Exome sequencing reveals a high proportion of causal and candidate gene variants in a large early-onset Primary Ovarian Insufficiency cohort

S. M. McGlacken-Byrne et al. (2022) European Society for Paediatric Endocrinology Abstracts, 95, P1-371

Nonacus Products: Cell3 Target: Constitutional Genetics

Background: The presentation of early-onset Primary Ovarian Insufficiency (EO-POI), most often with primary amenorrhea, is at one end of a spectrum spanning 40 years. The aetiology of POI is frequently unclear but next generation sequencing of varied age groups has identified several associated genetic variants. Whether girls with EO-POI are more likely to have a genetic aetiology than those with later presentations remains unknown.

Methods: We performed exome sequencing (Nonacus) in a large cohort of young females with unexplained EO-POI and their unaffected family members where possible. Analysis was performed in QCI (Qiagen) following appropriate inheritance models. Variants were retained if rare/novel (minor allele frequency <0.01%), predicted pathogenic in silico, and enriched in the cohort compared to controls (gnomAD v3.1.2; Fisher’s exact testing). Hierarchical filtering considered genes associated with: A) POI with functional models (n=113); B) POI without functional models (n=315); C) animal models of ovarian insufficiency (n=120); D) differential expression during critical human fetal ovary developmental stages.

Results: A total of 147 women with EO-POI were recruited (29 familial POI (16 kindreds, 8 consanguineous); 118 sporadic POI). Of these, 81.6% (n=120) had primary amenorrhea and 61.9% (n=91) pubertal delay/arrest. Pathogenic/likely pathogenic variants in POI-associated genes were found in 50.0% of familial POI kindred (n=8; 22 affected). These included variants in STAG3, PSMC3IP, YTHDC2, PLEC, MCM9 (biallelic); NLRP11, PRKD1, WRN (heterozygous); ANKRD31, POLR2C, PDE3A, POLR3H, CLPP, MSH6 (oligogenic). Variants in novel candidate genes (MRPS14, PCHD15) segregated with the phenotype in two further families. Variants with established pathogenicity in POI were found in 22.9% of women with sporadic POI (27/118), likely explaining their diagnosis. These included variants in GDF9, BUB1B, MCM9, MCM8, SETX, NBN, BMP15, NOBOX, AMH, ATG7, EIF4ENIF1, FOXO1, PRDM1, and BNC1. A further 34.7% (41/118) had variants with recognised pathogenicity but which followed oligogenic inheritance or inheritance patterns not yet supported by functional models (e.g, digenic variants in DNA repair genes). Variants were biallelic in 13.2% (9/68), heterozygous in 54.4% (37/68), and oligogenic in 32.4% (22/68). Novel candidate genes were also identified (e.g., FANCD2, C4orf33, TDRD9).

Conclusion: Causal and possibly contributory variants within POI-associated genes were found in a high proportion of this EO-POI cohort. Frequent polygenic involvement and enrichment of rare heterozygous variants suggest possible haploinsufficiency/dominant-negative models, multiallelic interactions, or threshold effects of rare variants. POI is remarkably genetically heterogeneous and we demonstrate a categorical, hierarchical approach to exome analysis in this condition.