Identification of Germline, Ancestry-Specific Variants for Langerhans Cell Histiocytosis in Hispanic Patients

Background: Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasia characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate with recurrent, mutually exclusive somatic activating mutations in MAPK pathway genes in ~85% of LCH lesions. Our group and others have reported that Hispanic populations are more likely to develop LCH, particularly high-risk LCH, than non-Hispanic counterparts. Our group previously identified and validated a risk SNP in SMAD6 associated with a 3-fold increase in LCH risk that was also enriched in those of Hispanic ancestry; however, germline risk factors have yet to be fully elucidated in the higher-risk Hispanic population. Methods: Using targeted SMAD6 sequence data from 466 cases with LCH and aggregate data for 15,694 non-cancer controls from gnomAD v2.1.1, we evaluated 49 SNPs previously associated with case status to identify those that were enriched specifically in Hispanic populations. We conducted an additional genome-wide association study (GWAS) on 98 LCH cases and 1,158 controls, all inferred to be Hispanic based on global genomic ancestry. The GWAS was adjusted for the first 3 PCs. Population genetics were assessed in Ensembl, ancestry inference was conducted Admixture software (reference panel 1000 Genomes, Phase 3), and statistical analyses were conducted with PLINK, Stata, and SAS software. Results: In the population genetics analysis of the SMAD6 SNPs, the top 4 SNPs (Figure 1) have a lower minor allele frequency (MAF) of 2-9% across all populations. However, in Hispanic populations, the alternate/risk allele in the top 4 SNPs is increased (MAF range 15-23%). Furthermore, the LD between the top four SNPs is enriched among Hispanic populations (range of r 2: 0.51-0.92; Table 1), suggesting that Hispanic patients may have different risk loci compared to others. In the LCH GWAS of Hispanic patients, there were no statistically significant SNPs; however, this pilot study of our ongoing analyses identified 5 LCH risk loci in Hispanic patients that had suggestive significant associations ( P=1.0x10 -5). Strikingly, these loci differed from the SNPs identified in our GWAS of all patients. Conclusions: Using multiple approaches, we have identified LCH risk variants that were identified in Hispanic patients. These Hispanic ancestry-specific risk SNPs were more strongly associated with case status in Hispanic patients than the risk SNPs from our GWAS of all patients