BACKGROUND: Total serum IgE (tIgE) is elevated in individuals suffering from allergic diseases such as asthma, rhinitis and eczema, and elevated tIgE has also been associated with coronary artery disease. Of the genome-wide association study (GWAS) loci identified for tIgE, the human leukocyte antigen (HLA) region has been the most consistently associated. In this study, we used next generation sequence data from the NHLBI Trans-Omics for Precision Medicine (TOPMed) program and graph-based alignment to perform an HLA association study of tIgE levels.

METHODS: HLA-LA was used to conduct HLA typing on the NHLBI BioData Catalyst cloud-based platform. Subjects for whom tIgE levels and TOPMed freeze5b CRAM files were available were included in the analysis (subjects from the Barbados Asthma Genetics Study, the Genetic Epidemiology of Asthma in Costa Rica, COPDGene, Genetics of Cardiometabolic Health in the Amish and the Framingham Heart Study). Analysis strata were defined based on study, race/ethnicity and asthma status (n=5,580 total; n=818 African, n=4,298 European, n=465 Hispanic/Latino ancestry; and n=798 asthmatics). Linear mixed effect models were used to test for association between presence/absence of a specific HLA allele and tIgE, separately for each stratum. Analyses were limited to 159 2-digit HLA alleles with a frequency of at least 1% in one or more strata. Age, sex and the first five principal components of genetic ancestry were included as fixed effect covariates in the models, and a kinship matrix was included as random effect to account for relatedness between individuals. Results were combined using inverse-variance meta-analysis.

RESULTS: HLA allele calls were of high quality, with a mean proportion of 0.008 discordant calls between duplicated samples and a mean Mendelian error rate of 0.016 in parent-offspring trios. HLA DRB1*13:03 was associated with increased levels of tIgE (Bonferroni-corrected p=0.008) in the European ancestry meta-analysis. HLA-DRB1*13 has previously been reported to have a higher frequency in Alternaria-sensitive moderate-severe asthmatics compared to Alternaria-sensitive mild asthmatics; Alternaria spores are the most common airborne mold in the USA.

For the region/set-based association analysis of rare variants in family-based studies, we propose a general methodological framework that integrates higher criticism approaches, SKATs, burden, and multivariate tests into the FBAT approach. Using the haplotype algorithm for FBATs to compute the conditional genotype distribution under the null hypothesis of Mendelian transmissions, virtually any association test statistics can be implemented straightforwardly in our approach, requiring no assumptions about the asymptotic distribution or approximations. Given the conditional joint distribution of the rare variants, simulation-based or exact p-values can be computed without the need to estimate the genetic correlation/linkage disequilibrium (LD) structure between variants empirically. Using simulations, we compare the features of the proposed test statistics in our framework with the existing region-based methodology for family-based studies under various scenarios. Under realistic assumptions, the tests of our framework outperform the existing methodology. We provide general guidelines for which scenarios, e.g., the sparseness of the signals or local LD structure, which test statistic will provide distinct power advantages over the others. We illustrate our approach in an application to a whole-genome sequencing dataset with 900 asthmatic trios.