Analysis Of Cell-free Fetal DNA Research Articles

Usefulness of early morphological ultrasound in association with cell-free DNA testing in case of atypical serum markers in first trimester of pregnancy: A retrospective study over 5 years

BackgroundEarly morphologic ultrasound, generally carried out in case of atypical first trimester serum markers (PAPP-A and/or free hCGβ <0.30 MoM), has not been re-evaluated since the possibility of performing a cell-free fetal DNA analysis in this indication. Our objective was to evaluate the usefulness of early morphological ultrasound in case of atypical profile of serum markers performed in association with Non-Invasive Prenatal Testing (NIPT). MethodsThis was a single-center retrospective study in a tertiary maternity. Between January 2017 and December 2021, women with an atypical first trimester serum markers and low/intermediate risk for trisomy 21 (<1/50) were included. The clinical data, results of first trimester serum markers, NIPT, early morphological ultrasound and subsequent ultrasounds and other investigations (amniocentesis, pregnancy outcomes) were analyzed. ResultsAfter exclusion of women with high-risk of trisomy 21 and lost to follow-up, 163 women were included. In 72 % of cases (117/163), women had a low risk of trisomy 21, and 39 % (59/163) had an early morphological ultrasound. Early morphological ultrasound was useful to detect severe IUGR leading to the suspicion of triploidy (3/163, 1.8 %). In all other situations, it did not allow earlier management. After analysis of the 3 triploidy cases, a collapsed profile for both serum markers was demonstrated (<0.25 MoM). ConclusionsSystematic early morphological ultrasound in case of an atypical serum marker profile seems useless considering the performance of NIPT. An ultrasound restricted to women with both markers below 0.25 MoM would allow the early detection of triploidy.

Detection of pathogenic variants related to severe dominant monogenic diseases by non-invasive prenatal testing (NIPT-SGD)

Non-invasive prenatal testing (NIPT) as a screening method for common chromosomal abnormalities such as trisomy 21, 18, and 13 has been widely adopted. In the last five years, the possibility of NIPT to detect common single-gene disorders (SGD) due to de novo mutations or paternal inherited had been reported worldwide. Our report describes the first cases in Vietnam that identified pathogenic/likely pathogenic variants by NIPT-SGD in fetuses. These findings were compared with the diagnostic testing (whole exome sequencing/WES) on amniotic fluid/placenta tissue/umbilical cord blood samples. Single-gene NIPT detected pathogenic variants in the fetuses on TSC2, FGFR3, FGFR2 (two cases), and PTPN11 genes. All results coincided with the subsequent diagnosis. Preliminary research showed the potential of cell-free fetal DNA analysis for prenatal screening of dominant single-gene mutations.

New insights on partial trisomy 3q syndrome: de novo 3q27.1-q29 duplication in a newborn with pre and postnatal overgrowth and assisted reproductive conception

BackgroundDuplications of the long arm of chromosome 3 are rare, and associated to a well-defined contiguous gene syndrome known as partial trisomy 3q syndrome. It has been first described in 1966 by Falek et al., and since then around 100 patients have been reported. Clinical manifestations include characteristic facial dysmorphic features, microcephaly, hirsutism, congenital heart disease, genitourinary anomalies, hand and feet abnormalities, growth disturbances and intellectual disability. Most of cases are due to unbalanced translocations, inherited from a parent carrying a balanced aberration (reciprocal translocation or inversion), and rarely the genomic anomaly arises de novo. Very few studies report on the prenatal identification of such rearrangements.Case presentationHereby, we report on a newborn with a rare pure duplication of the long arm of chromosome 3. Noninvasive prenatal test (cell free fetal DNA analysis on maternal blood), performed for advanced parental age and use of assisted reproductive technique, evidenced a partial 3q trisomy. Then, invasive cytogenetic (standard and molecular) investigations, carried out through amniocentesis, confirmed and defined a 3q27.1-q29 duplication spanning 10.9 Mb, and including about 80 genes. Our patient showed clinical findings (typical facial dysmorphic features, esotropia, short neck, atrial septal defect, hepatomegaly, mild motor delay) compatible with partial trisomy 3q syndrome diagnosis, in addition to pre- and postnatal overgrowth.ConclusionsAdvanced parental age increases the probability of chromosomal and/or genomic anomalies, while ART that of epigenomic defects. Both conditions, thus, deserve more careful prenatal monitoring and screening/diagnostic investigations. Among the latter, cell free fetal DNA testing can detect large segmental aneuploidies, along with chromosomal abnormalities. It identified in our patient a wide 3q rearrangement, then confirmed and defined through invasive molecular cytogenetic analysis. Neonatologists and pediatricians must be aware of the potential risks associated to duplication syndromes. Therefore, they should offer to affected subjects an adequate management and early and careful follow-up. These may be able to guarantee to patients satisfactory growth and development profiles, prevent and/or limit neurodevelopmental disorders, and timely recognition of complications.

