Comparison between single nucleotide polymorphism array and karyotyping in prenatal diagnosis in Down's screening abnormal pregnancy

AIM: To evaluate the clinical application of single nucleotide polymorphism array (SNP array) in prenatal diagnosis for screening the abnormality of women with Down's syndrome (DS).METHODS: The amniotic fluid samples (n=312) collected by amniocentesis for the DS screening abnormality women were tested by karyotyping and SNP array analysis, respectively. The findings of karyotyping and SNP array analysis were compared.RESULTS: Two cases of trisomy 21 were identified by karyotyping and SNP array analysis, but SNP array analysis failed to identify 6 cases of chromosome balanced structural rearrangement. SNP detected 176 cases copy number variants (CNVs) in 303 cases normal karyotype were detected by SNP, including 106 benign CNVs, 61 variants of unknown significance (VOUS), 9 de novo CNVs, and none of them was pathogenic. The distribution difference of CNVs in DS screening positive group and DS screening positive plus advanced maternal age group was not statistically significant (P>0.05). Furthermore, we reported 14 kinds of CNVs for the first time in population.CONCLUSION: SNP array can further assure chromosome microduplication/microdeletion. In normal karyotype fetus of prenatal diagnosis, SNP can detect some clinical significant CNVs.