Candidate gene investigation of non-immune hydrops fetalis with whole exome sequencing

Non-immune hydrops fetalis is one of the important prenatal anomalies with lethal course detected during routine pregnancy follow-up. It is a shared presentation of many genetic disorders. Standard routine genetic testing with prenatal karyotyping or chromosomal microarray analysis can diagnose only 25% of cases and cannot detect single gene disorders known to be involved in the etiology. Although the role of single gene diseases in the etiology of non-immune hydrops fetalis cases is not clear, it is thought to be significant. An accurate diagnosis makes it possible for focused prenatal management, early directed neonatal care. It also enables to apply prenatal and preimplantation genetic diagnosis for the consecutive pregnancies of the index case and accurate risk calculation for the other family members. In this study six unexplained non-immune hydrops fetalis cases that were defined by the presence of fetal ascites, pleural or pericardial effusions, skin edema, cystic hygroma, increased nuchal translucency, or a combination of these conditions were evaluated by trio whole exome sequencing. In the first step the detected variants were filtered according to their minor allele frequencies, their effects on the protein and classified based on the current ACMG guideline criteria. The cases that could not be diagnosed at the end the first step were examined using STRING, DAVID databases and in-silico pathogenicity scores to identify candidate genes and pathways. The aim of this study was to elucidate the role of single gene diseases in the etiology of non-immune hydrops fetalis cases and to define candidate genes by in-silico functional analysis. The average of 42,468 variants detected per case as a result of whole exome sequencing. Diagnostic variants of RIT1: c.297T> G and RIT1: c.321G>C were detected in two cases after the first step filtering. As a result of second step in-silico functional analysis performed on four cases whose diagnostic variant could not be detected at the end of first step filtering, a total of 66 candidate variants and COL2A1: c.1300C> T, SMARCC2: c.3128del potentially diagnostic variants were detected. No common cellular pathway was detected in the variant load analysis. When the cases were examined alone a significantly increased variant burden in pantothenate and coenzyme-A biosynthesis, and thyroid hormone synthesis pathways were found. The study shows that whole exome sequencing can be clinically beneficial in non-immune hydrops fetalis cases whose chromosome analyzes are detected normal. At the end of study, two diagnostic variant and two clinically relevant variant was found. Candidate variants and candidate genes associated with the non-immune hydrops fetalis were also pointed by in-silico analysis in cases where a diagnostic variant could not be detected but additional studies are needed to confirm the pathophysiological effects of these variants. By increasing knowledge about the etiology of non-immune hydrops fetalis accurate and fast diagnosis, treatment, follow-up and prevention algorithms may be developed in the future.