Noninvasive Prenatal Screening Research Articles

O45: Concurrent non-invasive prenatal screening for aneuploidies, microdeletions, and monogenic diseases in high-risk pregnancies: A prospective, multicenter study*

O45: Concurrent non-invasive prenatal screening for aneuploidies, microdeletions, and monogenic diseases in high-risk pregnancies: A prospective, multicenter study*

P627: Early performance analysis for 22q11.2 deletion syndrome detection using a whole-genome sequencing-based noninvasive prenatal screen

P627: Early performance analysis for 22q11.2 deletion syndrome detection using a whole-genome sequencing-based noninvasive prenatal screen

Paired-end sequencing technology in noninvasive prenatal screening reduces screen positive rate for monosomy X

Paired-end sequencing technology in noninvasive prenatal screening reduces screen positive rate for monosomy X

O39: Comprehensive, high-resolution, and non-invasive prenatal screening of coding variation*

O39: Comprehensive, high-resolution, and non-invasive prenatal screening of coding variation*

P616: Cell-based noninvasive prenatal screening for a comprehensive fetal genome profiling for pathogenic submicroscopic CNVs in circulating trophoblasts from maternal blood

P616: Cell-based noninvasive prenatal screening for a comprehensive fetal genome profiling for pathogenic submicroscopic CNVs in circulating trophoblasts from maternal blood

P626: A novel, iteratively designed and highly multiplexed droplet digital PCR assay for non-invasive prenatal screening

P626: A novel, iteratively designed and highly multiplexed droplet digital PCR assay for non-invasive prenatal screening

Noninvasive prenatal screening for cystic fibrosis using circulating trophoblasts: Detection of the 50 most common disease-causing variants.

Cystic fibrosis (CF) is one of the most common severe autosomal recessive disorders. Prenatal or preconception CF screening is offered in some countries. A maternal blood sample in early pregnancy can provide circulating trophoblasts and offers a DNA source for genetic analysis of both the mother and the fetus. This study aimed to develop a cell-based noninvasive prenatal test (NIPT) to screen for the 50 most common CF variants. Blood samples were collected from 30 pregnancies undergoing invasive diagnostics and circulating trophoblasts were harvested in 27. Cystic fibrosis testing was conducted using two different methods: by fragment length analysis and by our newly developed NGS-based CF analysis. In all 27 cases, cell-based NIPT provided a result using both methods in agreement with the invasive test result. This study shows that cell-based NIPT for CF screening provides a reliable result without the need for partner- and proband samples.

Phenotypic findings and pregnancy outcomes of fetal rare autosomal aneuploidies detected using chromosomal microarray analysis

BackgroundAneuploidies are the most common chromosomal abnormality and the main genetic cause of adverse pregnancy outcomes. Since numerous studies have focused on common trisomies, relatively little is known about the association between phenotypic findings and rare autosomal aneuploidies (RAAs). We conducted a retrospective study of 48,904 cases for chromosomal microarray analysis in a large tertiary referral center and reported the overall frequencies, clinical manifestations, and outcomes of prenatal RAAs.ResultsA total of 90 RAAs were detected, of which 83 cases were mosaic trisomies and 7 were non-mosaic trisomies. Chromosomes 16, 22, and 9 were identified as the major chromosomes involving RAAs. The four predominant indications for prenatal diagnosis in our RAA cases were RAA-positive in noninvasive prenatal screening, advanced maternal age, ultrasound abnormalities, and high-risk for serum prenatal screening. Cardiovascular defects were the most frequently observed structural abnormalities, followed by musculoskeletal anomalies. Increased nuchal translucency and persistent left superior vena cava, the major soft marker abnormalities involved, were also observed in our RAA cases. Clinical outcomes were available for all RAAs, with 63 induced abortions and 27 live births recorded.ConclusionsVariable phenotypes and outcomes were observed, which were highly heterogeneous in cases of prenatal RAAs. Thus, a cautious and comprehensive strategy should be implemented during prenatal counseling for RAAs.

