In maialab/quincunx: REST API Client for the 'PGS' Catalog

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Polygenic scores

A polygenic score (PGS) aggregates the effects of many genetic variants into a single number which predicts genetic predisposition for a phenotype. PGS are typically composed of hundreds-to-millions of genetic variants (usually SNPs) which are combined using a weighted sum of allele dosages multiplied by their corresponding effect sizes, as estimated from a relevant genome-wide association study (GWAS).

PGS nomenclature is heterogeneous: they can also be referred to as genetic scores or genomic scores, and as polygenic risk scores (PRS) or genomic risk scores (GRS) if they predict a discrete phenotype, such as a disease.

PGS Catalog

The PGS Catalog is an open database of published polygenic scores (PGS). Each PGS in the Catalog is consistently annotated with relevant metadata; including scoring files (variants, effect alleles/weights), annotations of how the PGS was developed and applied, and evaluations of their predictive performance.

Getting PGS scores

You can search PGS scores by three criteria:

• pgs_id: PGS identifier
• efo_id: EFO trait identifier
• pubmed_id: PubMed identifier

While these criteria are not terribly useful, as normally you do not know these identifiers beforehand, these are the search criteria provided by the PGS Catalog REST API (the service quincunx communicates with).

Instead of using these criteria directly, we show you how you may retrieve polygenic score information by starting with a trait or disease of interest. See vignette('pgs-scores-mavaddat') for how to get polygenic scores if starting with a publication of interest.

Let's say you are interested in basophil count. Basophils are one of the several kinds of white blood cells and make up less than 1% of all circulating white blood cells. Basophils play a part in immune surveillance, and varying levels of basophils are associated with different medical conditions, e.g., allergies, inflammation, infection, leukemia or anemia.

We start by querying the PGS Catalog for traits with the term "basophil" --- you may check vignette('getting-traits') for more details on how to use the get_traits() function.

(basophil_traits <- get_traits(trait_term = 'basophil', exact_term = FALSE))

The table (slot) pgs_ids in basophil_traits provides the associated PGS identifiers.

basophil_traits@pgs_ids

These identifiers can now be used to query score information using the function get_scores():

get_scores(pgs_id = basophil_traits@pgs_ids$pgs_id)

maialab/quincunx documentation built on Aug. 18, 2022, 5:31 a.m.