Genome-wide association for sarcoidosis identifies novel risk loci and genetic heritability in African and European ancestries: a meta-analysis from the Finngen, Million Veteran Program, UK Biobank, and Biobank Japan datasets

Introduction: Sarcoidosis is an inflammatory disease driven by immune-mediated mechanisms, characterized by the formation of epithelioid cell granulomas and a wide range of clinical manifestations. Its phenotype is the result of a complex interplay of genetic and environmental factors, the precise roles and interactions of which remain poorly defined. Aim: To identify candidate genes and risk loci associated with sarcoidosis from large population datasets. To estimate the genetic heritability of the phenotype in selected ancestries. Population and methods: Public summary statistics from the FinnGen release 12 (European ancestry), pan UK BioBank Project (UKBB - European and African ancestry), Million Veteran Program (MVP - European and African ancestry), and Japan BioBank (East Asian ancestry) were included for European, African and multi-ancestry meta-analysis through sample size-based analysis. Novel risk loci and single nucleotide polymorphisms (SNPs) significantly associated with the disease were critically reviewed on the basis of the available literature. For each risk locus, SNPs highly correlated with the lead SNP were selected based on Combined Annotation Dependent Depletion (CADD) scores. Genetic heritability (h2) scores were obtained through ancestry-specific linkage-disequilibrium score calculation. Result: Overall 9659 cases (7559 European, 1880 African, 220 East Asian) and 1,665,804 controls (1,361,726 European, 126,411 African, 177,667 East Asian) were analysed. Nineteen and two risk loci were identified in European and African ancestry, respectively; h2 scores were 0.25 (European) and 0.19 (African). Candidate non-MHC genes for further explorations through functional studies included IL23R, PUS10, ACOXL, PLCL1, FAM117B, BMPR2, PPARG, ESYT2, ANXA11, CCDC88B, ATXN2, CCL24, RP11−540O11.1, HOMER2, CD19, UBASH3A, RNF215, and others. Interferon gamma signaling, meiotic recombination/condensation of prophase chromosomes, and DNA methylation were the most enriched gene sets in European and multi-ancestry meta-analysis. Multi-ancestry meta-analysis was confronted with FinnGen+UKBB+MVP meta-analysis (released by FinnGen freeze 12) yielding consistent results (18 risk loci identified) Conclusion: Nineteen and two risk loci were significantly associated with sarcoidosis for European and African ancestries, respectively. Moderate genetic heritability was observed for both ancestries. A set of significantly associated non-MHC genes and SNPs was obtained to investigate functional validation. Although further studies are warranted, epigenetic alterations may contribute to the risk of developing sarcoidosis