Maternal carrier screening with single-gene NIPS provides accurate fetal risk assessments for recessive conditions

PurposeThe purpose of this study was to evaluate the clinical performance of carrier screening for cystic fibrosis, hemoglobinopathies, and spinal muscular atrophy with reflex single-gene noninvasive prenatal screening (sgNIPS), which does not require paternal carrier screening. MethodsAn unselected sample of 9151 pregnant individuals from the general US pregnant population was screened for carrier status, of which 1669 (18.2%) were identified as heterozygous for one or more pathogenic variants and reflexed to sgNIPS. sgNIPS results were compared with newborn outcomes obtained from parent survey responses or provider reports for a cohort of 201 pregnancies. ResultsOverall, 98.7% of pregnant individuals received an informative result (no-call rate = 1.3%), either a negative carrier report or, if identified as heterozygous for a pathogenic variant, a reflex sgNIPS report. In the outcomes cohort, the negative predictive value of sgNIPS was 99.4% (95% CI = 96.0%-99.9%) and average positive predictive value (PPV) of sgNIPS was 48.3% (95% CI = 36.1%-60.1%). Importantly, personalized PPVs accurately reflected the percentage of affected pregnancies in each PPV range, and all pregnancies with a sgNIPS fetal risk of >9 in 10 (90% PPV) were affected. ConclusionAlthough traditional carrier screening is most effective when used to assess reproductive risk before pregnancy, more than 95% of the time it is pursued during a pregnancy and is complicated by incomplete uptake of paternal carrier screening (<50%) and misattributed paternity (∼10%). Even in an idealized setting, when both partners have carrier screening, the maximum risk for having an affected pregnancy is 1 in 4 (equivalent of a 25% PPV). Carrier screening with sgNIPS during pregnancy is an alternative that does not require a paternal sample and provides accurate fetal risk in a timely manner that can be used for prenatal counseling and pregnancy management.

Combined Model-Based Prediction for Non-Invasive Prenatal Screening

The risk of chromosomal abnormalities in the child increases with increasing maternal age. Although non-invasive prenatal testing (NIPT) is a safe and effective prenatal screening method, the accuracy of the test results needs to be improved owing to various testing conditions. We attempted to achieve a more accurate and robust prediction of chromosomal abnormalities by combining multiple methods. Here, three different methods, namely standard Z-score, normalized chromosome value, and within-sample reference bin, were used for 1698 reference and 109 test samples of whole-genome sequencing. The logistic regression model combining the three methods achieved a higher accuracy than any single method. In conclusion, the proposed method offers a promising approach for increasing the reliability of NIPT.

Residual risk of noninvasive prenatal screening in pregnancies with ultrasound anomalies

ObjectivesTo discuss the residual risk (RR) of noninvasive prenatal screening (NIPS) for the mothers with fetal ultrasound abnormalities. Methods880 pregnant women with fetal ultrasound abnormalities accepted prenatal diagnosis by chromosomal microarray analysis (CMA) after amniocentesis. Furthermore, the detection efficiency of NIPS was evaluated and calculated based on our previous studies and other literatures. The RR of the chromosome abnormality results was then analyzed. ResultsA total of 103 cases were confirmed as fetal chromosome abnormalities, including 65 (63.1%) of aneuploidies and 38 (36.9%) of clinical significant copy number variations (CNVs). Of which, based on the estimated NIPS efficacy, 87 cases could also be detected by NIPS. The detection rate (DR) was 84.5%, while 16 cases would be missed. The total of RR of NIPS in the fetuses with ultrasound anomalies was 2.0% (16/793), approximately one in 51. The top three RR of fetal ultrasound abnormalities were echogenic bowel (5.9%), multiple systems of structural anomalies (4.5%), and nervous system anomalies (4.2%). ConclusionThe overall residual risk of NIPS in the fetuses with ultrasound anomalies was approximately 2.0%, especially in echogenic bowel, multiple systems of structural anomalies and nervous system anomalies.

Negotiating Awareness: Dutch Midwives' Experiences of Noninvasive Prenatal Screening Counseling.

Discussion of the topic of noninvasive prenatal screening (NIPS) has become a standard part of Dutch maternity care practice. This means that pregnant women who are contemplating NIPS can receive counseling from their midwife or obstetrician. The aim of this study is to understand the communicative practices and decision-making principles regarding first-tier use of NIPS, as experienced by Dutch midwives. Qualitative analysis of in-depth interviews with Dutch midwives (n = 10) exploring their conversations about NIPS counseling and decision making. Midwives value the autonomy of women in decisions on NIPS. They consider it a midwifery task to assess women's awareness of the risks and implications of using or not using this mode of screening. The optimal level of awareness may differ between women and midwives, creating novel challenges for informed decision making in midwifery communication. Negotiating awareness about NIPS in individual women is a relatively new and complex midwifery task in need of counseling time and skill. NIPS practices call for a reflection on midwifery values in the context of integrated maternity care.

The effect of abnormal placentation on maternal serum fetal fraction of cell-free DNA.