Noninvasive Prenatal Diagnosis of Beta-Thalassemia Disease by Using Digital PCR Analysis of Cell-Free Fetal DNA in Maternal Plasma

Introduction: Prenatal diagnosis of thalassemia disease was usually based on invasive technique. Noninvasive diagnosis using cell-free fetal DNA (cff-DNA) was described with various laboratory techniques. The aim of this study was to identify the performance of dPCR for analyzing cff-DNA in maternal plasma to diagnose fetal beta-thalassemia diseases. Methods: Thirty-five couples at risk of fetal beta-thalassemia disease caused by four common mutations of HBB were enrolled at 12–18 weeks. The dPCR assay was designed to detect and quantify paternally inherited beta-thalassemia allele (PIB) and maternally inherited beta-thalassemia allele (MIB) from cff-DNA in maternal plasma. Results: Of 29 couples with different paternal/maternal mutations, all cases who inherited paternal mutation had detectable PIB-M. The MIB-mutant/wild-type (MIB-M/MIB-N) ratio in the mothers whose fetuses did not inherit maternal mutation was 0.87 ± 0.07 which was significantly lower than that of the mothers whose fetuses inherited maternal mutation, 1.01 ± 0.05. The sensitivity and specificity of MIB-M/MIB-N ratio >0.95 in predicting fetus inheriting maternal mutation were 100 and 92.3%, respectively. In four couples with same paternal/maternal mutation, IB-M/IB-N ratio of >0.95 correctly predicted the presence of an inheritance of at least one beta-thalassemia allele. In two couples with paternal Hb E/beta-thalassemia, the presence of PIB-M and the MIB-M/MIB-N ratio of >0.95 correctly predicted the presence of paternal/maternal mutations, respectively. Conclusions: The method of analyzing cff-DNA in maternal plasma by dPCR is efficient for prenatal diagnosis of beta-thalassemia.

Cell-Free Fetal DNA and Non-Invasive Prenatal Diagnosis of Chromosomopathies and Pediatric Monogenic Diseases: A Critical Appraisal and Medicolegal Remarks.

Cell-free fetal DNA (cffDNA) analysis is a non-invasive prenatal diagnostic test with a fundamental role for the screening of chromosomic or monogenic pathologies of the fetus. Its administration is performed by fetal DNA detection in the mother's blood from the fourth week of gestation. Given the great interest regarding its validation as a diagnostic tool, the authors have set out to undertake a critical appraisal based on a wide-ranging narrative review of 45 total studies centered around such techniques. Both chromosomopathies and monogenic diseases were taken into account and systematically discussed and elucidated. Not surprisingly, cell-free fetal DNA analysis for screening purposes is already rather well-established. At the same time, considerable interest in its diagnostic value has emerged from this literature review, which recommends the elaboration of appropriate validation studies, as well as a broad discourse, involving all stakeholders, to address the legal and ethical complexities that such techniques entail.

