title: Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies.
abstract: OBJECTIVE
  To report the clinical performance of massively parallel sequencing-based non-invasive prenatal testing (NIPT) in detecting trisomies 21, 18 and 13 in over 140,000 clinical samples and to compare its performance in low-risk and high-risk pregnancies.
  
  
  METHODS
  Between 1 January 2012 and 31 August 2013, 147,314 NIPT requests to screen for fetal trisomies 21, 18 and 13 using low-coverage whole-genome sequencing of plasma cell-free DNA were received. The results were validated by karyotyping or follow-up of clinical outcomes.
  
  
  RESULTS
  NIPT was performed and results obtained in 146,958 samples, for which outcome data were available in 112,669 (76.7%). Repeat blood sampling was required in 3213 cases and 145 had test failure. Aneuploidy was confirmed in 720/781 cases positive for trisomy 21, 167/218 cases positive for trisomy 18 and 22/67 cases positive for trisomy 13 on NIPT. Nine false negatives were identified, including six cases of trisomy 21 and three of trisomy 18. The overall sensitivity of NIPT was 99.17%, 98.24% and 100% for trisomies 21, 18 and 13, respectively, and specificity was 99.95%, 99.95% and 99.96% for trisomies 21, 18 and 13, respectively. There was no significant difference in test performance between the 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 false-positive and false-negative NIPT results were maternal copy number variant and fetal/placental mosaicism, but fetal fraction had no effect.
  
  
  CONCLUSIONS
  Using a stringent protocol, the good performance of NIPT shown by early validation studies can be maintained in large clinical samples. This technique can provide equally high sensitivity and specificity in screening for trisomy 21 in a low-risk, as compared to high-risk, population.
authors.affiliation: BGI-Diagnostics, Shenzhen, China; BGI Clinical Laboratories-Shenzen, Shenzhen, China.
authors.forename: H
authors.initials: H
authors.lastname: Zhang
authors.forename: Y
authors.initials: Y
authors.lastname: Gao
authors.forename: F
authors.initials: F
authors.lastname: Jiang
authors.forename: M
authors.initials: M
authors.lastname: Fu
authors.forename: Y
authors.initials: Y
authors.lastname: Yuan
authors.forename: Y
authors.initials: Y
authors.lastname: Guo
authors.forename: Z
authors.initials: Z
authors.lastname: Zhu
authors.forename: M
authors.initials: M
authors.lastname: Lin
authors.forename: Q
authors.initials: Q
authors.lastname: Liu
authors.forename: Z
authors.initials: Z
authors.lastname: Tian
authors.forename: H
authors.initials: H
authors.lastname: Zhang
authors.forename: F
authors.initials: F
authors.lastname: Chen
authors.forename: T K
authors.initials: TK
authors.lastname: Lau
authors.forename: L
authors.initials: L
authors.lastname: Zhao
authors.forename: X
authors.initials: X
authors.lastname: Yi
authors.forename: Y
authors.initials: Y
authors.lastname: Yin
authors.forename: W
authors.initials: W
authors.lastname: Wang
mesh_terms: D000328:Adult; D002474:Cell-Free System; D002681:China / Q000453:epidemiology; D025063:Chromosome Disorders / Q000175:diagnosis* / Q000196:embryology / Q000235:genetics; D002882:Chromosomes, Human, Pair 13 / Q000235:genetics; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D004247:DNA / Q000235:genetics*; D019175:DNA Methylation; D004314:Down Syndrome / Q000175:diagnosis* / Q000196:embryology / Q000235:genetics; D005260:Female; D005500:Follow-Up Studies; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D007231:Infant, Newborn; D062145:Maternal Serum Screening Tests; D011247:Pregnancy; D011256:Pregnancy Outcome; D011296:Prenatal Diagnosis; D015203:Reproducibility of Results; D014314:Trisomy / Q000175:diagnosis* / Q000235:genetics; D000073839:Trisomy 13 Syndrome; D000073842:Trisomy 18 Syndrome
chemical_list: D004247:DNA
keywords: CNV; NIPT; cell-free DNA; clinical performance; false negative; false positive; low-risk population; mosaicism; trisomy