Expanding the Scope of Non-invasive Prenatal Testing to Detect Fetal Chromosomal Copy Number Variations

Songchang Chen; Lanlan Zhang; Jiong Gao; Shuyuan Li; Chunxin Chang; Yiyao Chen; Hongjun Fei; Junyu Zhang; Yanlin Wang; Hefeng Huang; Chenming Xu; Daru Lu

doi:10.3389/fmolb.2021.649169

Expanding the Scope of Non-invasive Prenatal Testing to Detect Fetal Chromosomal Copy Number Variations

Front Mol Biosci. 2021 May 12:8:649169. doi: 10.3389/fmolb.2021.649169. eCollection 2021.

Authors

Songchang Chen^{1

2

3

4

5}, Lanlan Zhang^{1

3

4

5

6}, Jiong Gao⁷, Shuyuan Li^{3

4

5}, Chunxin Chang^{3

4

5}, Yiyao Chen^{3

4

5}, Hongjun Fei^{3

4

5}, Junyu Zhang^{3

4

5}, Yanlin Wang^{3

4

5}, Hefeng Huang^{3

4

5}, Chenming Xu^{2

3

4

5}, Daru Lu^{1

8}

Affiliations

¹ State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China.
² Genetics Center of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.
³ The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
⁴ Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
⁵ Shanghai Municipal Key Clinical Specialty, Shanghai, China.
⁶ Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
⁷ Shanghai Medical Laboratory, BGI-Shanghai, BGI-Shenzhen, Shanghai, China.
⁸ Key Laboratory of Birth Defects and Reproductive Health of National Health Commission, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China.

Abstract

Non-invasive prenatal testing (NIPT) for common fetal trisomies is effective. However, the usefulness of cell-free DNA testing to detect other chromosomal abnormalities is poorly understood. We analyzed the positive rate at different read depths in next-generation sequencing (NGS) and identified a strategy for fetal copy number variant (CNV) detection in NIPT. Pregnant women who underwent NIPT by NGS at read depths of 4-6 M and fetuses with suspected CNVs were analyzed by amniocentesis and chromosomal microarray analysis (CMA). These fetus samples were re-sequenced at a read depth of 25 M and the positive detection rate was determined. With the increase in read depth, the positive CNV detection rate increased. The positive CNV detection rates at 25 M with small fragments were higher by NGS than by karyotype analysis. Increasing read depth in NGS improves the positive CNV detection rate while lowering the false positive detection rate. NIPT by NGS may be an accurate method of fetal chromosome analysis and reduce the rate of birth defects.

Keywords: copy number variation; microdeletion/microduplication syndromes; next generation sequencing; non-invasive prenatal testing; sequencing depth.