While most common variants associated with celiac disease have now been identified through genome-wide association studies (GWAS), outstanding questions still exist regarding the validity of previously identified common variants, the presence of common variants associated with celiac disease within the major histocompatibility complex (MHC) region of chromosome 6 that are independent of the high-risk HLA genotypes, and the presence of low-frequency and rare variants associated with celiac disease within previously implicated genomic regions. This dissertation sought to study all of these questions by employing GWAS, fine-mapping methods, meta-analysis methods, imputation, and next-generation sequencing (NGS) of targeted genomic regions.

In the first study of this dissertation, two large-scale celiac disease GWASs were re-analyzed using alternative random-effects meta-analysis models in addition to the fixed-effects approach employed in each GWAS meta-analysis. Implementing a random-effects meta-analysis model did not appreciably increase or decrease the power to detect an association and nearly all of the previously implicated loci were found to be genome-wide significant in the re-analysis. In the second study, a fine-mapping approach of the MHC region that takes into account the effect of the high-risk HLA genotypes was implemented. After adjustment for the high-risk HLA genotypes and the linkage disequilibrium in the MHC region, seven novel loci were found to be associated with celiac disease. In the third study, targeted NGS-based resequencing was performed on previously implicated genomic regions to test for the presence of low-frequency and rare variants associated with celiac disease. Gene-based collapsing tests revealed that dozens of genes harbor low-frequency and rare variants that are associated with celiac disease, particularly in the MHC region and within non-coding regions of genes. The fourth study implemented a variant imputation method to impute low-frequency and rare variants into a large GWAS dataset to increase the statistical power to detect low-frequency and rare variants. Nearly all of the low-frequency and rare variant associations from the third study were replicated in this fourth study along with novel associations, using both gene-based tests and single-marker association tests.

These studies reveal that there are many more loci that need to be carefully followed-up in larger resequencing studies and functional studies than previously acknowledged by large-scale celiac disease GWAS that do not account for the role of the high-risk HLA genotypes or the low-frequency and rare variants within genomic regions that harbor common variants previously found to be associated with celiac disease.

Melanomas accumulate a high burden of mutations that could potentially generate neoantigens, yet somehow suppress the immune response to facilitate continued growth. In this study, we identify a subset of human melanomas that have loss-of-function mutations in ATR, a kinase that recognizes and repairs UV-induced DNA damage and is required for cellular proliferation. ATR mutant tumors exhibit both the accumulation of multiple mutations and the altered expression of inflammatory genes, resulting in decreased T cell recruitment and increased recruitment of macrophages known to spur tumor invasion. Taken together, these studies identify a mechanism by which melanoma cells modulate the immune microenvironment to promote continued growth.

Celiac disease is an increasingly recognized disorder in Caucasian populations of European origin. Little is known about its prevalence in non-Caucasians. Although it is thought to be a cause of iron deficiency anemia, little is known about the extent to which celiac disease contributes to iron deficiency in Caucasians, and especially non-Caucasians. We analyzed samples collected from participants in the Hemochromatosis and Iron Overload Screening (HEIRS) study to identify individuals with iron deficiency and assess the frequency of celiac disease.

We analyzed serum samples from white men (25 y old or older) and women (50 y old or older) who participated the HEIRS study; cases were defined as individuals with iron deficiency (serum level of ferritin ≤12 mg/L) and controls were those without (serum level of ferritin >100 mg/L in men and >50 mg/L in women). All samples were also analyzed for human recombinant tissue transglutaminase immunoglobulin A; positive results were confirmed by an assay for endomysial antibodies. Patients with positive results from both celiac disease tests were presumed to have untreated celiac disease, and those with a positive result from only 1 test were excluded from analysis. We analyzed HLA genotypes and frequencies of celiac disease between Caucasians and non-Caucasians with iron deficiency.

Celiac disease occurred in 14 of 567 of cases (2.5%) and in only 1 of 1136 controls (0.1%; Fisher’s exact test, P=1.92 × 10⁻⁶). Celiac disease was more common in Caucasian cases (14/363, 4%) than non-Caucasian cases (0/204; P=.003). Only 1 Caucasian control and no non-Caucasian controls had celiac disease. The odds of celiac disease in individuals with iron deficiency was 28-fold (95% confidence interval, 3.7–212.8) that of controls; 13/14 cases with celiac disease carried the DQ2.5 variant of the HLA genotype.

Celiac disease is associated with iron deficiency of Caucasians. Celiac disease is rare among non-Caucasians—even among individuals with features of celiac disease, such as iron deficiency. Celiac disease is also rare among individuals without iron deficiency. Men and post-menopausal women with iron deficiency should be tested for celiac disease.