IPDGC - RISK SCORES
Polygenic and Genetic Risk Scores: how to calculate and understand them

Apart from a very small fraction of neurodegenerative disorders that are caused by strong acting rare mutations in single genes, most are complex diseases, like Parkinson’s disease, that are caused by sophisticated interaction between many factors. Even though the entirety of the biological underpinnings behind such heterogeneous disorders remain elusive. Given recent efforts with genome-wide association studies (GWAS), we have discovered a set of genetic loci involved that cumulatively contribute to risk of Parkinson’s disease. At the moment, these are not entirely comprehensive, nor do they explain all the intricacies, but can shed light on complex diseases.

On GitHub , you can find these calculators, ready to use on your datasets, with the appropriate context, validation, and interpretation. Below is also a link to a Binder environment so you can run this online.

GitHub BINDER
PLINK

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PRSice-2

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Pathways PRS

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App

What is a PRS?

A polygenic risk score (PRS) is a subtype of a genetic risk score (GRS), and is used to evaluate one's overall risk or predisposition to a disease, taking in account comprehensive genetic architecture including the effects of both protective and risk variants.

This value is calculated by comparing individual-level genotype and phenotype data to a larger collection of weighted alleles from genome-wide association study summary (GWAS) statistics and indicates an individual's susceptibility based on alleles present in their genome.

How is PRS Useful?

  1. 1. Calculating PRS can differentiate cases from controls on a population or group level: Cases are expected to have a significantly higher mean PRS than controls
  2. 2. Can advise exploration on different pathways or biomarkers: We can expect that a true biomarker of genetic risk will be more likely be present in persons with a high PRS than with a low PRS
  3. 3. We can stratify Parkinson’s disease patients with a higher scores: You can calculate linear PRS based on a limited number of GWAS SNPs enriched in given cellular pathways like mitochondrial pathways and identify patients with higher mitochondrial burden, and then treat using particular medications which have been shown to boost up the mitochondrial functions
  4. 4. Don’t need a large sample size: You can generate a PRS for any individual and get meaningful results
App
App

What is the relationship between PRS and PD?

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PRS and non-European Populations

The vast majority of whole genome sequence data currently available for use in calculating PRS comes mainly from European populations, leading to an overrepresentation in global studies and potentially limiting accuracy when applied to other ethnic populations.There has been a large effort to collect data from underrepresented populations, especially of those of Asian, African, and indigenous descent, sparking initiatives like Global Parkinson's Genetics Program (GP2), which aims to collect, sequence, and analyze data from around the world.

App
App

Next Steps

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Calculators

UNDER DEVELOPMENT

Genetic Risk Score

PD-GRS European
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Polygenic Risk Score

PD-PRS European
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10 Million people estimated to be affected with Parkinson's disease globally
30 20-30% Estimated heritability of Parkinson's disease
92 Core SNPs associated with risk of Parkinson's disease

Limitations

Although someone’s PRS can include actionable information in giving impressions about genetic predisposition of a person to Parkinson’s disease, it is important to take some caveats into consideration with regard to the limitations in both the construction and interpretation of PRS to efficiently use them

PRS are only able to show correlations and not causations, given the fact that genetic risk is not going to be the only determinant in complex disorders such as Parkinson's disease

PRS only indicate correlations!

Building a PRS might have discrepancies due to different ethnic backgrounds, given that disease-associated alleles can have significantly different frequencies between populations

PRS discrepancies might be due to different ethnic backgrounds!

Depending on the strategy used to calculate the PRS, either linkage disequilibrium-based pruning or adjustments can contribute to bias due to the limited reference haplotype panels for diverse populations

PRS, likely any calculation, comes with inherent biases!

Publications

These are recommended publications for further reading and the sources for the content on this website

Genetic Risk score (GRS): Used to Evaluate Effects of Genetic Susceptiblity Factors in Risk Prediction Models

Other types of PRS models based on incorporation of different types of data
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Polygenic Risk Scores: a Biased Prediction?

Looking at using PRS beta values derived from one population and applied to another, and how this can affect bias
Read More

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Example4

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Example5

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Example6

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Resources

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Polygenic Score Catalog

An open database of polygenic scores and the relevant metadata required for accurate application and evaluation

Global Parkinson's Genetics Program

An initiative working to sequence and analyze data from around the world