Evaluating the clinical utility and strategy of whole exome sequencing testing for fetuses with increased nuchal translucency

The routine recommendation for detecting monogenic disease in fetuses with increased nuchal translucency (NT) remains controversial. This study aimed to evaluate the clinical significance and optimal strategy of whole exome sequencing (WES) in fetuses with increased NT. This retrospective study included pregnancies that underwent amniocentesis due to advanced maternal age, positive screening results, or abnormal ultrasound findings between January 2018 and December 2019. Chromosomal abnormalities were diagnosed using chromosome microarray analysis (CMA). WES testing was sequentially performed in fetuses with NT ≥ 3.5 mm. Newborns were followed up regularly until they reached 48-60 months of age. Of 11,774 pregnancies undergoing amniocentesis, 607 fetuses (5.16%) had NT ≥ 3 mm. Chromosomal abnormalities were detected in 23.56% (143/607), including aneuploidy (13.18%, 80/607) and chromosome deletion/duplication or regions of homozygosity (10.38%, 63/607). The diagnostic yield of CMA for aneuploidies and pathogenic/likely pathogenic (P/LP) chromosome abnormalities was 17.63% (107/607), after excluding 36 cases with variants of uncertain significance (VUS). Among 464 fetuses with NT ≥ 3 mm and negative CMA results, 240 cases had fetal NT ≥ 3.5 mm, of which 96 cases underwent WES testing. WES identified diagnostic variants in genes associated with an increased NT phenotype in 10.42% (10/96) of cases. These variants involved genes of DDX3X, RIT1, NIPBL, ANKRD11, PIEZO2, NF1, ASXL1, CCDC22, and TUBB3, which are inherited in either an X-linked (XL) or autosomal dominant (AD) pattern. Adverse outcomes were observed in 80% (8/10) of these cases, including four induced abortions, three cases of developmental delay, and one neonatal death. A total of 86 fetuses (14.17%, 86/607) had additional ultrasound findings. Fetuses with NT ≥ 3.5 mm and additional ultrasound findings identified during the second trimester exhibited a significantly higher rate of chromosomal abnormalities compared to those without additional findings (44.62% vs. 19.00%, P = 0.00). Among fetuses with NT ≥ 3 mm and negative CMA and/or WES testing results, 90.39% (395/437, after excluding 27 pregnancies lost to follow-up) were healthy during follow-up. The remaining approximately 10% (42 cases) experienced miscarriage, induced abortion, intrauterine fetal death, or developmental delay. CMA identified chromosomal abnormalities in 17.63% of fetuses with NT ≥ 3 mm. Fetuses with increased NT and additional ultrasound findings exhibited a significantly higher rate of chromosomal abnormalities. WES provided an additional diagnostic yield of 10.42% for monogenic disorders in fetuses with NT ≥ 3.5 mm. WES testing, combined with data reanalysis based on subsequent prenatal/postnatal phenotypes, offers an optimal strategy for diagnosing monogenic diseases in fetuses with increased NT.