Exome Sequencing For Prenatal Diagnosis In Nonimmune Hydrops Fetalis

Nonimmune hydrops fetalis (NIHF) is a condition complicating approximately 1 in 1700 to 3000 pregnancies where the fetus develops an overload of fluid, causing a wide range of outcomes such as stillbirth, pretermbirth, neonatal complications, or neonatal death. Standard genetic testing with microarray or karyotype identifies a genetic cause of hydrops approximately only 25% of the time. The goal of this study was to establish the diagnostic yield of exome sequencing in unexplained NIHF.This study enrolled patients from the 5 University of California Fetal-Maternal Consortium sites, as well as across the United States. Nonimmune hydrops fetalis was defined as the presence of 1 or more pathologic fetal fluid conditions, including an increased nuchal translucency measurement (>= 3.5 mm), cystic hygroma, pleural effusion, pericardial effusion, ascites, skin edema, or a combination of these fluid collections. Women were included if they had a fetus diagnosed with NIHF prenatally and a nondiagnostic karyotype and/or microarray.Participants completed informed consent via a phone or video call. Pregnancy-related medical records were obtained following informed consent, as well as fetal samples and parental samples. Fetal samples were collected prenatally from chorionic villus sampling or amniocentesis or postnatally from umbilical cord sampling, buccal swab, or other tissue. Parental samples were collected as saliva or blood. When possible, trio exome sequencing for both parents and the fetus was performed at the University of California, San Francisco, Genomic Medicine Laboratory. Duo exome sequencing was performed in cases in which only the mother was available, and only the proband was sequenced in 1 case in which the pregnancy resulted from donor egg and sperm. In a few cases where the older sibling was affected by NIHF, quad exome sequencing was performed including a sample from the older sibling.In all, 233 cases of NIHF were referred from October 2018 toMay 2020, and ultimately 127 were enrolled, excluding those who were lost to follow-up, did notmeet inclusion criteria, or did not have fetal sample remaining. Prior to exome sequencing, all patients had a normal karyotype and/or microarray. Trio exome sequencing was performed in 114 cases (90%), duo exome sequencing in 9 cases (7%), quad exome sequencing in 3 cases (2%), and proband-only sequencing in 1 case (1%). Exome sequencing results were returned in 2 to 4 weeks for cases with ongoing pregnancies and live births and 8 to 12 weeks for cases of stillbirth, termination, and neonatal demise. Of the 127 cases, 29 (23%) had an increased nuchal translucency or cystic hygroma at the time of enrollment, 21 (17%) had a single abnormal fluid collection, and 77 (61%) had at least 2 abnormal fluid collections.Diagnostic variants from exome sequencing were identified in 37 of the 127 fetuses (29%). The majority of diagnostic variants found were RASopathies, which are genetic disorders of the RAS-mitogen-activated protein kinases (MAPK) signaling pathway involved in cell communication (30%), followed by inborn errors of metabolism and musculoskeletal disorders (11% each); lymphatic, neurodevelopmental, cardiovascular, and hematologic disorders (8% each); immunologic disorders (5%); and renal disorders, ciliopathies, overgrowth syndromes, and others (3% each). For the cases with an initial presentation of an increased nuchal translucency or cystic hygroma with or without a concurrent structural anomaly, 31% had a diagnostic variant. Among the cases with at least 2 abnormal fluid collections, 34% had a diagnostic variant. An additional 9% had a variant identified as a variant of potential clinical significance but did not meet the criteria to be pathogenic or likely pathogenic. Furthermore, 91% of families agreed to the receipt of secondary findings, and 3% had a pathogenic or likely pathogenic secondary finding identified.Overall, exome sequencing was useful in identifying a pathogenic or likely pathogenic variant in 29% of cases with unexplained NIHF. This diagnostic yield is higher than previously reported prenatal exome sequencing studies, where the yield was 8.5% to 10%. This information is useful in categorizing recurrence risk for any future pregnancies. In cases where the variant identified was autosomal dominant, a 50% recurrence risk was quoted for inherited disorders, and a 1% to 2% recurrence risk was quoted for variants that were de novo. In cases where the variant identified was autosomal recessive, nearly all cases were identified as having a 25% recurrence risk. In the future, more studies are needed to further assess the underlying genetic causes of NIHF. Overall, this study highlights the clinical utility of exome sequencing in cases with unexplained NIHF.