SBTengine® GPS

 

Introduction

 

SBTengine GPS is a tool in SBTengine that helps you to select GSSPs upfront and resolve ambiguities more efficiently. This tool is only available when using IMGT/HLA database 3.43 or lower.

If pretyping information of a sample is available, it is often possible to determine which ambiguities can be expected and which GSSPs will resolve these ambiguities. Applying them in the first sequencing run will resolve the ambiguities, thus speeding up results and reducing analysis time.

Based on low-res pretyping information, GPS uses allele frequency tables to calculate the expected frequency of the sample being ambiguous after applying the core typing. Then it calculates which GSSPs will resolve these ambiguities and to which extend.

 

How to use GPS


  1. Create ambiguity lists

 

GPS uses lists describing ambiguities. These lists can be generated before you use GPS for the first time. The lists will be saved, but need to be regenerated with any change of IMGT library or allele frequency table.

Lists can be generated by selecting 'Help' -> 'Calculate GPS data' -> 'All frequency lists'

 



This takes some time.



 

  1. Select the GPS tab in SBTengine
  2. Select an allele frequency table

 

 

  1. Add samples. Enter sample names and their low-resolution or high-resolution typings

 

 

or load a pretyping table saved previously

 

 

Save the list of pretypings by clicking the save button.


  1. Click the Analyze button. The list with recommended GSSPs is shown.

 

 


Click on 'Open PDF Report' to open the report, to enable printing.

 

 

 

Applying the GSSPs recommended together with the core typing (exon 2 & 3) wil resolve the ambiguities.

The report contains 2 statistical numbers:

 

%W: The probability of the sample being ambiguous without applying any GSSPs

% A: The probability of the sample being ambiguous after applying the recommended GSSPs.

 

Since the GPS is based on allele frequencies, and on low-resolution pretyping data, the GSSPs recommended may differ from the GSSPs recommended by SBTengine after performing core typing. This is because the low resolution typing may also include ambiguities which will be resolved after core typing. In addition, GPS does not try to resolve between genotypes with very low frequencies, whereas SBTengine does.

 

It can be chosen whether silent variants should be resolved. Also the mimimum improvement can be set.

 

 

Settings

 

The GPS lists and the PDF files by default are saved in the 'GPS' folder located in the active workfolder. In the menu File, Preferences, tabsheet Library and Data Folders, the selection of GPS Data, the location can be changed.