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Volume 11
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10.3390/genes11121397
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Article

Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes

by
Qingwei Qi
1,*,
Yulin Jiang
1,
Xiya Zhou
1,
Hua Meng
2,
Na Hao
1,
Jiazhen Chang
3,
Junjie Bai
4,
Chunli Wang
5,
Mingming Wang
4,
Jiangshan Guo
4,
Yunshu Ouyang
2,
Zhonghui Xu
2,
Mengsu Xiao
2,
Victor Wei Zhang
5 and
Juntao Liu
1
1
Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
2
Department of Ultrasound, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
3
Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
4
Be Creative Lab Co., Ltd. Beijing 101111, China
5
AmCare Genomics Lab, Guangzhou 510335, China
*
Author to whom correspondence should be addressed.
Genes 2020, 11(12), 1397; https://doi.org/10.3390/genes11121397
Submission received: 6 September 2020 / Revised: 9 November 2020 / Accepted: 16 November 2020 / Published: 25 November 2020
(This article belongs to the Special Issue Advances in Prenatal Genetic Screening and Diagnosis Technologies)
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Abstract

The routine assessment to determine the genetic etiology for fetal ultrasound anomalies follows a sequential approach, which usually takes about 6–8 weeks turnaround time (TAT). We evaluated the clinical utility of simultaneous detection of copy number variations (CNVs) and single nucleotide variants (SNVs)/small insertion-deletions (indels) in fetuses with a normal karyotype with ultrasound anomalies. We performed CNV detection by chromosomal microarray analysis (CMA) or low pass CNV-sequencing (CNV-seq), and in parallel SNVs/indels detection by trio-based clinical exome sequencing (CES) or whole exome sequencing (WES). Eight-three singleton pregnancies with a normal fetal karyotype were enrolled in this prospective observational study. Pathogenic or likely pathogenic variations were identified in 30 cases (CNVs in 3 cases, SNVs/indels in 27 cases), indicating an overall molecular diagnostic rate of 36.1% (30/83). Two cases had both a CNV of uncertain significance (VOUS) and likely pathogenic SNV, and one case carried both a VOUS CNV and an SNV. We demonstrated that simultaneous analysis of CNVs and SNVs/indels can improve the diagnostic yield of prenatal diagnosis with shortened reporting time, namely, 2–3 weeks. Due to the relatively long TAT for sequential procedure for prenatal genetic diagnosis, as well as recent sequencing technology advancements, it is clinically necessary to consider the simultaneous evaluation of CNVs and SNVs/indels to enhance the diagnostic yield and timely TAT, especially for cases in the late second trimester or third trimester.
Keywords: fetal ultrasound anomalies; prenatal diagnosis; CMA; CNV-seq; clinical exome sequencing (CES) fetal ultrasound anomalies; prenatal diagnosis; CMA; CNV-seq; clinical exome sequencing (CES)

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MDPI and ACS Style

Qi, Q.; Jiang, Y.; Zhou, X.; Meng, H.; Hao, N.; Chang, J.; Bai, J.; Wang, C.; Wang, M.; Guo, J.; et al. Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes. Genes 2020, 11, 1397. https://doi.org/10.3390/genes11121397

AMA Style

Qi Q, Jiang Y, Zhou X, Meng H, Hao N, Chang J, Bai J, Wang C, Wang M, Guo J, et al. Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes. Genes. 2020; 11(12):1397. https://doi.org/10.3390/genes11121397

Chicago/Turabian Style

Qi, Qingwei, Yulin Jiang, Xiya Zhou, Hua Meng, Na Hao, Jiazhen Chang, Junjie Bai, Chunli Wang, Mingming Wang, Jiangshan Guo, and et al. 2020. "Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes" Genes 11, no. 12: 1397. https://doi.org/10.3390/genes11121397

APA Style

Qi, Q., Jiang, Y., Zhou, X., Meng, H., Hao, N., Chang, J., Bai, J., Wang, C., Wang, M., Guo, J., Ouyang, Y., Xu, Z., Xiao, M., Zhang, V. W., & Liu, J. (2020). Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes. Genes, 11(12), 1397. https://doi.org/10.3390/genes11121397

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