Noninvasive prenatal diagnosis of common aneuploidies by semiconductor sequencing

Abstract

Massively parallel sequencing (MPS) of cell-free fetal DNA from maternal plasma has revolutionized our ability to perform noninvasive prenatal diagnosis. This approach avoids the risk of fetal loss associated with more invasive diagnostic procedures. The present study developed an effective method for noninvasive prenatal diagnosis of common chromosomal aneuploidies using a benchtop semiconductor sequencing platform (SSP), which relies on the MPS platform but offers advantages over existing noninvasive screening techniques. A total of 2,275 pregnant subjects was included in the study; of these, 515 subjects who had full karyotyping results were used in a retrospective analysis, and 1,760 subjects without karyotyping were analyzed in a prospective study. In the retrospective study, all 55 fetal trisomy 21 cases were identified using the SSP with a sensitivity and specificity of 99.94% and 99.46%, respectively. The SSP also detected 16 trisomy 18 cases with 100% sensitivity and 99.24% specificity and 3 trisomy 13 cases with 100% sensitivity and 100% specificity. Furthermore, 15 fetuses with sex chromosome aneuploidies (10 45,X, 2 47,XYY, 2 47,XXX, and 1 47,XXY) were detected. In the prospective study, nine fetuses with trisomy 21, three with trisomy 18, three with trisomy 13, and one with 45,X were detected. To our knowledge, this is the first large-scale clinical study to systematically identify chromosomal aneuploidies based on cell-free fetal DNA using the SSP and provides an effective strategy for large-scale noninvasive screening for chromosomal aneuploidies in a clinical setting.

Fig. 1.

Characterization of pregnant subjects included in the retrospective and prospective studies.

Fig. 2.

Z scores obtained for each sample in group I (n = 515) and the cutoffs for detection of fetal aneuploidy. (A–C) Z scores for chromosome 13 (A), chromosome 18 (B), and chromosome 21 (C). (D and E) Z scores for male and female fetuses for chromosome X (D) and chromosome Y (E).

Fig. 3.

Comparison of z scores obtained from technical repeat experiments. Results from nine samples involving a fetus with trisomy are shown (open circles), including three samples that were tested a third time (solid circles).

Fig. 4.

Workflow for the noninvasive prenatal diagnosis of trisomy 21, 18, and 13 using the SSP.