The major histocompatibility complex (MHC) of chromosome 6 and the killer cell immunoglobulin-like receptor (KIR) region of chromosome 19 are among the most variable and medically important regions of the human genome. The MHC encodes the highly polymorphic human leukocyte antigens (HLA) that are central to immunity and reproduction, and another 140 genes, many with supporting roles in immunity. A subset of HLA allotypes interact with KIR, which are expressed by Natural Killer (NK) cells, modulating their activities in initiating and controlling the immune response. Specific alleles as well as compound genotypes of MHC and KIR have been implicated in susceptibility or resistance to infectious, allergic, inflammatory, and autoimmune diseases, as well as to outcomes of hematopoietic cell transplantation and reproductive success. Asthma is one of the most common inflammatory diseases affecting over 30 million Americans, with 5,000 deaths per year. Atopic dermatitis (AD) occurs in 20% of children and predisposes to asthma. Together they pose significant burden on the health and economy of the country, costing an estimated $82 billion per year. Common to these diseases are a strong genetic component, an environmental or infection trigger, and complex interplay between innate and adaptive immunity. Accordingly, there are long standing associations with MHC diversity and asthma susceptibility, which have been confirmed by recent large scale genome studies, but they remain poorly refined due to the complexity and difficulty of sequencing the region. For the same reasons, the KIR region has never been studied to high resolution in AD or asthma. To overcome difficulties in analyzing these complex genomic regions, we developed a targeted sequencing and bioinformatics approach to analyze MHC and KIR regions at high throughput and resolution. In Aim 1 we will use the methods to analyze the complete MHC genomic regions from 5,000 patients and 5,000 controls, investigating each gene as well as their pathways of interaction. We will study well defined cohorts of individuals from diverse backgrounds, focusing on African ancestry, which associates with the highest prevalence and poorest outcome. We will sequence the entire MHC with high accuracy to determine the full context of any variants associated with asthma susceptibility. In Aim 2 we will perform the first high resolution analysis of NK cell diversity in asthma, supported by directed functional analyses of the activity and specificity of NK cells in disease. By combining high- resolution analysis of KIR and HLA genes with known functional properties of these interactions, we will be able to determine the role of NK cell diversity in asthma. To enhance our methodology and solve the most difficult genomic structural variation, in Aim 3 we will design and implement the first methods to target long-read sequencing specifically to the MHC and KIR regions, and a bioinformatics pipeline to annotate and analyze the...