Abnormal placentation may affect the maternal serum fraction of cell-free fetal DNA (fetal fraction) determined as part of non-invasive prenatal screening (NIPS). This study aimed to assess whether the fetal fraction can predict placenta accreta spectrum (PAS) with or without placenta previa (PP). We also investigated the impact of trophoblastic invasion depth on the fetal fraction. This is a retrospective case-control study of pregnant women with and without abnormal placentation carrying a singleton and having undergone NIPS prior to 20weeks of gestation. The eligible subjects were selected from a cohort managed at our institution for PAS suspected antenatally. We compared women with normal placentation (controls) to PAS, PP, or PAS+PP cases. Data were abstracted from electronic medical records, and PAS was confirmed histologically. Of the 146 patients in our cohort, 8 controls, 10 PP, 6 PAS, and 7 PAS+PP cases were eligible for the study. Among the groups, there were no significant differences in baseline demographic and clinical characteristics except the median number of prior uterine surgeries. Also, the groups did not significantly differ in their median fetal fraction. The fetal fraction did not discriminate any group when stratified according to the depth of placental invasion, i.e.,no PAS, abnormally adherent, and abnormally invasive placenta. The maternal serum fraction of cell-free fetal DNA measured before 20weeks of gestation is not predictive of PAS with or without concurrent PP or the depth of trophoblastic invasion.

Live-Born Double Aneuploidy at the Johns Hopkins Cytogenomics Laboratory: Case Report and Review of the Literature

Double aneuploidy is the co-occurrence of aneuploidy of two different chromosomes within the same individual. Genomic imbalance associated with two aneuploidies in humans is associated with early lethality, and observation in live-born humans is rare. In isolation, trisomy of chromosomes 13, 18, 21, X, and Y may be better tolerated, whereas monosomy of X is the only such type of aberration that may be compatible with life. It is hypothesized that two successive malsegregation events must occur in early development to be observed constitutionally. Mechanisms like trisomy rescue or selection against aneuploidies may result in mosaicism and promote subsequent survival in live-born individuals, depending on the chromosomes involved. From the literature, double aneuploidy in the live-born is rare, with (acrocentric) autosomal with gonosomal aneuploidy more common than double autosomal aneuploidy. A retrospective case study of patients who underwent routine postnatal cytogenetic testing at The Johns Hopkins Hospital (JHH) Cytogenomics Laboratory (from its inception in the early 1960s-present) was carried out to identify mosaic and/or non-mosaic forms of double aneuploidy. One case each of non-mosaic [Klinefelter with Edwards Syndrome] and non-mosaic [Klinefelter with Down Syndrome] is identified. No gonosomal and autosomal cases in females nor double autosomal trisomies were identified in live-born individuals at the JHH Cytogenomics Laboratory. Given the advancements in non-invasive prenatal screening for common aneuploidies, the need for diagnostic confirmation studies persists. Providers should be aware of the possibility of early detection of pregnancies bearing double aneuploidy (common or rare) when maternal malignancy is not suspected. Additionally, clinicians should consider the possibility of double aneuploidy in rare situations of atypical or blended phenotypes reminiscent of dual diagnoses. Further work is needed to identify and compile these and even rarer double aneuploidy cases to improve genotype-phenotype correlations.

Noninvasive Prenatal Screening for Trisomy 21 in Patients with a Vanishing Twin.

A vanishing twin (VT) occurs in up to 30% of early diagnosed twin pregnancies and is associated with an increased risk of fetal aneuploidy. Here, we describe our experience in a large VT population of 847 patients that underwent noninvasive prenatal testing (NIPT) for common fetal trisomies over a three-year period. All patients underwent an ultrasound examination prior to NIPT. Two comparison populations were included, namely, the singleton (n = 105,560) and the viable multiple gestation pregnancy samples (n = 9691) collected over the same period. All NIPT samples in the VT population received a result, of which 14 were high-risk for trisomy 21 (1.6%), nine for trisomy 18 (1.1%), and six for trisomy 13 (0.7%). Diagnostic testing confirmed the presence of trisomy 21 in 6/12 samples, giving a positive predictive value of 50%. One trisomy 18 case and no trisomy 13 cases were confirmed. The time between fetal demise and NIPT sampling did not appear to affect the number of true- or false-positive cases. In conclusion, NIPT is an effective screening method for trisomy 21 in the surviving fetus(es) in VT pregnancies. For trisomies 18 and 13, a positive NIPT should be interpreted carefully and ultrasound monitoring is preferrable over invasive diagnostic testing.

Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening

Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.

