Table 2.
Information of detection failure on the originally submitted and resubmitted samples.
| No. | Failure Reasons | Blood/Plasma Samples 1 | DNA/Library 2 | Sequencing Data Analysis 3 | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A | B | C | D | E | F | G | H | I | J | K | ||
| 1. | Original samples | |||||||||||
| 1.1. | Experiment failure cases (first tube plasma) | 204 | 222 | 20 | 132 | 1145 | 65 | 152 | 85 | 133 | 1077 | 22 |
| Experiment failure rate% (first tube plasma, total cases) |
0.52 (446/86,262) | 1.48(1277/86,262) | 1.78(1534/86,262) | |||||||||
| 1.1.1. | Re-experiment rate% (second or third tube plasma, re-examining) |
/ | 1.48(1277/86,262) | 1.58 (1359/86,262) |
||||||||
| 1.1.2. | Re-experiment failure rate% | / | 0.06(48/86,262) | 0.15(128/86,262) | ||||||||
| 2. | Resampling procedure | |||||||||||
| 2.1. | Resampling rate% (required resampling) | 0.52 (446/86,262) | 0.06(48/86,262) 4 | 0.35(303/86,262) 5 | ||||||||
| 2.2. | Actual resampling rate% (accepted and obtained) |
0.52 (446/86,262) | 0.03(22/86,262) | 0.32 (279/86,262) | ||||||||
| 2.3. | Experiment failure rate% (redrawing samples) |
/ | 0(0/22) | 6.81(19/279) | ||||||||
| 2.4. | Experiment successful rate% (redrawing samples) |
100(446/446) | 100(22/22) | 93.19(260/279) | ||||||||
| 3. | Final failure rate% | |||||||||||
| 3.1. | Final test failure rate% (no results, original and resampling) |
/ | 0.03 ((48–22)/86,262) |
0.03 ((303–279) + 19)/86,262) 6 |
||||||||
| Final test failure cases (total cases) 7 | 0.08(69/86,262) | |||||||||||
| 4. | Average fetal fraction% (accepted and obtained) | n = 125 | ||||||||||
| 4.1. | Result group 8 | 12.61 (5.49%, n = 110) | ||||||||||
| 4.2. | No-call group 8 | 10.59 (2.82%, n = 15) | ||||||||||
1 Poor quality of whole blood or plasma: A, hemolysis; B, coagulation; C, others, e.g., lipemia, hemolysis with coagulation. 2 DNA/library issues: D, high/low concentration of DNA extraction; E, abnormal peak, low concentration of library construction. 3 Sequencing data issues: F, GC content bias (>42 or <38); G, insufficient data amount; H, multiple chromosome abnormalities; I, low fetal fraction (FF), FF < 3.0%; J, borderline Z-score; K, multiple factors, failed samples with more than one failing factor, including high GC, insufficient data amount and low fetal fraction, multiple chromosome abnormalities, etc. 4 These samples received a non-reportable NIPS results even after re-experiment with the second or third plasma of the original samples. 5 In total, 0.35% of cases required resampling totally. Among these cases, 0.15% (n = 128) still failed in the re-experiment with the second or third plasma of the original samples, and 0.2% (n = 175) were required for resampling directly, mainly due to low FF (n = 133). 6 A total of 0.03% failure cases were included 24 re-experiment cases and 19 resampling cases. 7 All of these failure cases chose to terminate the test. 8 Result/no-call groups: defined as with/without results yielded from the direct resampling due to low FF (n = 125).