Protocol for analyzing human leukocyte antigen variants and sexually transmitted infections: from genotyping to...

This chapter describes experimental and analytical procedures that can be used to decipher the specific role of human leukocyte antigen (HLA) variants in infectious diseases. The techniques are distilled from more than one decade of active immunogenetics research, primarily on sexually transmitted infections (STIs) caused by viral and bacterial pathogens, including human immunodeficiency virus type 1 (HIV-1), hepatitis B virus (HBV), and Chlamydia trachomatis. The specific approaches cover (1) sequence-specific oligonucleotide (SSO) probe hybridization for low-resolution genotyping, (2) sequencing-based typing (SBT) for high-resolution, (3) statistical methods for testing associations between HLA variants and phenotypic traits, and (4) enzyme-linked immunospot (ELISpot) assay for enumerating HLA-restricted and epitope-specific T-lymphocyte responses. Proper application of these mature and robust techniques should help establish the importance of individual HLA alleles, haplotypes, and supertypes to host-pathogen interactions.