Analysis of cell-free fetal DNA in 16,843 pregnant women from a single center in China using targeted sequencing approach

IntroductionNon-invasive prenatal testing (NIPT) using cell-free fetal DNA (cffDNA) has been widely accepted for detecting common fetal chromosome aneuploidies, but few large-scale studies have reported the kinetics of cffDNA concentration during gestation. This study examines cffDNA kinetics spanning gestational periods. MethodsIn this retrospective cohort study, cffDNA concentration from maternal plasma of 16,843 pregnant women between 4 and 39 weeks of pregnancy were determined by SNP-based targeted deep sequencing. ResultsMaternal plasma cffDNA could be detected as early as the fourth gestational week. After detection, cffDNA concentration begun to increase to the 39th week showing three conspicuous inflection points characterized by growth and stabilization phases. The rapid increase in cffDNA (∼1.19% per week) from the 4th to 9th week represents the first growth stage. The first plateau phase spanned from the 10th to 19th week (∼0.03% increase per week). cffDNA begun to rise dramatically (∼0.85% per week) from the 19th to 29th week, stabilizing at week 30 and onwards with only 0.27% increase per week representing the second plateau period. The proportion of cases with cffDNA ≥4% increased rapidly before the 10th gestational week with no significant increase from the 10th week onwards. About 92.00% of all the maternal plasma had a cffDNA greater than 4% from 10 weeks. DiscussionWe indicate that cffDNA had 3 inflection points at the 10th, 19th and 30th week of gestation, an observation not yet reported. Moreover, we show that cffDNA concentration has met the NIPT requirements after 9 weeks gestational age.

The Next Frontier in Noninvasive Prenatal Diagnostics: Cell-Free Fetal DNA Analysis for Monogenic Disease Assessment.

With the widespread clinical adoption of noninvasive screening for fetal chromosomal aneuploidies based on cell-free DNA analysis from maternal plasma, more researchers are turning their attention to noninvasive prenatal assessment for single-gene disorders. The development of a spectrum of approaches to analyze cell-free DNA in maternal circulation, including relative mutation dosage, relative haplotype dosage, and size-based methods, has expanded the scope of noninvasive prenatal testing to sex-linked and autosomal recessive disorders. Cell-free fetal DNA analysis for several of the more prevalent single-gene disorders has recently been introduced into clinical service. This article reviews the analytical approaches currently available and discusses the extent of the clinical implementation of noninvasive prenatal testing for single-gene disorders.

Correction to “Performance of a universal prenatal screening program incorporating cell-free fetal DNA analysis in Ontario, Canada”

CMAJ has been made aware of an error that occurred in the Aug. 3, 2021, issue.[1][1] In Figure 3, the number of pregnant people in Ontario who underwent first-tier cell-free fetal DNA screening should have been 5750, not 575. This has been corrected at [cmaj.ca][2]. 1. [↵][3]1. Dougan SD

Performance of a universal prenatal screening program incorporating cell-free fetal DNA analysis in Ontario, Canada.

