> For the complete documentation index, see [llms.txt](https://allelica-1.gitbook.io/saas/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://allelica-1.gitbook.io/saas/master.md).

# Introduction

![](/files/-MGx2ohnFyhJc7lm-BUk)

Allelica enables users to impute Low-Coverage and Microarray data, discover new Polygenic Risk Scores (PRSs), validate their predictive performance and construct reports on individual PRS.

This user guide provides assistance for: 

* [Allelica Modules](/saas/master.md#allelica-app)
* [Low Pass Impute (Illumina BaseSpace App)](/saas/master.md#loss-pass-impute)

## Allelica Modules

The [Allelica Modules](https://saas.allelica.com/site/app) support the following functions:

* [Discover](/saas/allelica-app-user-guide/discover.md) 
* [Validate](/saas/allelica-app-user-guide/validate.md)
* [Predict](/saas/allelica-app-user-guide/predict.md)

One of the major barriers to PRS usage in clinical practice is the computational complexity needed to calculate per-individual PRSs. Extensive bioinformatics expertise is required to run the entire pipeline, from imputing genomic data, through quality control to result visualization. For these reasons, we developed Software as a Service (SaaS) for genomic risk prediction of complex diseases. Allelica's SaaS is fully automated, GDPR complaint and has been certified as a CE-marked medical device. Researchers wishing to use this SaaS can [contact](mailto:%20research@genomicriskscore.io) us directly.

The synergy of large Human Genome Biobanks with improved statistical methods to model genomes has revolutionized our ability to predict phenotypic expression from a person's genetic makeup. Allelica's SaaS provides a set of tools to estimate disease risk. The PRS metric that Allelica provides estimates the genetic risk of an individual to develop a disease based on a combination of a large number of genetic variants.

Allelica utilizes the largest prospective genotyped cohort available to date, the [UK Biobank](https://www.ukbiobank.ac.uk/). The predicted efficacy of this SaaS tool has [been confirmed against](https://www.biorxiv.org/content/10.1101/763722v2) Coronary Artery Disease (CAD), Breast Cancer (BC), and Prostate Cancer (PC) at the time of writing (May 2020).

## Low Pass Impute

[Low Pass Impute](/saas/impute-app-user-guide-and-benchmark/impute.md) allows users to analyze their data directly from [Illumina's dashboard](https://basespace.illumina.com/dashboard).