title: Cell-free DNA screening in clinical practice: abnormal autosomal aneuploidy and microdeletion results.
abstract: BACKGROUND
  Since its commercial release in 2011 cell-free DNA screening has been rapidly adopted as a routine prenatal genetic test. However, little is known about its performance in actual clinical practice.
  
  
  OBJECTIVE
  We sought to investigate factors associated with the accuracy of abnormal autosomal cell-free DNA results.
  
  
  METHODS
  We conducted a retrospective cohort study of 121 patients with abnormal cell-free DNA results from a referral maternal-fetal medicine practice from March 2013 through July 2015. Patients were included if cell-free DNA results for trisomy 21, trisomy 18, trisomy 13, or microdeletions (if reported by the laboratory) were positive or nonreportable. The primary outcome was confirmed aneuploidy or microarray abnormality on either prenatal or postnatal karyotype or microarray. Secondary outcomes were identifiable associations with in vitro fertilization, twins, ultrasound findings, testing platform, and testing laboratory. Kruskal-Wallis or Fisher exact tests were used as appropriate.
  
  
  RESULTS
  A total of 121 patients had abnormal cell-free DNA results for trisomy 21, trisomy 18, trisomy 13, and/or microdeletions. In all, 105 patients had abnormal cell-free DNA results for trisomy 21, trisomy 18, and trisomy 13. Of these, 92 (87.6%) were positive and 13 (12.4%) were nonreportable. The results of the 92 positive cell-free DNA were for trisomy 21 (48, 52.2%), trisomy 18 (22, 23.9%), trisomy 13 (17, 18.5%), triploidy (2, 2.2%), and positive for >1 parameter (3, 3.3%). Overall, the positive predictive value of cell-free DNA was 73.5% (61/83; 95% confidence interval, 63-82%) for all trisomies (by chromosome: trisomy 21, 83.0% [39/47; 95% confidence interval, 69-92%], trisomy 18, 65.0% [13/20; 95% confidence interval, 41-84%], and trisomy 13, 43.8% [7/16; 95% confidence interval, 21-70%]). Abnormal cell-free DNA results were associated with positive serum screening (by group: trisomy 21 [17/48, 70.8%]; trisomy 18 [7/22, 77.8%]; trisomy 13 [3/17, 37.5%]; nonreportable [2/13, 16.7%]; P = .004), and abnormal first-trimester ultrasound (trisomy 21 [25/45, 55.6%]; trisomy 18 [13/20, 65%]; trisomy 13 [6/14, 42.9%]; nonreportable [1/13, 7.7%]; P = .003). There was no association between false-positive rates and testing platform, but there was a difference between the 4 laboratories (P = .018). In all, 26 patients had positive (n = 9) or nonreportable (n = 17) microdeletion results. Seven of 9 screens positive for microdeletions underwent confirmatory testing; all were false positives.
  
  
  CONCLUSIONS
  The positive predictive value of 73.5% for cell-free DNA screening for autosomal aneuploidy is lower than reported. The positive predictive value for microdeletion testing was 0%. Diagnostic testing is needed to confirm abnormal cell-free DNA results for aneuploidy and microdeletions.
authors.affiliation: Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.
authors.forename: Stephanie G
authors.initials: SG
authors.lastname: Valderramos
authors.affiliation: Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.
authors.forename: Rashmi R
authors.initials: RR
authors.lastname: Rao
authors.affiliation: Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.
authors.forename: Emily W
authors.initials: EW
authors.lastname: Scibetta
authors.affiliation: Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.
authors.forename: Neil S
authors.initials: NS
authors.lastname: Silverman
authors.affiliation: Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA.
authors.forename: Christina S
authors.initials: CS
authors.lastname: Han
authors.affiliation: Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA. Electronic address: ldplatt@gmail.com.
authors.forename: Lawrence D
authors.initials: LD
authors.lastname: Platt
mesh_terms: D000328:Adult; D015415:Biomarkers / Q000097:blood; D002872:Chromosome Deletion; D025063:Chromosome Disorders / Q000175:diagnosis* / Q000235:genetics; D004247:DNA / Q000097:blood; D005260:Female; D005500:Follow-Up Studies; D006801:Humans; D062145:Maternal Serum Screening Tests; D008875:Middle Aged; D011237:Predictive Value of Tests; D011247:Pregnancy; D012189:Retrospective Studies; D014314:Trisomy
chemical_list: D015415:Biomarkers; D004247:DNA
keywords: aneuploidy; cell-free DNA; genetic screening; microdeletion; noninvasive prenatal testing; positive predictive value; prenatal diagnosis; trisomy 13; trisomy 18; trisomy 21