BACKGROUND:The emergence of cell-free fetal DNA (cfDNA) testing technology has disrupted the landscape of prenatal screening for trisomies 21 (T21) and 18 (T18). Publicly funded systems around the world are grappling with how to best integrate this more accurate but costly technology, as there is limited evidence about its incremental value in real-world conditions. The objectives of this study were to describe the population-based performance of Ontario’s prenatal screening program, which incorporates publicly funded cfDNA screening for specific indications, and the effect of cfDNA testing on the screening and diagnostic choices made by pregnant people.METHODS:We conducted a retrospective, descriptive cohort study using routinely collected data from Better Outcomes & Registry Network (BORN) Ontario, which captures linked population data for prenatal and neonatal health encounters across Ontario. We included all singleton pregnancies with an estimated due date between Sept. 1, 2016, and Mar. 31, 2019, that underwent publicly funded prenatal screening in Ontario, and a comparison cohort from Apr. 1, 2012, and Mar. 31, 2013. We assessed performance of the screening program for the detection of T21 or T18 by calculating sensitivity, specificity, positive predictive value and negative predictive value against diagnostic cytogenetic results or birth outcomes. We assessed the impact of the program by calculating the proportion of T21 screen-positive pregnancies undergoing subsequent cfDNA screening and invasive prenatal diagnostic testing.RESULTS:The study cohort included 373 682 pregnancies. The prenatal screening program had an uptake of 69.9%, a screen-positive rate and sensitivity of 1.6% and 89.9% for T21, and 0.2% and 80.5% for T18, respectively. The test failure rate for cfDNA screening was 2.2%. Invasive prenatal diagnostic testing decreased from 4.4% in 2012–2013 to 2.4% over the study period; 65.2% of pregnant people who received a screen-positive result from cfDNA testing went on to have invasive prenatal diagnostic testing.INTERPRETATION:This publicly funded screening program, incorporating cfDNA analysis for common aneuploidies, showed robust performance, a substantial reduction in invasive prenatal diagnostic testing and that pregnant people exercise autonomy in their choices about prenatal screening and diagnosis.

Contingent prenatal screening for frequent aneuploidies with cell-free fetal DNA analysis

ObjectiveTo analyze the results of contingent screening for common aneuploidies at our center from June 2017 to June 2019. Materials and methodsTraditional screening tests were performed using a combination of biochemical markers and ultrasound measurements in the first and second trimesters to assess the risk of trisomies 21 (T21), 18 (T18) and 13 (T13). Cell-free DNA (cf-DNA) testing was offered (Harmony test) to pregnant women at high risk (>1/280 for T21 and > 1/150 for T13 and T18) and a normal early morphology scan. In positive cases, prenatal sampling was strongly recommended to confirm the results by gold standard methods (QF-PCR and karyotyping). Newborns' phenotypes were corroborated after birth in all cases. ResultsIn this prospective study, 8153 pregnant women were enrolled, resulting in 390 at high risk according to traditional screening tests. cfDNA testing was offered to 383 women. Traditional screening tests showed a false negative rate of 9.68% for T21. Traditional test sensitivity for T21 was 90.3%, for a false positive rate of 4.17% and a positive predictive value of 7.6%. The positive and negative predictive value for cfDNA testing was 100%. The approach used avoided invasive procedures in 91.3% of women at high risk. The prevalence of chromosomal abnormalities in the population analyzed was 1 in 164, and 1 in 210 for T21. ConclusionsOur results show that offering cf-DNA testing to women at high risk in traditional tests (including those with risks >1 in 50) significantly reduces false positives and, therefore, the number of invasive tests. Extending the use of cf-DNA testing to intermediate risk categories may be cost effective.

Cell-free fetal DNA coming in all sizes and shapes.

Cell‐free fetal DNA analysis has an established role in prenatal assessments. It serves as a source of fetal genetic material that is accessible non‐invasively from maternal blood. Through the years, evidence has accumulated to show that cell‐free fetal DNA molecules are derived from placental tissues, are mainly of short DNA fragments and have rapid post‐delivery clearance profiles. But questions regarding how they come to being short molecules from placental cells and in which physical forms do they exist remained largely unanswered until recently. We now know that the distributions of ending sites of cell‐free DNA molecules are non‐random across the genome and bear correlations with the chromatin structures of cells from which they have originated. Such an insight offers ways to deduce the tissue‐of‐origin of these molecules. Besides, the physical nature and sequence characteristics of the ends of each cell‐free DNA molecule provide tell‐tale signs of how the DNA fragmentation processes are orchestrated by nuclease enzymes. These realizations offered opportunities to develop methods for enriching cell‐free fetal DNA to facilitate non‐invasive prenatal diagnostics. Here we aimed to collate what is known about the biological and physical characteristics of cell‐free fetal DNA into one article and explain the implications of these observations.

