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

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.

Trio-Based Low-Pass Genome Sequencing Reveals Characteristics and Significance of Rare Copy Number Variants in Prenatal Diagnosis

“…The results indicated the size distributions were significantly different (Kruskal–Wallis rank sum test: p = 0.0054, Figure 2B ). The large mosaic CNVs reported and the large proportion of small CNVs (<100 kb) in our study may explain the differences in size distribution ( Zhou et al, 2021 ).…”

“…The majority of rare CNVs were smaller than 1 Mb (562/603, 93.2%), while the six mosaic CNVs were all larger than 1 Mb ( Figure 2A ). We further compared the size distribution of CNVs to those reported by Zhou et al (2021) in a trio-based high read-depth GS study utilizing an independent algorithm ( n = 111). The results indicated the size distributions were significantly different (Kruskal–Wallis rank sum test: p = 0.0054, Figure 2B ).…”

“…The frequency of rare CNVs in each chromosome is provided in the top panel. (B) Comparison of the rare CNVs identified in our study and in a trio-based high read-depth genome sequencing study ( Zhou et al, 2021 ; n = 111). In each bar, each segment in green, purple, and yellow indicates the percentage of constitutional duplications (digits in dark green), constitutional deletions (digits shown in purple), and mosaic CNVs (digits in orange) identified.…”

“…We also curated CNVs from several published studies on the spectrum of CNVs in prenatal diagnosis for comparison: (1) 428 P/LP CNVs detected in 23,865 prenatal diagnosis cases by CMA, of which clinically relevant CNVs smaller than 10 Mb were included; 25% of the CNVs did not have parental inheritance information ( Chau et al, 2019 ), (2) 51 P/LP CNVs detected in 3,429 cases by low-coverage GS; fetuses with ultrasound anomalies were excluded and only 20% of the CNVs had parental inheritance information ( Wang et al, 2018 ); and (3) 217 CNVs (seven P/LP) in 111 cases by trio-based high read-depth GS ( Zhou et al, 2021 ), in which parental inheritance was not provided for CNVs smaller than 100 kb.…”

“…Recent studies have demonstrated the feasibility of applying genome sequencing (GS) for CNV detection in prenatal diagnosis ( Choy et al, 2019 ; Zhou et al, 2021 ), particularly using a low-pass (low-coverage and high-through) approach ( Liang et al, 2014 ; Dong et al, 2016 ; Wang et al, 2018 ; Chau et al, 2020 ; Wang H. et al, 2020 ). It offers higher resolution of CNV detection (e.g., CNVs < 100 kb in size) and improved sensitivity in detecting low-level mosaic variants.…”