Copy number variations in ultrasonically abnormal late pregnancy fetuses with normal karyotypes

Many fetuses are found to have ultrasonic abnormalities in the late pregnancy. The association of fetal ultrasound abnormalities in late pregnancy with copy number variations (CNVs) is unclear. We attempted to explore the relationship between types of ultrasonically abnormal late pregnancy fetuses and CNVs. Fetuses (n = 713) with ultrasound-detected abnormalities in late pregnancy and normal karyotypes were analyzed. Of these, 237 showed fetal sonographic structural malformations and 476 showed fetal non-structural abnormalities. Single nucleotide polymorphism (SNP)-based chromosomal microarray (CMA) was performed on the Affymetrix CytoScan HD platform. Using the SNP array, abnormal CNVs were detected in 8.0% (57/713) of the cases, with pathogenic CNVs in 32 cases and variants of uncertain clinical significance (VUS) in 25 cases. The detection rate of abnormal CNVs in fetuses with sonographic structural malformations (12.7%, 30/237) was significantly higher (P = 0.001) than that in the fetuses with non-structural abnormalities (5.7%, 27/476). Overall, we observed that when fetal sonographic structural malformations or non-structural abnormalities occurred in the third trimester of pregnancy, the use of SNP analysis could improve the accuracy of prenatal diagnosis and reduce the rate of pregnancy termination.


Scientific RepoRtS
| (2020) 10:15094 | https://doi.org/10.1038/s41598-020-72157-6 www.nature.com/scientificreports/ The relationships between fetal ultrasound abnormalities during pregnancy and chromosomal copy number variations (CNVs) have been extensively investigated 3,6,7 . In recent years, CMA has been recommended as the preferred diagnostic method for prenatal diagnosis of fetal ultrasound abnormalities 8 . However, there was little research assessment of the utility of CMA used in fetuses with abnormal ultrasound in late pregnancy. This study retrospectively analyzed the results of SNP analysis of 713 cases, from 2016 to 2019, and explored the relationship between types of ultrasonically abnormal late pregnancy fetuses and CNVs.
Methods patient data. The data regarding pregnancies with abnormal ultrasound findings (n = 713) from November 2016 to July 2019 were collected at the Fujian Maternal and Child Health Hospital. The exclusion criteria were abnormal karyotype analysis results and normal fetal ultrasound findings. The inclusion criteria were fetal sonographic structural malformations and non-structural abnormalities. According to the anatomical system affected, sonographic structural malformations were divided into: (1) central nervous system; (2) cardiovascular system; (3) urogenital system; (4) skeletal system; (5) respiratory system; (6) digestive system; and (7) craniofacial region malformations. Non-structural abnormalities were divided into: (1) ultrasound soft markers (including an echogenic bowel, absence of nasal bone, lateral ventricle widening, intracardiac echogenic focus, and tricuspid regurgitation); (2) fetal growth restriction (FGR); and (3) amniotic fluid volume abnormality and pericardial effusion. Indications for late cordocentesis included fetal sonographic structural malformations (n = 237) and fetal non-structural abnormalities (n = 476) (Fig. 1).

