Systematic analysis of the causes of NIPS sex chromosome aneuploidy false‐positive results

Abstract

Objective To investigate the underlying causes of false positives in NIPT of fetal sex chromosomal aneuploidies using fetal cell‐free DNA from maternal plasma. Methods In the present study, we focus on a cohort of 23,984 pregnancy cases with NIPT. Karyotyping and FISH analysis were employed to verify the NIPT detected false‐positive results of fetal sex chromosomal aneuploidies, and a comparative CNV sequencing on positive and negative NIPT cases was uniquely performed to elucidate the underlying causes. Results A total of 166 cases (0.69%) were identified as fetal sex chromosomal abnormalities, while 84 cases were found to be false‐positive results possibly associated with maternal X chromosomal aneuploidies (n = 8), maternal X chromosomal structural abnormalities (n = 1), maternal CNVs (n = 4) as well as known placental mosaicism (n = 1). Furthermore, our study showed that the maternal chromosome CNV between 1–1.6 Mb was associated with false‐positive NIPT results in sex chromosomal abnormalities. Conclusion Our research demonstrated the spectrum of factors causing false positives in NIPT of fetal sex chromosomal abnormalities based on a large cohort. The effective maternal CNV size cut‐off identified in our study could integrate into bioinformatics algorithms for reducing the false‐positive rate, however, further investigation is necessary to confirm this.

Multicenter clinical experience with non‐invasive cell‐free DNA screening for monosomy X and related X‐chromosome variants

“…First, we evaluated the performance of cfDNA screening for Turner syndrome in this mixed‐risk population in general and in relation to prenatal ultrasound findings. We found that a high‐risk cfDNA result was confirmed by diagnostic genetic testing more often than previously reported in most studies 21–26,29,50,57,58 . This is not surprising, since there was a relatively high number of fetuses in our cohort that had anomalies identified by ultrasound.…”

“…We found that a high-risk cfDNA result was confirmed by diagnostic genetic testing more often than previously reported in most studies. [21][22][23][24][25][26]29,50,57,58 This is not surprising, since there was a relatively high number of fetuses in our cohort that had anomalies identified by ultrasound. This is also consistent with findings by Grati et al and Sandow et al 41,59 and has also been shown for trisomy 13 and 18.…”

“…However, the positive predictive value (PPV) for detection of 45,X by cfDNA screening is much lower than for trisomy 21, ranging from 9% to 40%, and various factors limit its performance. [20][21][22][23][24][25][26] Confined placental mosaicism (CPM) and true fetal mosaicism are more common for monosomy X than for other chromosomal abnormalities. 27 The performance of cfDNA testing for SCA can also be affected by undiagnosed maternal sex chromosome abnormalities, such as X-chromosome deletions or mosaic Xchromosome aneuploidy, including the well-described somatic maternal loss of the second X chromosome with increasing maternal age.…”

“…Cell‐free DNA (cfDNA)‐based non‐invasive prenatal screening for common aneuploidies and additional sex chromosome aneuploidies (SCA), including monosomy X, is now offered by commercial laboratories and has resulted in a larger number of pregnancies identified to be at an increased risk for fetal Turner syndrome. However, the positive predictive value (PPV) for detection of 45,X by cfDNA screening is much lower than for trisomy 21, ranging from 9% to 40%, and various factors limit its performance 20–26 . Confined placental mosaicism (CPM) and true fetal mosaicism are more common for monosomy X than for other chromosomal abnormalities 27 .…”