epitope-demo

This repository contains sample files and instructions for a live PIRCHE and HLA-EMMA demo

Contents

• "Slides" contains power point presentation, with an introduction to the epitope concepts.
• "CaseStudies" contains the input and output files for PIRCHE and HLA-EMMA analysis
• You may still interpret the output files if the software is not available at this moment.

How to Download Demo Files

It is possible to access all of the files directly here on Github, or optionally, you may download the files to your own computer, to open them in Excel or another software.

1. (If you're not already here) Go to the github website in your browser: https://github.com/bmatern/epitope-demo

2. Click the green [Code] button, then Select [Download ZIP]

3. Extract the .zip file (It might be in your "Downloads" folder)

How to register for PIRCHE

We have created temporary accounts to use PIRCHE during EFI 2022, you should have received an email inviting you to join Ben Matern's Laboratory in PIRCHE.com.

Please change your password.

If there are troubles creating the account

• We can try to resolve it
• If it is a larger issue, the PIRCHE analysis output files are also provided in this repository

Analysis in PIRCHE

1. Login at the PIRCHE Website

2. In the home page, choose "SOT" (solid organ transplantation) option (top right screen), then select "Single Patient":

3. For the Patient, and then the Donors, Copy-paste the patient and donor HLA strings from the Case Study above into the "Input Wizard" fields:

4. For both Patient and Donors, push the [dna/ser] button to switch to "dna", because our HLA genotypes are DNA-based, not Serological types. The default for PIRCHE program is serological types ("ser") and therefore before you switch to "dna", the program will give an error message.

5. Analyze your results....

Analysis in HLA-EMMA

1. Go to https://hla-emma.com/ to download the software. The software runs only in Windows. In the webpage of HLA-EMMA there is a temporary licence for the tutorial (valid until 1st of June 2022), which you can use to finalize your installation. If you need help with installation, please check the manual

2. The steps of the HLA-EMMA analysis are explained in detail in this file

What if you don't have a Windows computer?

• Output files for HLA-EMMA are provided in this repository

Case-study I

(provided by Kirsten Geneugelijk)

Patient_O., blood group B, is a 34 year old male who is on kidney dialysis for almost 4 years. He is registered on the active waiting list since September 2016. He has the following HLA typing (Copy-Paste this text into Patient Input Wizard):

Patient_O,A*02:01,A*01:01,B*07:02,B*08:01,C*07:01,C*07:02,DRB1*15:01,DRB1*03:01,DQB1*06:02,DQB1*02:01

The patient is not immunized, which means that he doesn’t have detectable levels of preformed HLA antibodies. The father of patient O. is willing to donate her kidney to his son. The HLA typing of the father is the following:

Father,A*02:01,A*02:01,B*08:01,B*07:02,C*06:02,C*07:01,DRB1*03:01,DRB1*13:01,DQB1*06:02,DQB1*02:02

In the meantime the patient O. is still registered on the active kidney transplantation waiting list. At a certain time the patient get two deceased donor kidney offers.

Deceased donor 1 has the following HLA typing:

Deceased_1,A*02:01,A*01:01,B*44:03,B*08:01,C*01:02,C*07:02,DRB1*15:01,DRB1*03:01,DQB1*06:02,DQB1*02:01

Deceased donor 2 has the following HLA typing:

Deceased_2,A*02:01,A*01:01,B*07:02,B*08:01,C*07:01,C*01:02,DRB1*15:01,DRB1*03:01,DQB1*06:01,DQB1*02:01

These are the three potential donor strings combined (Copy-Paste this text into Donors Input Wizard):

Father,A*02:01,A*02:01,B*08:01,B*07:02,C*06:02,C*07:01,DRB1*03:01,DRB1*13:01,DQB1*06:02,DQB1*02:02
Deceased_1,A*02:01,A*01:01,B*44:03,B*08:01,C*01:02,C*07:02,DRB1*15:01,DRB1*03:01,DQB1*06:02,DQB1*02:01
Deceased_2,A*02:01,A*01:01,B*07:02,B*08:01,C*07:01,C*01:02,DRB1*15:01,DRB1*03:01,DQB1*06:01,DQB1*02:01

Which donor would you prefer to use for this kidney transplantation?

Case-study II

(provided by Matthias Niemaan)

For another patient R with the following HLA typing (Copy-Paste this text into Patient Input Wizard): Patient_R,A*02:01,A*24:02,B*15:01,B*51:01,C*07:04,C*14:02,DRB1*01:01,DRB1*14:54,DQB1*05:01,DQB1*05:03

We have two donors:

D1,A*24:02,A*02:01,B*07:02,B*44:02,C*07:02,C*05:01,DRB1*15:01,DQB1*06:02 D2,A*02:01,A*03:02,B*15:17,B*51:01,C*07:01,C*15:02,DRB1*13:02,DQB1*06:04

These are the two potential donor strings combined (Copy-Paste this text into Donors Input Wizard):

D1,A*24:02,A*02:01,B*07:02,B*44:02,C*07:02,C*05:01,DRB1*15:01,DQB1*06:02
D2,A*02:01,A*03:02,B*15:17,B*51:01,C*07:01,C*15:02,DRB1*13:02,DQB1*06:04

As you see both donors are rather similar: HLA-DR and HLA-DQ are homozygous, so not a lot of PIRCHE-II are to be expected. Moreover, both donors have only two matches on Class I - besides from that fully mismatched.

Are these two donors as likely to be succesfull transplantation candidates.