Karyotype analysis.
According to the routine methods established in our laboratory, umbilical cord blood was routinely cultured for 72 h, and then the chromosomes were harvested, fixed and prepared. Cultured cells were analyzed by karyotype analysis using Giemsa banding at a resolution of 450-550 bands.
Single-nucleotide polymorphism (SNP) array. Ultrasound-guided cordocentesis was used to extract umbilical cord blood for prenatal SNP-array testing. To avoid maternal cell contamination during cordocentesis, short-tandem repeats analysis was conducted before testing fetal samples. Genomic DNA extraction from fetal umbilical cord blood cells was performed using a QIAamp DNA blood mini kit (Qiagen, Germany). The concentration and purity of genomic DNA were measured using a NanoDrop One Microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific, USA). DNA digestion, amplification, purification, fragmentation, labeling, hybridization, washing, staining, scanning, and other steps were carried out according to the manual for an Affymetrix Genome CytoScan 750K gene chip. The reporting thresholds for CNVs were 400 kb deleted and 400 kb duplicated. Data analysis was carried out using the Chromosome Analysis Suite software 3.3 (Affymetrix, Santa Clara, CA, USA). Based on the nature of CNVs detected, CNVs were classified as pathogenic, variants of uncertain clinical significance (VUS), and benign, according to the American College of Medical Genetics guidelines 9 .  pathogenic cnVs detected in fetuses with ultrasound abnormalities and normal karyotypes using an Snp array. Among the 32 cases with pathogenic CNVs, 24 were related to known chromosomal disorders, namely, 22q11 deletion syndrome (n = 5), 22q11.2 duplication syndrome (n = 3), 17q12 deletion syndrome (n = 3), cat eye (n = 1), 16p11.2 deletion syndrome (n = 4), Prader-Willi syndrome (n = 1), Miller-Dieker syndrome (n = 1), Wolf-Hirschhorn syndrome (n = 1), Sotos syndrome (n = 1), 7q11.23 duplication syndrome (n = 2), and 1q21.1 duplication syndrome (n = 2). Additionally, the pathogenic CNVs were associated with a loss at 17p12, 1p36.33p36.23, and 22q13.33 and a gain at 15q13.3, 1q21.1q21.2, 3q29, Xq28, and 10q11.22q11.23 (Table 3). Benign cnVs detected in fetuses with ultrasound abnormalities and normal karyotypes using Snp array. The seven benign CNVs in fetuses were inherited from their healthy parents (Table 5). According to the Database of Genomic Variants (DGV), these genes have not been reported previously.
Genealogical analysis and pregnancy outcomes. The parents of nine fetuses with pathogenic CNVs were tested, and it was found that five CNVs were de nova and four were inherited. Among the 25 cases of fetuses with VUS, the parents refused genetic testing in seven cases. In the other 18 cases, the variants were confirmed to be inherited. Some pregnant women with fetuses with pathogenic CNV (n = 29) and VUS (n = 7) chose to terminate the pregnancies. However, 15 cases with VUS CNVs women chose to continue the pregnancy and showed good growth and development on postnatal examination. In the seven cases in which fetuses were found to have inherited a benign CNV from one of the normal parents, the pregnancies were continued and had a favorable outcome.

