A retrospective study of noninvasive prenatal testing for chromosome aneuploidies and subchromosomal copy number variations in 24359 single pregnancies

Abstract Background: With the development of whole-genome sequencing, small subchromosomal deletions and duplications could be found by non-invasive prenatal testing(NIPT). Our study is aimed to review the efficacy of NIPT as a screening test for aneuploidies and subchromosomal copy number variations (CNVs) in 24359 single pregnancies.Methods: A total of 24359 single pregnancies with different clinical features were retrospectively analyzed. Pathogenicity of abnormal NIPT results were assessed according to American College of Medical Genetics and Genomics(ACMG). Chromosome aneuploidies and subchromosomal CNVs were confirmed by karyotyping and chromosomal microarray analysis(CMA). Results: A total of 442 pregnancies (442/24359,1.9%) were with abnormal NIPT results. The positive predictive value (PPV) for trisomy 21(T21), trisomy 18 (T18), trisomy 13 (T13), and sex chromosome aneuploidies (SCAs) was 84.8%, 54.2%, 11.1% an 40.5% respectively. The PPV for subchromosomal CNVs was 59.0% (46/78). The clinical information, prenatal diagnosis results and follow-up results of 46 true positive cases, 6 cases with subchromosomal CNVs inconsistent with NIPT and 1 case of false negative were also demonstrated in detail.Conclusion: Our data have potential significance in demonstrating the significance of NIPT not only for common whole chromosome aneuploidies but also for subchromosomal CNV. Besides, the clinical information, prenatal diagnosis results and follow-up results of 52 cases with subchromosomal CNV and 1 case of false negative would provide important guidance for genetic counseling.