Diseasome

Calculation of multiple risk profiles for
23andme reports,using the PGS Catalog.


PRS

A prototype personal risk score calculator , created for research purposes, was developed to demonstrate how the PGS Catalog can be privately and readily applied to readily available direct-to-consumer genetic testing services, such as 23andMe. No software download, installation, or configuration is needed. The PRS web calculator matches individual PGS catalog entries with an individual's 23andMe genome data composed of 600k to 1.4 M single-nucleotide polymorphisms (SNPs). Beta coefficients provide researchers with a convenient assessment of risk associated with matched SNPs. This in-browser application was tested in a variety of personal devices, including smartphones, establishing the feasibility of privately calculating personal risk scores with up to a few thousand reference genetic variations and from the full 23andMe SNP data file (compressed or not).

OpenSNP

OpenSNP.org is a repository to which users can upload their SNP-sets (and exome-VCFs) from a variety of direct-to-consumer genetic testing brands including 23andMe.

Select an openSNP datatype below:

OpenSNP phenotypes

The Polygenic Score (PGS) Catalog

The PGS Catalog is an open database of published polygenic scores (PGS), annotated with relevant metadata; including scoring files (variants, effect alleles/weights).

Select a PGS category below:


Select a PGS category below:
Select an EFO id below:

Privacy:
All data and calculations take place in the browser. No data or calculations circulate by a server. This application is, foremost, an exercise in privacy-preserving biomedical informatics for consumer genomics data.
Scope/Limitations:
This calculator was devised as an implementation proof of concept. It has a number of important limitations for epidemiology research and it does not meet criteria for clinical use. The current tool uses pre-imputation genotype data and thus results in a low number of SNP matches. Most important, only the relative risk model (Box 1, eq 2) is calculated, with no effort to determine absolute risk of disease. Finally, the risk calculation will only be attempted for PGS catalog entries reporting effects as beta values under "effect_weight".