Prenatal Screening Via cfDNA – Paired‐End Sequencing Utilizing Fragment Size Information Reduces the Screen Positive Rate for X Chromosome Aneuploidies

ABSTRACT Objective Prenatal cfDNA screening has transformed care, yet it remains difficult to determine whether X aneuploidy signals originate from the patient or fetus, inflating screen positive and false positive rates. One potential solution is to incorporate fragment size data from paired‐end sequencing (PES). Method We use a large clinical cohort to examine the effect of incorporating fragment size information via PES on the performance of cfDNA screening for X chromosome aneuploidies. Within the same patients ( n = 118,859), we compare screen positive rates for monosomy X (MX) and trisomy X (XXX) before and after incorporation of fragment size data. Additionally, we examine the rate of reported false positives from patients tested via PES versus single‐end sequencing (SES, n = 141,364), which lacks fragment size. Results Incorporation of fragment size data from PES significantly reduced the screen positive rates for MX (−49.1%, 227/446) and XXX (−42.9%, 60/105). The rate of voluntarily reported MX false positives was lower among patients with PES fragment size information (0.0033%) compared with SES (0.0085%). No XXX false positives were reported. Conclusion The results illustrate that the screen positive rate can be reduced by leveraging fragment size data from paired‐end sequencing. This has the potential to reduce false positive rates in clinical cfDNA prenatal screening.