Prenatal Diagnosis of Fetuses With Increased Nuchal Translucency by Genome Sequencing Analysis

Abstract

Background: Increased nuchal translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single-nucleotide variants to those affecting millions of base pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA); however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT. Methods: We retrospectively applied GS (> 30-fold) for fetuses with increased NT (≥3.5 mm) who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy number variants, and structural rearrangements was performed simultaneously, and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available. Results: Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a twofold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications, and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion that disrupted an OMIM autosomal dominant disease-causing gene at the insertion site. Conclusions: Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turnaround time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.

Comprehensive genome sequencing analysis as a promising option in the prenatal diagnosis of fetal structural anomalies: a prospective study

“…Indeed, in our cohorts, 22 fetuses referred for CMA did not undergo serum screening or NIPS, and this resulted in 6 (27.3%) fetuses with trisomy 21/18/13 still being identified during GS implementation. We also note that the prenatal detection rate for P/LP SNVs/INDELs in our study was lower than that in a previous study of 50 fetuses with increased nuchal translucency (11.7% vs 14%) [18], possibly due to our larger cohort and the broader range of fetal structural anomalies in our study. However, the incremental diagnostic yield of ES in CMAnegative cases was higher in this study (12.7% vs 8.5%-10%) [8,9] than in previous prospective studies on the prenatal application of ES in fetuses with structural or growth anomalies who had normal CMA results.…”

“…Talkowski et al [17] identified precise translocation breakpoints that directly disrupted CHD7 and LMBRD1 by using ~12-fold GS in an undiagnosed prenatal sample, and this finding could not have been reliably inferred from conventional karyotyping. Choy et al [18] demonstrated that 30-fold GS could provide a two-fold increase in diagnostic yield (32.0%, 16/50) in fetuses with increased nuchal translucency (≥3.5 mm) compared with routine CMA and/or karyotyping (16.0%, 8/50). The additional diagnoses by GS include 7 (14%, 7/50) cases with pathogenic or likely pathogenic (P/LP) SNVs/INDELs, and their result demonstrated the potential of GS to replace the combination of CMA and ES in prenatal diagnosis.…”

Noninvasive prenatal sequencing for multiple Mendelian monogenic disorders among fetuses with skeletal dysplasia or increased nuchal translucency

“…[23][24][25] A recent study had also showed the feasibility of applying genome sequencing (GS) for prenatal diagnosis of fetuses with increased NT for comprehensive detection of various disease-causing genomic variants. 26 However, accurate prenatal diagnosis of skeletal dysplasia by invasive procedures is still under debate in the absence of a relevant family history, and the time from invasive testing to diagnosis can be lengthy. 12 On the other hand, the cost of WES and WGS is relatively high and clinical utility of these technologies in prenatal diagnosis is to be addressed by large-cohort prospective studies.…”

Clinical Significance of Non-Invasive Prenatal Screening for Trisomy 7: Cohort Study and Literature Review

“…Chromosomal abnormalities affect one of 150 live births, and the prevalence is even higher in pregnancies [ 1 , 2 ]. Prenatal diagnosis of chromosomal abnormalities can be performed by using advanced technologies such as chromosomal microarray analysis (CMA) and genome sequencing [ 3 , 4 ], which, however, requires an invasive procedure such as amniocentesis or chorionic villi sampling (CVS) to obtain a fetal sample for testing. These procedures carry a 0.1–0.2% procedure-related miscarriage risk [ 5 ].…”