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
To investigate factors associated with the accuracy of abnormal autosomal cell- free DNA results.
Study Design
Retrospective cohort study of 121 patients with abnormal cell-free DNA results from a referral maternal-fetal medicine practice from March 2013 to 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 non-reportable. 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’s exact tests were used as appropriate.
Results
121 patients had abnormal cell-free DNA results for for trisomy 21, trisomy 18, trisomy 13, and/or microdeletions. 105 patients had abnormal cell-free DNA results for for trisomy 21, trisomy 18, trisomy 13. Of these, 92 (87.6%) were positive and 13 (12.4%) were non-reportable. 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 (CI) 63% to 82%) for all trisomies (by chromosome: trisomy 21, 83.0% (39/47, CI 69% to 92%, trisomy 18, 65.0% (13/20, CI 41% to 84%), and trisomy 13, 43.8% (7/16, CI 21% to 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%; non-reportable 2/13, 16.7%; p=0.004), and abnormal first trimester ultrasound (trisomy 21 25/45, 55.6%; trisomy 18 13/20, 65%; trisomy 13 6/14, 42.9%; non-reportable 1/13, 7.7%; p=0.003). There was no association between false positive rates and testing platform, but there was a difference between the four laboratories (p=0.018). Twenty-six patients had positive (n=9) or non-reportable (n=17) microdeletion results. Seven of nine 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.