Abstract Background Small subchromosomal deletions and duplications caused by copy number variants (CNVs) can now be detected with noninvasive prenatal testing (NIPT) technology. However, the clinical utility and validity of this screening for CNVs are still unknown. Here, we discuss some special conditions in which both cases simultaneously exhibited false positives caused by maternal CNVs and false negatives due to limitations of the technology. Case presentation In case 1, NIPT indicated a 1.1 Mb deletion at 21q21.1, but the umbilical cord for array CGH (aCGH) revealed a 422 kb deletion at 15q13.3. Peripheral blood of the parents for aCGH showed a 1.1 Mb deletion at 21q21.1 in the mother’s sample, and the same deletion at 15q13.3 was detected in the father’s blood. In case 2, NIPT showed a 1.5 Mb deletion at 22q11.21, but aCGH of amniocytes revealed a 1.377 Mb duplication rather than a 1.5 Mb deletion at 22q11.21. Furthermore, aCGH analysis of the parental blood revealed a 647 kb deletion at 22q11.21 in the mother and a 2.8 Mb duplication of 22q11.21 in the father. Conclusions Our findings not only highlight the significance of diagnostic testing following a positive cfDNA sequencing result but also the necessity for additional analytical and clinical validation before routine use in practice.
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