Getting Cohorts

Cohorts

A cohort is a group of individuals with a shared characteristic. Cohorts are identified in quincunx by the cohort_symbol variable. Participants in cohorts are used to define samples, which in turn, are used to assemble sample sets. For more details on the relationship between the concepts of cohorts, samples and sample sets, see vignette('cohorts-samples-sample-sets').

Given that study participants typically come from one or more catalogued cohorts and that cohorts can have a strong bias ancestry composition — i.e., most cohorts are mostly composed of European-ancestry individuals —, it can be really important to know which cohorts have been used at the different stages of a Polygenic Score (PGS) life cycle to assess the transferability of PGS performance^1–3.

If you know beforehand the cohort acronyms (e.g., "23andMe") that you are interested in, then you can get their full name and associated PGS identifiers using the get_cohorts() function by providing their symbols with the parameter cohort_symbol:

library(quincunx)
get_cohorts(cohort_symbol = '23andMe')
#> An object of class "cohorts"
#> Slot "cohorts":
#> # A tibble: 1 × 2
#>   cohort_symbol cohort_name
#>   <chr>         <chr>      
#> 1 23andMe       23andMe    
#> 
#> Slot "pgs_ids":
#> # A tibble: 18 × 3
#>    cohort_symbol pgs_id    stage   
#>    <chr>         <chr>     <chr>   
#>  1 23andMe       PGS000336 gwas/dev
#>  2 23andMe       PGS000730 gwas/dev
#>  3 23andMe       PGS000731 gwas/dev
#>  4 23andMe       PGS000732 gwas/dev
#>  5 23andMe       PGS000766 gwas/dev
#>  6 23andMe       PGS000767 gwas/dev
#>  7 23andMe       PGS000780 gwas/dev
#>  8 23andMe       PGS000790 gwas/dev
#>  9 23andMe       PGS000800 gwas/dev
#> 10 23andMe       PGS000810 gwas/dev
#> 11 23andMe       PGS000867 gwas/dev
#> 12 23andMe       PGS000902 gwas/dev
#> 13 23andMe       PGS000903 gwas/dev
#> 14 23andMe       PGS001774 gwas/dev
#> 15 23andMe       PGS002235 gwas/dev
#> 16 23andMe       PGS000730 eval    
#> 17 23andMe       PGS000731 eval    
#> 18 23andMe       PGS000732 eval

The pgs_ids slot contains a tibble of associated PGS identifiers with the queried cohorts. The stage variable indicates the PGS stage in which the cohort was used.

To get all catalogued cohorts in the PGS Catalog, leave the cohort_symbol parameter as NULL (default). Note that, in this case, it may take a few minutes for the download to complete.

References

1. Reisberg, S., Iljasenko, T., Läll, K., Fischer, K. & Vilo, J. Comparing distributions of polygenic risk scores of type 2 diabetes and coronary heart disease within different populations. PLOS ONE 12, e0179238 (2017).

2. Martin, A. R. et al. Clinical use of current polygenic risk scores may exacerbate health disparities. Nature Genetics 51, 584–591 (2019).

3. Duncan, L. et al. Analysis of polygenic risk score usage and performance in diverse human populations. Nature Communications 10, (2019).