Discussion
We retrospectively analyzed the SNP analysis data of 713 cases, and explored the correlation between phenotype characteristics of the fetuses and pathogenic CNVs. All 713 fetuses with abnormal ultrasound findings and normal karyotypes were investigated by CMA. We detected abnormal CNVs in 8.0% (57/713) of the cases, including pathogenic CNVs in 32 cases (4.5%, 32/713) and VUS in 25 cases (3.5%, 25/713). This rate of detection of abnormal CNVs was somewhat higher than that reported in previous studies [10][11][12] . We suggest that CMA should be considered for genetic analysis in cases with abnormal ultrasound findings in the second and third trimesters of pregnancy. With the growth of the fetus, more fetal ultrasound abnormalities (structural and non-structural) are found during the second and third trimesters of pregnancy. In our study, the detection rate of abnormal CNVs in fetuses with sonographic structural malformations (12.7%, 30/237) was significantly higher (P = 0.001) than in fetuses with non-structural abnormalities (5.7%, 27/476). Among the fetuses with sonographic structural malformations, those with multiple malformations showed the greatest rate of CNVs (31.8%, 7/22), followed by fetuses with central nervous system malformations (25%, 4/16), congenital anomalies of the kidney and urinary tract (18.0%, 7/39), and congenital heart malformations (8%, 10/125). These findings are slightly different from those of a previous study 13 , in which cardiovascular, central nervous, gastrointestinal, and musculoskeletal system malformations were mostly associated with pathogenic CNVs.
At present, the consensus regarding the application of CMA in prenatal diagnosis does not include cases with non-structural abnormalities. There are few studies reporting the relationships between sonographic nonstructural abnormalities and chromosomal duplications/deletions. In our study, among the fetuses with nonstructural abnormalities, those with amniotic fluid volume abnormality and pericardial effusion showed the greatest rate of CNVs (20%, 4/20), followed by fetuses with FGR (5.8, 7/120) and abnormal soft indications (4.8%, 16/336). Compared with that reported in another study 14 , the CNV detection rate in the fetuses with sonographic non-structural abnormalities was slightly higher in this study, likely due to differences in the selected cohorts of fetuses with ultrasound anomalies in late pregnancy.
In most cases, there are direct causal relationships between pathogenic CNVs and fetal phenotypes. However, the use of genotype-phenotype associations is not always reliable in prenatal diagnosis. Our findings revealed 32 cases of pathogenic CNVs. The most common was 22q11 deletion syndrome 15 , which is associated with congenital heart disease. We also found three fetuses with 17q12 deletion syndrome 16 , which is associated with congenital anomalies of the kidney and urinary tract. The only ultrasonographic manifestations in these fetuses were double kidney echo enhancements. A CNV on human chromosome 16p11.2 is associated with autism spectrum www.nature.com/scientificreports/ disorders 17,18 . We detected this known 16p11.2 deletion syndrome in four fetuses, with different ultrasonographic manifestations. The ultrasonographic manifestations in three of the fetuses were hydrocephalus, spinal dysplasia, and lateral ventricle widening. The fourth fetus presented with a widened lateral ventricle, echogenic bowel, and echogenic foci within the left ventricle. Owing to the limitations of ultrasound, fetal phenotypes are often incomplete, which may complicate prenatal counseling 19 . Therefore, the application of genomic detection techniques is important in fetuses with ultrasound abnormalities. We detected 25 fetuses with VUS, of which three fetuses had 16p13.11 duplications and one had a 16p13.11 deletion. According to the literature 20-23 , gain and loss at 16p13.11 have been associated with autism, schizophrenia, and epilepsy. The carrier frequencies of duplications and deletions at the 16p13.11 locus are less than 1% in the general population, but the penetrance is 5-10% 24 ; therefore, we defined the CNVs at 16p13.11 as VUS. We also detected 15q11.2 deletions in three fetuses. The ultrasonographic manifestations in these fetuses included ventricular septal defect (VSD), a Dandy-Walker malformation, an echogenic bowel, and a subcutaneous cyst at the back of the neck. Genetic analysis showed that these deletions were inherited from one of the normal parents. However, there are some reports of 15q11.2 deletions causing neurodevelopmental alterations 25,26 . Thus, we also defined the 15q11.2 deletions as VUS. Another 15 mutations were defined as VUS because these CNVs have not been reported in the DGV and were identified as de novo variants by pedigree analysis. Two cases were identified to lack heterozygosity. The parents of these two cases refused to undergo a pedigree test, and therefore, we defined the lack of heterozygosity as VUS. Seven fetuses were found to have inherited their CNVs from their normal parents. As there are no reports of these CNVs in the DGV, they were defined as benign CNVs. At present, the greatest difficulty in the use of SNP-array results in prenatal diagnosis lies in the correct interpretation of VUS. Literature reports show that the rates of VUS detection are 1.4-12.3% 11,27,28 ; hence, the rate found in our study (3.5%) was consistent with previous findings.
Following the application of an SNP array to rule out genomic abnormalities, pregnant women generally choose to deliver their babies, thus avoiding unnecessary termination of pregnancy. This outcome emphasizes the importance of CMA in genetic counseling. In our study, 29 cases of fetal sonographic structural malformations with pathogenic CNVs resulted in pregnancy termination; however, in three cases, the parents chose to deliver and neonates had good outcomes no other abnormalities were found except one with VSD. Of the 25 cases of fetuses with VUS, in 15 cases, the parents chose to deliver, and the babies showed good growth and development after birth. We also found that seven cases associated with benign CNVs continued their pregnancies and had a  www.nature.com/scientificreports/ favorable outcome. According to our experience, if the observations by ultrasound associated with chromosomal anomalies and other fatal malformation are excluded, the pregnant women may have increased confidence in continuing pregnancy, especially CNVs were inherited. There were some limitations to our study. First, we only used the SNP array to detect CNVs in fetuses with ultrasound-detected abnormalities and normal karyotyping analysis results. Thus, we cannot rule out single-gene mutations. In recent years, next-generation sequencing has been used as a new technique for genetic testing to detect single-gene mutations and CNVs. This technology may provide a more comprehensive prenatal genetic diagnosis for fetuses with ultrasound-detected abnormalities and a better assessment of the fetal prognosis. Second, the origins of some VUS were not traced, and thus, the sample size should be increased to further study these VUS. In addition, the numbers of cases in the subsystems of some ultrasound abnormalities were insufficient, and therefore, it was impossible to group those cases at a deeper level. In the future, more cases need to be analyzed, or multicenter collaborations are required, to improve the statistical reliability of the findings. conclusion CMA can be used as an effective method for genetic diagnosis of ultrasonically abnormal late pregnancy fetuses. The detection rate of CMA was different for different types of ultrasonically abnormal late pregnancy fetuses. CMA can improve the detection rate of chromosomal abnormalities that cannot be detected by karyotype analysis. In genetic counselling, CMA should be utilized based on the type of ultrasonic abnormality observed.

Data availability
All data generated during and/or analyzed during the current study are available upon request by contact the corresponding author.