Non-Invasive Prenatal Genetic Screening to Detect Trisomies In Singleton and Twin Pregnancies

Background Screening for fetal anomalies is one of the most critical parts of prenatal testing to reduce the burden of chromosomal aberrations and improve clinical outcomes in pregnancy. The available literature suggests that India carries a strong economic, emotional, and health care burden of new-born genetic diseases. Material and Methods: We present a single-center retrospective study of 200 singletons and 6 dichorionic diamniotic twin gestations screened for chromosomal abnormalities and trisomies using NIPT. The patients were presented with a gestation period of 10-12 (plus a few days) weeks, clinically confirmed with singleton or diamniotic dizygotic twins, who underwent NIPT between the years 2021-2022 (mid) at our center. All the patients underwent sonographic examination and biochemical investigations with regular follow-up and genetic counseling. The clinical history and family history of the presence of any genetic disease or any other disease were previously taken by the clinician in all cases. The main clinical indications were increased risk of trisomies found in markers test, advanced maternal age, or presented with some mild complications in pregnancy. Results; Out of the total (206) pregnancies, only 2 singleton cases were found at high risk in NIPT screen, prospectively followed up, and showed normal twins in six cases of twin pregnancy growing successfully. The high-risk cases were genetically counselled and further tests using amniotic or chorionic villi samples were recommended by the clinician with regular clinical follow-up. Conclusion: This retrospective study clearly indicates that non-invasive prenatal testing in pregnancy is a safe and effective screening test to rule out certain chromosomal abnormalities and to omit the need of further invasive tests among low-risk cases.

Noninvasive prenatal screening (NIPS) results for participants of the eXtraordinarY babies study: Screening, counseling, diagnosis, and discordance.

Sex chromosome aneuploidies (SCAs), including 47,XXY, 47,XXX, 47,XYY, and supernumerary variants, occur collectively in approximately one of 500 live births. Clinical phenotypes are highly variable resulting in previous ascertainment rates estimated to be only 10%-25% during a lifetime. Historically, prenatal SCA diagnoses were incidental findings, accounting for ≤10% of cases, with the majority of diagnoses occurring postnatally during evaluations for neurodevelopmental, medical, or infertility concerns. The initiation of noninvasive prenatal screening (NIPS) in 2012 and adoption into standardized obstetric care provides a unique opportunity to significantly increase prenatal ascertainment of SCAs. However, the impact NIPS has had on ascertainment of SCAs is understudied, particularly for those who may defer diagnostic testing until after birth. This study evaluates the timing of diagnostic testing following positive NIPS in 152 infants with SCAs and potential factors influencing this decision. Eighty-seven (57%) elected to defer diagnostic testing after a positive NIPS until birth, and 8% (7/87) of those confirmed after birth were found to have discordant results on postnatal diagnostic testing, most of which would have influenced genetic counseling.

Cell-Free Fetal Deoxyribonucleic Acid (cffDNA) Analysis as a Remarkable Method of Non-Invasive Prenatal Screening

The cell-free fetal DNA (cffDNA) analysis for screening fetal genetic anomalies has increased dramatically since its commercialization in 2011 worldwide. In the early weeks of pregnancy, it offers a hassle-free, non-invasive procedure of antenatal screening. It guides and protects mothers from undergoing unwanted risk-laden invasive prenatal testing. cffDNA testing is accurate at detecting the abnormal fetus chromosome among a large pool population. Patau syndrome, Edward syndrome, and Down syndrome are currently being accurately screened by this method. Due to their sensitivity and specificity, they now have become the screening method of choice, approaching almost 100% in various studies with a large sample pool. The latest procedures to analyze cffDNA, like the new digital droplet polymerase chain reaction (ddPCR) and sophisticated next-generation sequencing (NGS), haveincreased detection rates with decreased analyzing time. The latest techniques make it possible to screen large numbers of the population with faster report generation. Screening for Rh incompatibility and its timely prevention is now more accessible and more accurate with the help of cffDNA analysis. The problem arises when we deviate from the primary disease and start testing for anomalies not intended to be screened by cffDNA in the first place. Fetal sex chromosome aneuploidy screening by cffDNA is one area where the test gives mixed results either due to differences in machinery, laboratory parameters, or human error. Other rare occurrences like trisomes, such as trisomy 7, trisomy 16, trisomy 22, and a few microdeletion syndromes are also being screened but with less accuracy. Like every technology, cffDNA analysis is not entirely free of criticism. Its high testing cost, potential to accurately prognosticate the gender of the developing fetus and absence of standard testing practices will become an issue as the test becomes routine worldwide.

Residual Risk for Clinically Significant Copy Number Variants in Low-Risk Pregnancies, Following Exclusion of Noninvasive Prenatal Screening–Detectable Findings

(Abstracted from Am J Obstet Gynecol 2022;226:562.e1–562.e8) Recent developments in available techniques for prenatal genetic analysis have significantly changed genetic screening and diagnosis; these include chromosomal microarray analysis (CMA) and cell-free DNA (cfDNA) screening. However, both tests have benefits and drawbacks.