Table of contents
Allelica Modules User Guide
Impute App User Guide and Benchmark

Predict

Predict allows users to calculate the Polygenic Risk Score (PRS) of single individual or a batch of samples.

Login to saas.allelica.com to access these functions in the PRS Predict App:

Step 1 – Upload Individual(s) Data

1.1 Verify your data format

The first step to ensure successful processing of your file requires the data to be formatted correctly.

For example, a VCF must provide the data in 2 tab-delimited columns (not comma delimited, as previously described).

The phenotype ID must correspond to that applied by the UK Biobank. They provide a search engine for this purpose.

Other data-standards that may be parsed include:

  • Oxford genotype format (bgen/bfam/bsam)

  • Plink genotype format (pgen/psam/pfam)

  • Binary format (bim/bed/fam)

Null values are not acceptable.

1.2 Once you have your data in the correct format, use our file picker to upload it. Click "Browse". Navigate to your file and upload.

1.3 Click "Done".

Finalizing Upload Validation Population

1.4 A successful upload is confirmed with an "Actions done" verification providing a date/time stamp.

Step 2– Select PRS

There are 2 paths available to users:

2.1 Use the UK Biobank data as the population for comparison.

2.2 Provide your custom population for comparison.

Path 2.1

2.1.1 To use the UK Biobank data as the population for comparison, check the boxes for the disease/s you wish to validate:

2.1.2 Click "Select" to confirm your checkbox selections.

2.1.3 Click "Done".

Path 2.2

Alternatively, you may provide your custom population for comparison by uploading your own dataset.

2.2.1 Verify your data format

To ensure successful processing of your file, the data must be formatted as 3 tab-delimited fields. The file extension type must be .csv. Your column layout must be:

  1. rs ID

  2. Effective allele

  3. Weight

Matching your data to the expected structure is a vital step. You must setup your data appropriately pre-submission.

rs ID

Effective allele

Weight

rs12345

A

0.0003

rs12346

C

0.021

A tab-delimited file provides these 3 columns with an even spacing (tab) between them such as:

rs12345 A 0003

A comma-delimited file will be rejected, such as:

rs12345,A,0.0003

2.2.2 Once you have your data in the correct format, use our file picker to upload it. Click "Browse". Navigate to your file and upload.

2.2.3 Check the boxes for the disease/s you wish to validate:

2.2.4 Click "Select" to confirm your selections.

2.2.5 Click "Done".

Step 3 – Select PRS Percentile

There are 2 paths available to users:

3.1 Use the UK Biobank data as the population for computing the PRS percentile.

3.2 Provide your custom population for computation.

Path 3.1

3.1 To use the UK Biobank data as the population for comparison, click "Done".

Path 3.2

3.2.1 To upload your own population use the link in "upload it here".

3.2.2 Once you have your data in the correct format This may deserve further description, use our file picker to upload it. Click "Browse". Navigate to your file and upload.

Finalizing Select PRS

3.3 Success is confirmed with a "Task completed" verification providing a date/time stamp.

If you want to revert the upload of your data or your selections at any time, simply use the "Reset" option.

Step 4 – Run the Model

You are able to return to any of the previous steps to verify or update your choices at any time.

Once you have finalized all your selections, click "Run".

Step 5 – Download the Report

The processing power required to run the analysis is substantial. The main factors that will influence your run-time are the algorithm selected and your population size. You will receive an email notification when your report is available to download within 3–5 days.

Troubleshooting?

If you need assistance, please reach out.