A standardized approach for case selection and genomic data analysis of maternal exomes for the diagnosis of oocyte maturation and early embryonic developmental arrest in IVF

OBJECTIVE: To develop a methodology for case selection and whole-exome sequencing (WES) analysis in infertile women due to recurrent oocyte maturation defects(OOMD) and/or preimplantation embryo lethality (PREMBL). DESIGN: Cross-sectional study. SETTING: IVF patients attending the Istanbul Memorial Hospital (2015-2021). WES and bioinformatics were performed at Igenomix and National Research Council,Italy. PATIENTS: A statistical methodology for identification of infertile endophenotypes (recurrent low oocyte maturation rate, LMR, low fertilization rate, LFR, and preimplantation developmental arrest, PDA, was developed using a large IVF dataset (11,221 couples). 28 OOMD/PREMBL infertile women were subsequently enrolled for WES. INTERVENTION: 30X-WES was performed on women's gDNA. Pathogenic variants were prioritized using a custom-made bioinformatic pipeline set to minimize false positive discoveries through resampling in control cohorts (i.e., HGDP and 1,343 WES from oocyte donors). Individual scRNAseq data from 18 human MII oocytes and antral granulosa cells(AGC) was used for genome-wide validation. MAIN OUTCOME MEASURE: Identification of High-impact variants and pathways causative of OOMD/PREMBL endophenotypes. RESULTS: Variant prioritization analysis identified 265 unique variants in 248 genes (average per sample 22.4). 87.8% of genes harbouring high-impact variants are expressed by MII oocytes and/or AGC, significantly higher compared to a random sample of 28 WES from the egg donors. Seven of the 28 women (25%) are homozygous carriers of missense pathogenic variants in known candidate genes for OOMD/PREMBL, including PATL2, NLRP5 (N=2), TLE6,PADI6, TUBB8 and TRIP13. CONCLUSIONS: This analytical framework revealed known and new genes/pathways associated with isolated recurrent OOMD/PREMBL, providing essential indications for scaling this strategy to larger studies.