Identification of copy number variations among fetuses with ultrasound soft markers using next-generation sequencing

Abstract

A prospective analysis investigating the associations between pathogenic copy number variations (pCNVs) and ultrasound soft markers (USMs) in fetuses and evaluating the clinical value of copy number variation sequencing (CNV-seq) in such pregnancy studies was carried out. 3,398 unrelated Chinese women with singleton pregnancies and undergone amniocentesis at 18-36 weeks of gestation for fetal CNV-seq were included. According to the prenatal fetal ultrasound screening results, the samples were divided into 3 groups: normal ultrasound (n = 2616), solitary USM (n = 663), and two or more USMs (n = 119). CNV-seq was performed successfully using all samples. The prevalence of pCNVs in fetuses with normal ultrasound and USMs was 3.03% (79/2616) and 2.94% (23/782), respectively. The risk of segmental aneuploidies was significantly higher in the two or more USMs group (5/119, 4.20%) than in the normal ultrasound (27/2616, 1.04%) or solitary USM (9/663, 1.36%) groups (p = 0.002 and p = 0.031, respectively). Assuming that the resolution of karyotyping is ~5 Mb, a cytogenetic analysis would miss 33 of 102 (32.35%) pCNVs in these samples. Our results suggest an association between pCNVs and fetal USMs; multiple USMs indicate an increased risk of fetal segmental aneuploidies. In prenatal diagnostic testing, CNV-Seq identified additional, clinically significant cytogenetic information.

Figure 1

The CNV-seq profiles and partial karyograms of the fetus. (A,B) CNV-seq profiles for dup1q32.2q44 and dup15q11.1q13.2 (arrows), data is plotted as copy number (Y-axis) versus 20 kb chromosomal read bins (X-axis). The mean copy number along the length of each chromosome is indicated by the blue line. (C,D) The amniocytes of P20 showed partial karyotype and ideogram with an additional derivative chromosome der (15) t(1; 15) (q32.2; q13).