Circulating anti-Müllerian hormone levels in pre-menopausal women: novel genetic insights from a genome-wide association meta-analysis

Abstract

Abstract STUDY QUESTION Can a genome-wide association study (GWAS) meta-analysis, including a large sample of young premenopausal women from a founder population from Northern Finland, identify novel genetic variants for circulating anti-Müllerian hormone (AMH) levels and provide insights into single-nucleotide polymorphism enrichment in different biological pathways and tissues involved in AMH regulation? SUMMARY ANSWER The meta-analysis identified a total of six loci associated with AMH levels at P < 5 × 10−8, three of which were novel in or near CHEK2, BMP4, and EIF4EBP1, as well as highlighted significant enrichment in renal system vasculature morphogenesis, and the pituitary gland as the top associated tissue in tissue enrichment analysis. WHAT IS KNOWN ALREADY AMH is expressed by preantral and small antral stage ovarian follicles in women, and variation in age-specific circulating AMH levels has been associated with several health conditions. However, the biological mechanisms underlying the association between health conditions and AMH levels are not yet fully understood. Previous GWAS have identified loci associated with AMH levels in pre-menopausal women, in or near MCM8, AMH, TEX41, and CDCA7. STUDY DESIGN, SIZE, DURATION We performed a GWAS meta-analysis for circulating AMH level measurements in 9668 pre-menopausal women. PARTICIPANTS/MATERIALS, SETTING, METHODS We performed a GWAS meta-analysis in which we combined 2619 AMH measurements (at age 31 years) from a prospective founder population cohort (Northern Finland Birth Cohort 1966, NFBC1966) with a previous GWAS meta-analysis that included 7049 pre-menopausal women (age range 15–48 years) (N = 9668). NFBC1966 AMH measurements were quantified using an automated assay. We annotated the genetic variants, combined different data layers to prioritize potential candidate genes, described significant pathways and tissues enriched by the GWAS signals, identified plausible regulatory roles using colocalization analysis, and leveraged publicly available summary statistics to assess genetic and phenotypic correlations with multiple traits. MAIN RESULTS AND THE ROLE OF CHANCE Three novel genome-wide significant loci were identified. One of these is in complete linkage disequilibrium with c.1100delC in CHEK2, which is found to be 4-fold enriched in the Finnish population compared to other European populations. We propose a plausible regulatory effect of some of the GWAS variants linked to AMH, as they colocalize with GWAS signals associated with gene expression levels of BMP4, TEX41, and EIFBP41. Gene set analysis highlighted significant enrichment in renal system vasculature morphogenesis, and tissue enrichment analysis ranked the pituitary gland as the top association. LARGE SCALE DATA The GWAS meta-analysis summary statistics are available for download from the GWAS Catalogue with accession number GCST90428625. LIMITATIONS, REASONS FOR CAUTION This study only included women of European ancestry and the lack of sufficiently sized relevant tissue data in gene expression datasets hinders the assessment of potential regulatory effects in reproductive tissues. WIDER IMPLICATIONS OF THE FINDINGS Our results highlight the increased power of founder populations and larger sample sizes to boost the discovery of novel trait-associated variants underlying variation in AMH levels, which aided the characterization of GWAS signals enrichment in different biological pathways and plausible genetic regulatory effects linked with AMH level variation for the first time. STUDY FUNDING/COMPETING INTEREST(S) This work has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the MATER Marie Sklodowska-Curie Grant Agreement No. 813707 and Oulu University Scholarship Foundation and Paulon Säätiö Foundation. (N.P.-G.), Academy of Finland, Sigrid Jusélius Foundation, Novo Nordisk, University of Oulu, Roche Diagnostics (T.T.P.). This work was supported by the Estonian Research Council Grant 1911 (R.M.). J.R. was supported by the European Union’s Horizon 2020 Research and Innovation Program under Grant Agreements No. 874739 (LongITools), 824989 (EUCAN-Connect), 848158 (EarlyCause), and 733206 (LifeCycle). U.V. was supported by the Estonian Research Council grant PRG (PRG1291). The NFBC1966 received financial support from University of Oulu Grant No. 24000692, Oulu University Hospital Grant No. 24301140, and ERDF European Regional Development Fund Grant No. 539/2010 A31592. T.T.P. has received grants from Roche, Perkin Elmer, and honoraria for scientific presentations from Gedeon Richter, Exeltis, Astellas, Roche, Stragen, Astra Zeneca, Merck, MSD, Ferring, Duodecim, and Ajaton Terveys. For all other authors, there are no competing interests.