Genetic findings in early miscarriage analysis by Chromosomal Microarray and Whole Exome Sequencing

Miscarriage is a condition that affects 10%-15% of all clinically recognized pregnancies, most of which occur in the first trimester. Approximately 50% of first-trimester miscarriages result from fetal chromosome abnormalities. Conventional karyotyping analysis is limited due to unsuccessful culture fetal tissue and poor chromosome quality. Chromosomal microarray analysis (CMA) provides a significant increase in test success rate and incremental diagnostic yield in early pregnancy loss, using fetal DNA. We aimed to estimate detection of pathogenic Copy Number Variants (CNVs) and variants of uncertain significance (VOUS) in early pregnancy losses. Moreover we integrate cytogenomic findings performing Whole Exome Sequencing (WES) in order to elucidate the genetic associations of gene variants clinically significant for the viability of a conceptus. We collected product of conception (POC) samples (n= 33), managed in our genetic unit between February 1, 2020, and July 31, 2021. Fetal tissue samples were obtained after informed consent from females of average age 37 years old, who experienced spontaneous pregnancy losses (□<20 weeks) (70%), medical abortion (9%) and miscarriage after assisted reproductive treatment (21%). In the 97% of cases, the cytogenomic and/or molecular analysis were performed and concluded with an informative results (n= 32) useful for couple counseling. To avoid risk of maternal cell contamination and to define sex chromosomes, before CMA, QF-PCR was performed. As aspected, autosomal trisomies are shown to be the most frequent anomalies (42%) associated with first-trimester miscarriage, followed by monosomy X (3%). 2 CNVs, are detected (6%): 1 pathogenic de novo deletion associated with monosomy 1pter and 1 duplication with uncertain clinical significance in region 7q21.13, segregated from healthy father. In this sample, we performed WES in order to understand the possible genetic cause of major malformations detected by ultrasound exploration. A missense variant in ITF80 gene was detected. The encoded protein is essential for the development and maintenance of primary cilia, but a single variant, inherited from father, is not enough to conclude the diagnosis. In another case, with a fetal peculiar clinical picture, the WES analysis performed, showed a compound heterozygosity in the CC2D2A gene, associated with Meckel syndrome, an autosomal recessive ciliopathy. Ciliopathies are an expanding disease spectrum that have been associated with over 40 genes to date. In this case, the genetic diagnosis allow us to determine the cause of miscarriage with a major impact on the future couple reproductive plans and prenatal care in future pregnancies. This study demonstrates that the DNA-based CMA technology overcomes many of the limitations of routine cytogenetic analysis of POC samples and, in selected cases, integration with WES analysis increase diagnostic rate and recurrence-risk for subsequent pregnancies can be also determined.