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

Huilin Wang,Kwong Wai Choy,Zhenjun Yang,Yanfang Wang,Tak Yeung Leung,Rui Zhang,Huanchen Yan,Yvonne K. Kwok,Matthew Hoi Kin Chau,Mengmeng Shi,Jingsi Chen,Shaoyun Chen,Min Chen,Olivia Y.M. Chan,Ye Cao,Zirui Dong,Yuanfang Zhu

doi:10.3389/fgene.2019.00761

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.

Highlights

From year 2014 to 2018, 50 pregnant women, whose fetus was diagnosed with increased nuchal translucency (NT) (≥3.5 mm) with/without structural malformations (Leung et al, 2011; Huang et al, 2014) and had undergone prenatal diagnosis by chromosomal microarray analysis (CMA) after a negative finding from quantitative fluorescent PCR (QF-PCR) (Choy et al, 2014), were recruited in this study
Written informed consent was obtained from each participant for the purpose of this study, and any findings from the genome sequencing would not be disclosed to the patients
Thirtyseven CVS samples were collected from the first trimester, and amniotic fluids (AF) samples were collected in later gestational weeks in the other 13 cases

Summary

Introduction

Detection of fetuses with increased nuchal translucency (NT) in routine first-trimester ultrasound screening has been widely used as a sensitive indication for fetal chromosomal abnormalities and/or fetal structural anomalies, such as congenital heart disorders or neurodevelopmental anomalies detected in later gestations (Leung et al, 2011; Huang et al, 2014; Socolov et al, 2017; Sinajon et al, 2019). Emerging studies show that WES has the ability to provide genetic diagnoses ranging from 9.1% to 32% for the fetuses with a structural anomaly (Drury et al, 2015; Fu et al, 2018; Leung et al, 2018; Normand et al, 2018; Lord et al, 2019; Petrovski et al, 2019), while among these cases, WES yielded diagnoses in 3.2% to 21% of the fetuses with increased NT with/without structural malformations (Drury et al, 2015; Lord et al, 2019; Petrovski et al, 2019) Most of these studies were conducted on prenatal cohorts after the exclusion of abnormal karyotypes and/ or CMA results attributed to the cost and the limited ability of WES in CNV detection (Belkadi et al, 2015).

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