Table 3.
Performance of NIPS in screening of chromosome abnormalities in 83,671 general pregnancies 1.
| No. | NIPS Result | N | TP (n) |
FP (n) |
UC (n) |
FN (n) |
Sensitivity (%) |
Specificity (%) |
PPV (%) |
NPV (%) |
FPR (%) |
FNR (%) |
SPR (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Part 1: Common aneuploidies | |||||||||||||
| 1. | Trisomy 21 | 368 | 330 | 38 | 51 | 3 | 99.1 | 99.95 | 89.67 | 99.996 | 0.05 | 0.9 | 0.5 |
| Trisomy 21(full) | 349 | 325 | 24 | 50 | 3 | 99.09 | 99.97 | 93.12 | 99.996 | 0.03 | 0.91 | ||
| Trisomy 21(mos) | 19 | 5 | 14 | 1 | 0 | 100 | 99.98 | 26.32 | 100 | 0.02 | 0 | ||
| 2. | Trisomy 18 | 100 | 84 | 16 | 8 | 1 | 98.82 | 99.98 | 84 | 99.999 | 0.02 | 1.18 | 0.13 |
| Trisomy 18 | 95 | 83 | 12 | 8 | 1 | 98.81 | 99.99 | 87.37 | 99.999 | 0.01 | 1.19 | ||
| Trisomy 18(mos) | 5 | 1 | 4 | 0 | 0 | 100 | 100 | 20 | 100 | 0 | 0 | ||
| 3. | Trisomy 13 | 57 | 30 | 27 | 2 | 0 | 100 | 99.97 | 52.63 | 100 | 0.03 | 0 | 0.07 |
| Trisomy 13 | 50 | 29 | 21 | 2 | 0 | 100 | 99.97 | 58 | 100 | 0.03 | 0 | ||
| Trisomy 13(mos) | 7 | 1 | 6 | 0 | 0 | 100 | 99.99 | 14.29 | 100 | 0.01 | 0 | ||
| 4. | Common aneuploidies (combined) | 525 | 444 | 81 | 61 | 4 | 99.11 | 99.9 | 84.57 | 99.995 | 0.1 | 0.89 | 0.7 |
| Part 2: SCAs | |||||||||||||
| 1. | Monosomy X | 191 | 23 | 168 | 48 | 3 | 88.46 | 99.8 | 12.04 | 99.996 | 0.2 | 11.54 | 0.29 |
| Monosomy X | 185 | 23 | 162 | 46 | 3 | 88.46 | 99.81 | 12.43 | 99.996 | 0.19 | 11.54 | ||
| Monosomy X (mat) | 6 | 0 | 6 | 2 | 0 | / | 99.99 | 0 | 100 | 0.01 | / | ||
| 2. | Other SCAs (XXX, XXY, XYY, combined) | 184 | 128 | 56 | 52 | 0 | 100 | 99.93 | 69.57 | 100 | 0.07 | 0 | 0.28 |
| XXX | 53 | 36 | 17 | 18 | 0 | 100 | 99.98 | 67.92 | 100 | 0.02 | 0 | 0.08 | |
| XXY | 113 | 78 | 35 | 29 | 0 | 100 | 99.96 | 69.03 | 100 | 0.04 | 0 | 0.17 | |
| XYY | 18 | 14 | 4 | 5 | 0 | 100 | 100 | 77.78 | 100 | 0 | 0 | 0.03 | |
| 3. | 46,XY(delX) | 25 | 1 | 24 | 5 | 0 | 100 | 99.97 | 4 | 100 | 0.03 | 0 | 0.04 |
| 4. | SCAs (combined) | 400 | 152 | 248 | 105 | 3 | 98.06 | 99.7 | 38 | 99.996 | 0.3 | 1.94 | 0.6 |
| Part 3: Other abnormalities | |||||||||||||
| 1. | CNVs (≥5 Mb) 2 | 12 | 4 | 8 | 1 | 16 | 20 | 99.99 | 33.33 | 99.981 | 0.01 | 80 | 0.02 |
| 2. | RATs 3 | 44 | 9 | 35 | 12 | 1 | 90 | 99.96 | 20.45 | 99.999 | 0.04 | 10 | 0.07 |
| 3. | Other abnormalities (combined) | 56 | 13 | 43 | 13 | 174 | 43.33 | 99.95 | 23.21 | 99.98 | 0.05 | 56.67 | 0.09 |
| Part 4: Common aneuploidies, SCAs and other abnormalities | |||||||||||||
| 1. | Common aneuploidies and SCAs (combined) | 925 | 596 | 329 | 166 | 7 | 98.84 | 99.6 | 64.43 | 99.992 | 0.4 | 1.16 | 1.3 |
| 2. | Totally (combined) | 981 | 609 | 372 | 179 | 24 | 96.21 | 99.55 | 62.08 | 99.971 | 0.45 | 3.79 | 1.39 |
NIPS, noninvasive prenatal screening; N, invasive diagnosis and clinical diagnosis; TP, true positive; FP, false positive; UC, refused to diagnosis; FN, false negative; PPV, positive predictive value; NPV, negative predictive value; FPR, false positive rate; FNR, false negative rate; SPR, screen-positive rate; Mos, mosaic. 1 A total of 83,671 pregnancies, included 1160 screening positive cases and 82,511 negative cases with follow-up data. 2 CNVs, copy number variants (≥5 Mb), these CNVs included fragments sizes of chromosome deletion and duplication ranged from 6 to 32.5 Mb and 5.5 to 99 Mb, respectively (Table A2). 3 RATs, rare autosomal aneuploidies (chrN+/-), including, increased dosage chromosomes (most likely trisomies, chrN+), decreased dosage chromosomes (most likely monosomies, chrN-) and multiple chromosomal abnormalities (Multis, more than two chromosomal abnormalities) (Table A2 and Table A3). Almost all the Multis were retested again. 4 A total of 17 false negative cases were all confirmed by SNP microarray.