candidates will join a team of internationally recognized scientists in genetic epidemiology and statistical genetics.

Position Openings 

Currently, the committee is looking to hire statisticians, bioinformaticians, epidemiologists, programmers, infectious disease researchers and human geneticists for post-doctoral fellowship positions, and we have several openings for these positions. We may require the work to be done remotely, and we may provide access to super computers and secure servers.  

Required skills

The skills required for these roles are any subset of the following:

  • Experience with imputation of missing phenotype data 
  • Familiarity with genotype imputation and phasing (software lines such as IMPUTE, SHAPEIT, PHASE and BEAGLE) 
  • Manipulating whole genome sequences using software such as Burrows Wheeler Aligner, samtools, Rainbow or related software (including R package such as SNPAssoc, sequinR) 
  • Computation of polygenic risk scores 
  • Genome-wide association studies using software such as plink, plink2, bgenie, snptest, ldak or qctool 
  • Genome-wide association studies using whole genome sequencing 
  • Rare and common variant analysis 
  • Computation of genetic correlation using software such as LDSC/LDSR, GCTA, GEMMA or phenix 
  • Functional annotation of genetic variants 
  • Imputation of HLA serotypes from sequencing data  
  • Database management and data preprocessing in R, matlab, python or SQL. 
  • Website development, including backend development using python or administration of apache servers (or prior experience with the pheweb software) 
  • X chromosome analysis (working knowledge of inactivation, formats and methods for pseudoautosomal regions, the XG blood group system, whole genome analysis of X or interaction between X and immunity)


The term of the contract is up to two (2) years. The initial contract will be one (1) year, with the possibility of extending to two years based on progress.

Required Qualifications

  • A Master’s or PhD Degree in a relevant discipline. 
  • Experience analyzing genetic data or developing genetic software. 
  • Demonstrated problem-solving skills, time management and written and oral communication skills. 
  • Demonstrated ability to think and work independently solving analytic challenges.


The salary will be determined based on the position and previous experience plus benefits. 

Application Instructions

Individuals interested in these openings should submit a cover letter indicating the specific skills they possess (from the Required Skills section, above). They should also list their interest and experience in the research area, a curriculum vitae, and a copy of a scientific paper they contributed to with a description of their role. This letter should explicitly address previous experience analyzing large scale genetic data, such as performing GWAS, calculating genetic risk scores and experience with study design. Applicants should include name and e-mail addresses of two potential referees and indicate the date they will be available to begin. All application materials must be submitted as PDFs at or in email to Review of application will begin immediately and continue until the openings are filled. We appreciate all expressed interest in these positions but only those candidates short listed for an interview will be contacted.

All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.

Diversity Statement 
The team is strongly committed to diversity within its community and especially welcomes applications from racialized persons / persons of colour, women, Indigenous / Aboriginal People of North America, persons with disabilities, LGBTQ persons, and others who may contribute to the further diversification of ideas.

Accessibility Statement 
The team strives to be an equitable and inclusive community, and proactively seeks to increase diversity among its community members. Our values regarding equity and diversity are linked with our unwavering commitment to excellence in the pursuit of our academic mission.

We are committed to the principles of the Accessibility for Ontarians with Disabilities Act (AODA). As such, we strive to make our recruitment, assessment and selection processes as accessible as possible and provide accommodations as required for applicants with disabilities.

We are not accepting applications for this position through AcademicJobsOnline.Org right now. Please apply at
Contact: Natalie Sun
Email: email
Postal Mail:
SickKids, University of Toronto
Administrative Contact: Lloyd Elliott
Peter Gilgan Centre for Research & Learning
The Hospital for Sick Children (SickKids)
686 Bay Street, Room 12.9801
Toronto, ON
M5G 0A4
Web Page:

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