The aim of this study was to report the clinical performance of massively parallel sequencing-based noninvasive prenatal testing (NIPT) in detecting T21, T18, and T13 in over 140,000 clinical samples. NIPT performance in low-risk pregnancies and high-risk pregnancies was also compared.
from January 1, 2012 to August 31, 2013, 147,314 NIPT requests were received for screening of fetal trisomy 21, 18, and 13 using low-coverage whole-genome sequencing of plasma cell free DNA. NIPT results were validated by karyotyping confirmation or follow-up of clinical outcomes.
NIPT was performed on 146,958 samples, of which outcome data were available in 112,669 (76.7%). 3,213 cases required repeat blood sampling, 145 had no report. Aneuploidy was confirmed in 720 of 781 T21-positive cases, 167 of 218 T18-positive cases, and 22 of 67 T13-positive cases. There were 9 false negative identified, including 6 T21 and 3 T18 cases. The overall sensitivity of NIPT was 99.17% for T21, 98.24% for T18, and 100% for T13, and the specificity was 99.95% for T21, 99.95% for T18, and 99.96% for T13. There was no significant difference in test performance between 72,382 high-risk and 40,287 low-risk subjects (sensitivity 99.21% vs. 98.97%, p = 0.82; specificity 99.95% vs. 99.95%, p = 0.98). The major factors contributing to NIPT false positive and false negative results were maternal copy number variant (CNV) and fetal/placental mosaicism, but not fetal fraction.
With stringent protocol, the high performance of NIPT showed by early validation studies could be maintained in large clinical services. NIPT can provide equally high sensitivity and specificity in screening T21 in low-risk population.
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