Whole Genome Sequencing in the Evaluation of Fetal Structural Anomalies: A Parallel Test with Chromosomal Microarray Plus Whole Exome Sequencing.

Jia Zhou,Xiuxiu Wei,Luming Sun,Xiaoyu Liu,Lipei Liu,Zhonghua Wang,Yaoshen Wang,Zhiyu Peng,Fengxia Liu,Jian Wang,Jun Sun,Xing Wei,Gang Zou,Tao Duan,Xinyao Zhou,Saiying Yan,Yun Zhang,Fanwei Zeng,Shuge Cui,Fengyu Wu,Ziying Yang,Shiyi Xiong,Yongzhong Xing ,Yazhou Yang

doi:10.3390/genes12030376

Abstract

Whole genome sequencing (WGS) is a powerful tool for postnatal genetic diagnosis, but relevant clinical studies in the field of prenatal diagnosis are limited. The present study aimed to prospectively evaluate the utility of WGS compared with chromosomal microarray (CMA) and whole exome sequencing (WES) in the prenatal diagnosis of fetal structural anomalies. We performed trio WGS (≈40-fold) in parallel with CMA in 111 fetuses with structural or growth anomalies, and sequentially performed WES when CMA was negative (CMA plus WES). In comparison, WGS not only detected all pathogenic genetic variants in 22 diagnosed cases identified by CMA plus WES, yielding a diagnostic rate of 19.8% (22/110), but also provided additional and clinically significant information, including a case of balanced translocations and a case of intrauterine infection, which might not be detectable by CMA or WES. WGS also required less DNA (100 ng) as input and could provide a rapid turnaround time (TAT, 18 ± 6 days) compared with that (31 ± 8 days) of the CMA plus WES. Our results showed that WGS provided more comprehensive and precise genetic information with a rapid TAT and less DNA required than CMA plus WES, which enables it as an alternative prenatal diagnosis test for fetal structural anomalies.

Highlights

Congenital fetal anomalies occur in approximately 3% of pregnancies [1], and many of these anomalies have an underlying genetic etiology
pathogenic or likely pathogenic (P/LP) single-nucleotide variants (SNVs)/insertions or deletions (INDELs) were validated by Sanger sequencing, while P/LP copy number variants (CNVs) identified by whole genome sequencing (WGS) were cross-validated with the results of chromosomal microarray (CMA)
Samples from a total of 320 individuals (106 fetus–parental trios, including 4 sets of twins and 5 fetus–parent dyads) were analyzed by WGS, while the 111 fetal samples were analyzed by CMA in parallel

Summary

Introduction

Congenital fetal anomalies occur in approximately 3% of pregnancies [1], and many of these anomalies have an underlying genetic etiology. Chromosomal microarray (CMA) has been broadly adopted to detect copy number variants (CNVs) in prenatal diagnoses with an additional 6% of diagnostic yield over standard karyotyping in fetuses with structural anomalies observed by ultrasound [2,3]. CMA can detect CNVs as small as 10–100 kb in length, depending on the probe density. Smaller variants, such as single-nucleotide variants (SNVs) and small insertions or deletions (INDELs), which contribute to a substantial portion of genetic disorders, remain undetectable by this approach [4,5,6,7]. Emerging studies have shown that WES has a detection rate of 8.5% to 10% in fetal structural abnormalities with normal karyotype and CMA results [8,9]

Methods

Results

Conclusion