Genomics of host–pathogen interactions

• Host and pathogen genomes can be analyzed jointly.
• Host and pathogen co-evolution results in signals of positive selection.
• Recent adaptation to pathogens generates genetic differences across human populations.
• Humans carry collectively abundant, individually rare variants in innate immunity genes.
• The ultimate aim of these analyses is to associate genomic signals with disease traits.

The study of immunity against infection can be framed in the context of genomics. First, long-term association with pathogens results in genomic signatures that result from positive selection. Evolutionary pressures tailor species or individual responses to pathogens, that may be associated with skewed patterns of immunity. Second, recent human population expansion carries an increasing burden of genetic mutation that can result in sporadic immunodeficiencies, and more generally, in diversity in susceptibility to infection. This review highlights current concepts and tools for the analysis of genomes and stresses the interest of these approaches in immunity.