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HCC_Immunity

Background information

Chronic hepatitis B virus (HBV) infection contributes to roughly 50% of all hepatocellular carcinoma (HCC), which is the most common form ofr liver cancer. Human leukocyte antigen (HLA), the human equivalent of major histocompatibility complex (MHC), is a group of proteins that the immune system uses to detect pathogens. HLA is highly polymorphic, especially in the peptide-binding groove, and this allows the HLA to bind a wide range of peptides.

In this project, we are interested in:

  1. Is HLA associated with HBV-mediated liver cancer?
  2. How is HBV binding affinity related to HBV-mediated liver cancer?

This project can be split into three parts:

  1. Predict HLA binding to HBV peptides
  2. Gather allele frequency from liver cancer population and the general population
  3. Perform Fisher's test to test allele association with HBV-mediated liver cancer

Methods

Predict HLA Binding

Software used: DTU Health Tech netMHCpan-4.1 and netMHCIIpan-4.0

Details can be found in hla_binding/README.md

Gather allele frequency

Software used: SyntekabioTools HLAScan

Fisher's test

Software used: R