Current relevance of non-invasive prenatal study of cell-free fetal DNA in the mother’s blood and prospects for its application in mass screening of pregnant women in the Russian Federation

This review article offers an analysis of application of cell-free fetal DNA non-invasive prenatal screening test for chromosome abnormalities in the mothers blood in different countries. The diagnostic capacities of the method, its limitations, execution models and ethical aspects pertinent to its application are discussed. The data for the discordant results is shown and analyzed. The advantages of the genome-wide variant of cell-free fetal DNA analysis and the problems concerning its application in the mass screening are described. The main suggestion is to implement the contingent cell-free fetal DNA testing model for the common trisomies (for the chromosomes 21, 18 and 13) into the prenatal diagnostic screening programs in the Russian Federation. This novel model is based on the results of the mass combined first trimester prenatal screening in four federal subjects of the country completed by 2019 and is offered as an additional screening in the mid-level risk group (with cut-off from 1 : 100 to 1 : 500 or from 1 : 100 to 1 : 1000) defined according to the first trimester prenatal screening results. The basic requirements for the implementation of the contingent model in the Russian Federation are stated.

Prenatal Testing or Screening?

Abstract Over the past 50 years, the scope and extent of prenatal diagnosis and screening for genetic disorders have improved geometrically. There has been a pendulum like swing from testing to screening back and forth as new technologies emerge. The concurrent developments of cell free fetal DNA analysis of maternal blood has dramatically changed patient's choices towards screening. However, with the use of array comparative genomic hybridization of fetal DNA that requires diagnostic procedures (Chorionic villus sampling and amniocentesis), much more extensive diagnosis can be obtained. Until noninvasive methods can replicate what can be done with diagnostic procedures there still will be a “price to be paid” for opting for the non-invasive methods.

Non-invasive fetal RHD genotyping

Immunization against RhD is the major cause of hemolytic disease of the fetus and newborn (HDFN), which causes fetal or neonatal death. The introduction of postnatal immune prophylaxis in the 1960s drastically reduced immunization incidents in pregnant, D-negative women. In several countries, antenatal prophylaxis is combined with postnatal prophylaxis to further minimize the immunization risk. Due to lack of knowledge of the fetal RhD type, antenatal prophylaxis is given to all D-negative women. In the European population, approximately 40% of pregnant women carry a D-negative fetus and are thus at no risk of immunization. Noninvasive fetal RhD genotyping enables antenatal prophylaxis to be targeted to only those women carrying a D-positive fetus to avoid unnecessary treatment. Based on an analysis of cell-free fetal DNA from the plasma of pregnant women, this approach has recently undergone technical improvements and rapid clinical implementation. As a screening assay, the sensitivity is >99.3% from a gestational age of approximately 10–11 weeks. In addition, fetal RhD genotyping is widely used to assess the risk of HDFN in anti-D immunized women.

Prenatal serum screening - a summary of our experience with high risk reporting

Objective The spectrum of pregnancy tests for screening of chromosomal disorders in the unborn child includes maternal serum testing through double, triple and quadruple marker as well as the emerging cell free fetal DNA analysis based noninvasive prenatal test. The aim of this short communication is to summarize our finding’s pertaining to high risk serum screening cases with reference to clinical indications and history. Methods Data of cases reported high-risk by serum screening including a total of 3368 women with median age of 32 years was included. Serum testing was done in the laboratory using the technology of Chemiluminescence micro particle two-step immunoassay for sensitive quantification of hormones routinely tested for in the double, triple and quadruple marker. Risk estimation using values of hormone levels and the resulting MoM was done using the PRISCA 5.0.2.37. Results A total of 16,608 samples were tested for serum screening in the study period and specific high risk analysis detected a total of 20% reported as high risk. Trisomy 21 was detected to be the most common finding at 86% followed by neural tube defects at 9%. Advanced maternal age (≥35 years) accounted for a total of 34% of the reported high risk cases. Conclusion The gap between absence of a nation-wide screening mandate, and guidelines for agencies involved in prenatal screening tests can be reduced with studies which focus on trends in recommendation and developing an understanding of the clinical backdrop leading to high risk screening results.

