Clinical application of single nucleotide polymorphism array in prenatal diagnosis: Experience with 8753 samples

Abstract

Background Single nucleotide polymorphism (SNP) array has been applied to prenatal diagnosis. This study aimed to assess the clinical significance of SNP array in diagnosing fetal chromosomal anomalies based on our experience. Methods A total of 8753 pregnant women with high-risk prenatal indications were enrolled in this retrospective study. Demographic characteristics, chromosomal abnormalities and follow-up results were collected. Results Data showed that the overall abnormality detection rate of SNP array was 16.9%, including the detection rate of 7.7% in aneuploidy, the detection rate of 4.2% and 4.4% in pathogenic copy number variations (CNVs) and variants of uncertain significance. The total abnormality detection rate was 15.3%, 22.0% and 38.4% for pregnant women with single risk indication, two kinds of indications and more than two kinds of indications, respectively. The detection rates in the three groups were statistically significant. Additionally, fetus with the positive noninvasive prenatal testing (NIPT) results had the highest abnormality detection rate (38.8%), followed by participants with the abnormal ultrasound findings (13.1%). 98.8% of pregnant women simultaneously chose traditional karyotyping and got their karyotype results. The concordant rate between karyotyping and SNP array was 89.0%, with some structural abnormalities and low-level mosaicism being missed by SNP array, while SNP array additionally found the microduplication/microdeletion. Conclusions SNP array would be a valuable technology in prenatal diagnosis, with different abnormality detection rate in pregnant women with various risk indications. SNP array combined with the traditional karyotyping could provide more information for prenatal diagnosis.