PyPresent

Quantified patient MHC presentation

Author: Rachel Marty

Introduction

PyPresent has been developed to improve the reproducibility of MHC-I and MHC-II presentation scores as seen in (Marty et al. 2017). It is a wrapper that is build around netMHCpan and netMHCIIpan. Users can get residue-centric presentation by single alleles and multi-allelic patients.

Requirements

PyPresent uses the following software:

1. NetMHCpan-3.0
2. NetMHCIIpan-3.1

Licensed only for academic use

And the following Python modules:

1. Pandas
2. Scipy
3. Bio

Anaconda makes downloading the python modules easy

Setup

1. Clone repository locally.
2. Download NetMHCpan and NetMHCIIpan.
3. Update paths for NetMHCpan, NetMHCIIpan and a temporary directory in the config.py file.
4. Download python modules.
5. Run example_usage.ipynb. The scores should be as follows:
   • HLA-A01:01 - 0.25
   • DRB1_1114 - 46.0
   • Patient MHCI - 1.810..
   • Patient MHCII - 5.379..

Inputs needed for scores

Single-Allelic Score (Best Rank)

• MHC-I/MHC-II allele
• Mutation information:
  • Gene sequence - string or fasta file
  • Residue position
  • New amino acid

Multi-Allellic Score (PHBR)

• All MHC-I/MHC-II alleles
• Mutation information:
  • Gene sequence
  • Residue position
  • New amino acid

Test examples

See example_usage.ipynb

Contact

ramarty [at] ucsd.edu

Citation

[Marty, Rachel, et al. "MHC-I genotype restricts the oncogenic mutational landscape." Cell 171.6 (2017): 1272-1283.] (https://www.cell.com/cell/fulltext/S0092-8674(17)31144-3)