614: Artificial Intelligence and epigenomic analysis of cell-free fetal DNA for Congenital Heart Defect (CHD) detection

614: Artificial Intelligence and epigenomic analysis of cell-free fetal DNA for Congenital Heart Defect (CHD) detection

Cell-free fetal DNA analysis: Translating innovations into clinical practice

Cell-free fetal DNA analysis: Translating innovations into clinical practice

Targeted Rhesus immunoglobulin for RhD-negative women undergoing an induced abortion: A clinical pilot study.

The aim of this clinical pilot study was to examine the accuracy of noninvasive fetal RHD genotyping in early pregnancy (8+0 to 11+6 weeks) and to clarify whether targeted administration of Rhesus immunoglobulin (RhIg) is possible for women undergoing an induced abortion such that unnecessary injections can be avoided. The study examines the correlation between gestational age and the amount of cell-free fetal DNA in maternal plasma, the fetal fraction of DNA and whether transportation time or body mass index affects these parameters. Fifty-two RhD-negative women undergoing a surgically induced abortion were included. A maternal blood sample was collected prior to the abortion and a tissue sample was collected from the placental part of the abortion material after the intervention. Fetal RhD type was determined by PCR analysis of cell-free fetal DNA extracted from maternal plasma and on DNA from the tissue sample, with the latter providing a reference standard. Copies of RHD/mL were determined on RHD-positive samples and the fetal fraction of DNA was calculated. We demonstrated complete concordance between results from plasma and tissue, with 31 RhD-positive and 21 RhD-negative samples, corresponding to 40% being RhD-negative, specificity 100% [95% confidence interval (CI) 88.8-100] and sensitivity 100% (95% CI 83.9-100). We found no significant correlation between gestational age and the amount or the fraction of cell-free fetal DNA in maternal plasma, nor did we find that transportation time or BMI significantly affected these factors in this setup. Fetal RHD genotyping can be accurately performed from the 8th week of gestation and unnecessary injections of RhIg can be avoided for women undergoing an induced abortion. A larger study is needed to determine a more accurate sensitivity for the analysis early in pregnancy.

Just choice: a Danielsian analysis of the aims and scope of prenatal screening for fetal abnormalities

Developments in Non-Invasive Prenatal Testing (NIPT) and cell-free fetal DNA analysis raise the possibility that antenatal services may soon be able to support couples in non-invasively testing for, and diagnosing, an unprecedented range of genetic disorders and traits coded within their unborn child’s genome. Inevitably, this has prompted debate within the bioethics literature about what screening options should be offered to couples for the purpose of reproductive choice. In relation to this problem, the European Society of Human Genetics (ESHG) and American Society of Human Genetics (ASHG) tentatively recommend that any expansion of this type of screening, as facilitated by NIPT, should be limited to serious congenital and childhood disorders. In support of this recommendation, the ESHG and ASHG cite considerations of distribution justice. Notably, however, an account of justice in the organization and provision of this type of screening which might substantiate this recommendation has yet to be developed. This paper attempts to redress this oversight through an investigation of Norman Daniels’ theory of Just health: meeting health needs fairly. In line with this aim, the paper examines what special moral importance (for Just health) screening for the purpose of reproductive choice might have where concerning serious congenital and childhood disorders in particular. The paper concludes that screening for reproductive choice where concerning serious congenital and childhood disorders may be important for providing women with fair opportunity to protect their health (by either having or not having an affected child).

Cell-free Fetal DNA Analysis in Maternal Plasma as Screening Test for Trisomies 21, 18, and 13 in Twin Pregnancy

(Abstracted from Ultrasound Obstet Gynecol 2018;52(3):318–324) Increased use of fertility treatment and advanced maternal age contribute to the increased prevalence of twin pregnancy, which is currently approximately 3% in the United States. Screening for trisomy 21 in twins largely relies on maternal age and nuchal translucency measurement in the first trimester, as well as first- and second-trimester serum screening.