Prenatal cell-free DNA screening for chromosomal aneuploidies after euploid embryo transfer shows high concordance with preimplantation genetic testing for aneuploidy results and low positive predictive values

Abstract

Objective: To evaluate the positive predictive value (PPV) of prenatal cell-free DNA (cfDNA) screening for chromosomal aneuploidies in pregnancies achieved either after single euploid transfer in in vitro fertilization or Preimplantation Genetic Testing for Aneuploidy (PGT-A) cycles or transfer of single untested embryo, and to assess the concordance of prenatal-cfDNA-screening and PGT-A results.

Design: Single center retrospective cohort study.

Setting: Fertility clinic.

Patient(s): A total of 2,973 prenatal-cfDNA-screening results for the most common trisomies (T13, T18, T21, X, and Y) and microdeletions (1p36, 4p16.3, 5p15.2, 15q11.2, and 22q11.2) from singleton pregnancies allocated into two groups: PGT-A group (n = 1,204) pregnant after single euploid transfer and non-PGT-A group (n = 1769) pregnant after transfer of single untested embryo, between 2016 and 2023.

Intervention(s): Not applicable.

Main outcome measure(s): The primary outcome measure was the accuracy of prenatal-cfDNA screening. Positive and negative prenatal-cfDNA-screening results and subsequent prenatal or postnatal diagnostic testing were used to classify each positive prenatal-cfDNA-screening result as a true or a false positive. Secondary endpoints were to evaluate the concordance of PGT-A and prenatal-cfDNA-screening results and to assess the differences in the fetal fraction of cfDNA used for prenatal-cfDNA-screening reports between the study groups.

Result(s): Prenatal-cfDNA screening was performed at a mean 11.3 ± 1.8 weeks gestational age, and yielded results in 99.9% of the patients (0.1% cancellation rate). There was no difference in the fetal fraction between PGT-A tested and not tested pregnancies (9.5% ± 4% vs. 10.3% ± 4%). 13 positive prenatal-cfDNA-screening results (two T21, two X0, four XXX, one XYY, one indeterminate sex, two 22q11 del/dup, and one 15q11.2del) were received for PGT-A group. Only one (22q11 dup) was confirmed with amniocentesis and fetal autopsy, giving a PPV for an abnormal prenatal-cfDNA screening of 7.7%, the rest had results concordant with PGT-A. Sex chromosomes were 100% concordant between prenatal-cfDNA-screening and PGT-A results, giving a 100% PPV for PGT-A for sex chromosomes and 100% negative predictive value for aneuploidies. Positive prenatal-cfDNA-screening results were received for 27 pregnancies from untested embryos (1.5%), follow-up testing was electively performed for 21, and 8 had confirmed the prenatal-cfDNA-screening result, giving a PPV for the non-PGT-A group of 38%.

Conclusion(s): This study demonstrates that patients undergoing in vitro fertilization/PGT-A and single euploid embryo transfer can reliably do prenatal-cfDNA screening during their first trimester. Fetal fraction in singleton pregnancies after PGT-A tested embryos is not different from pregnancies with untested embryos. Positive predictive value for an abnormal prenatal-cfDNA-screening result after euploid embryo transfer was reassuringly low (7.7%). PGT-A reliably selects against aneuploidy with 100% concordance with fetal sex.

Keywords: NPV; PGT-A; PPV; prenatal-cfDNA-screening.