OR20-02 Trans-Ethnic Analysis Of PCOS Subtype Genomewide Association Signals Reveals 3 Shared Subtype-Specific Loci
Authors: Brewer Kelly , Sisk Ryan , Lee Hyejin , Elisabeth Moolhuijsen Loes Melanie , van der Ham Kim , Louwers Yvonne , Visser Jenny A , Dapas Matthew , Franks Stephen , Laven Joop S E , Li Chun , Dunaif Andrea Elizabeth 
Published: October 2023

Abstract
Disclosure: K. Brewer: None. R. Sisk: None. H. Lee: None. L.M. Moolhuijsen: None. K. van der Ham: None. Y. Louwers: None. J.A. Visser: None. M. Dapas: None. S. Franks: None. J.S. Laven: None. C. Li: None. A.E. Dunaif: None.
The phenotypic variation observed in PCOS is suggestive of underlying genetic heterogeneity, but a recent meta-analysis of European ancestry (EA) PCOS cases found that the genetic architecture of PCOS defined by NIH and Rotterdam diagnostic criteria was similar, suggesting that these criteria do not identify biologically distinct disease phenotypes. Using Hierarchical Clustering (HC) in EA NIH PCOS cases, we have identified discrete, stable PCOS subtypes, which we called reproductive and metabolic (Dapas. PLoS Med, 2020); cases that did not cluster were designated as “background”. These subtypes appeared to capture biologically meaningful differences because they were associated with distinct genomewide significant loci. We were unable to replicate 4 of 6 loci since the lead SNPs were neither genotyped nor imputed on the array used for replication, the Metabochip custom array for cardiometabolic traits with additional PCOS-relevant SNPs. Here, we report an updated EA genomewide association study (GWAS) meta-analysis with additional EA NIH PCOS cases, and a trans-ethnic meta-analysis including a Korean ancestry (KA) NIH PCOS cohort (Lee. Hum Reprod, 2015). HC was applied to cases in both cohorts to identify PCOS subtypes. The EA discovery cohort, 620 cases and 2951 controls, was genotyped with the Illumina OmniExpress array. The replication EA cohort, 371 cases and 926 controls, was genotyped with the Metabochip. The KA cohort, 417 cases and 926 controls, was genotyped with the HumanOmni1-Quad v1 array. The imputation of previously reported genotype data was updated using the larger, more deeply sequenced TOPMed (R2) imputation panel. Nine loci were genomewide significant in the EA meta-analysis: 5 novel loci (reproductive subtype); 2 loci (metabolic subtype), including c9orf3; 2 loci (background subtype), including FSHB/ARL14P. Five of 6 other lead SNPs in the original analysis remained nominally significant. Three loci were significant in the trans-ethnic meta-analysis: a novel locus on chr 3, EPHA6, a receptor tyrosine kinase that binds promiscuously GPI-anchored ephrin-A family ligands (rs140766105, p=1.08 x 10-8, reproductive subtype); a previously identified GWAS locus on chr 9, c9orf3 (AOPEP), an aminopeptidase that catalyzes the hydrolysis of amino acid residues from the N-terminus of peptides (rs10761370, p=4.12 x 10-9, metabolic subtype); a previously identified GWAS locus on chr 11, FSHB/ARL14P, FSHB encodes the β-subunit of FSH and is associated with general fertility status, (rs10835649, 1.23 x 10-11, background subtype). We have replicated the 9 distinct subtype loci in the EA meta-analysis providing orthogonal (independent) validation suggesting these subtypes have distinct genetic architecture. For the first time, a trans-ethnic meta-analysis demonstrates that 3 subtype-specific loci play a role in PCOS pathogenesis across diverse populations.
Presentation Date: Saturday, June 17, 2023