Fetal Fraction in Maternal Plasma Cell-Free DNA at 11–13 Weeks’ Gestation: Effect of Maternal and Fetal Factors

Abstract

Objective: It was the aim of this study to examine the possible effects of maternal and fetal characteristics on the fetal fraction in maternal plasma cell-free DNA (cfDNA) at 11–13 weeks’ gestation. Methods: In a nested case-control study, cfDNA was extracted from maternal plasma obtained before chorionic villous sampling from 300 euploid, 50 trisomy 21 and 50 trisomy 18 pregnancies at 11–13 weeks’ gestation. Chromosome-selective sequencing of maternal cfDNA non-polymorphic and polymorphic loci, where fetal alleles differ from maternal alleles, was used to determine the proportion of DNA which is of fetal origin. Multivariate regression analysis was used to determine which of the factors amongst maternal weight, racial origin, smoking status, plasma storage time, serum pregnancy-associated plasma protein (PAPP)-A and free β-subunit of human chorionic gonadotropin (β-hCG), fetal crown-rump length, nuchal translucency thickness, gender and karyotype were significant predictors of the fetal fraction. Results: Significant independent prediction of fetal fraction was provided by maternal weight, serum PAPP-A and serum free β-hCG multiples of the median, but not by other maternal characteristics, fetal karyotype, crown-rump length or nuchal translucency thickness. Fetal fraction increased with serum metabolite levels and decreased with maternal weight. Conclusions: The fetal fraction in maternal plasma cfDNA increases with serum PAPP-A and free β-hCG and decreases with maternal weight.

Diagnostic cytogenetic testing following positive noninvasive prenatal screening results: a clinical laboratory practice resource of the American College of Medical Genetics and Genomics (ACMG)

“…Furthermore, it has been reported that discordant results can be due to variations in the maternal DNA contribution, including low-level sex chromosome and autosomal chromosome mosaicism, maternal malignancies, and maternal copynumber variants. 9,17,[25][26][27] It is well known that some women may have low-level age-related losses and gains of the X chromosome. 28,29 There are a few reports of concurrent maternal malignancies when multiple or rare aneuploidies (e.g., autosomal monosomies) are detected by NIPS.…”

“…[13][14][15][16] While NIPS can be performed in the late first trimester of pregnancy, and CVS is a possibility for confirmatory studies (and often desired by the patient due to timing), CVS may simply reflect the same DNA/cells that were detected by NIPS, as both are derived from the placenta. 17 Certain aneuploidies, including trisomy 13 and monosomy X, are more likely to be found in the mosaic form on CVS, which may influence genetic counseling about the preferred diagnostic test for confirmatory studies. 18 When CVS shows mosaicism for the suspected trisomy, it is impossible to determine if this is CPM or true fetal mosaicism (TFM).…”

Cell-free fetal DNA in maternal blood – an update of the method and clinical practice

“…The fetal fraction is significantly lower in overweight mothers and is increased in cases with high levels of free beta-hCG and PAPP-A. It is not significantly related to maternal age, storage time, smoking status, nuchal translucency thickness, fetal crown-rump length, gender or karyotype (12). In his study Nicolaides KH et al found that the fetal fraction declines from a mean of about 12% at a 60 kg maternal weight to as low as 6% at 120 kg.…”

Cell-Free RNA Is a Reliable Fetoplacental Marker in Noninvasive Fetal Sex Determination

“…The cffDNA represents on average 6%-10% of the total cfDNA in first-and second-trimester pregnancies, and increases to 10%-20% in third-trimester pregnancies (2,3 ). However, the fetal fraction can remain Ͻ4% in the first trimester (4,5 ). To conclude whether a negative result of an NIPD assay is a true or false negative, a marker to confirm the presence of fetal nucleic acids (a fetal marker) is crucial.…”

“…To date, in general, 2 methods are used to confirm that cffDNA is present in the sample. The first is the detection of paternally inherited alleles (17 ), and the second is the amplification of hypermethylated placental genes, such as RASSF1A [Ras association (RalGDS/AF-6) domain family member 1, isoform A], 5 after removing maternal unmethylated gene sequences by a methylationsensitive endonuclease (18 ). Both approaches have drawbacks.…”