Test performance and clinical utility of expanded non-invasive prenatal test: Experience on 71,883 unselected routine cases from one single center

OBJECTIVE

The balance between benefits and risks of discordant outcomes makes the Genome-Wide Non-Invasive Prenatal Test (GW-NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation.

METHOD

In 2 years, over 70,000 pregnant patients underwent GW-NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home-made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes.

RESULTS

Among 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected.

CONCLUSIONS

Integrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome-wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.

Clinical outcomes of screen-positive genome-wide cfDNA cases for trisomy 20: results from the global expanded NIPT Consortium

Trisomy 20 has been shown to be one of the most frequent rare autosomal trisomies in patients that undergo genome-wide noninvasive prenatal testing. Here, we describe the clinical outcomes of cases that screened positive for trisomy 20 following prenatal genome-wide cell-free (cf.) DNA screening. These cases are part of a larger cohort of previously published cases. Members of the Global Expanded NIPT Consortium were invited to submit details on their cases with a single rare autosomal aneuploidy following genome-wide cfDNA screening for retrospective analysis. Clinical details including patient demographics, test indications, diagnostic testing, and obstetric pregnancy outcomes were collected. Genome-wide cfDNA screening was conducted following site-specific laboratory procedures. Cases which screened positive for trisomy 20 (n = 10) were reviewed. Clinical outcome information was available for 90% (9/10) of our screen-positive trisomy 20 cases; the case without diagnostic testing ended in a fetal demise. Of the nine cases with outcome information, one was found to have a mosaic partial duplication (duplication at 20p13), rather than a full trisomy 20. Only one case in the study cohort had placental testing; therefore, confined placental mosaicism could not be ruled out in most cases. Adverse pregnancy outcomes were seen in half of the cases, which could suggest the presence of underlying confined placental mosaicism or mosaic/full fetal trisomy 20. Based on our limited series, the likelihood of true fetal aneuploidy is low but pregnancies may be at increased risk for adverse obstetric outcomes and may benefit from additional surveillance.

Placental, maternal, fetal, and technical origins of false-positive cell-free DNA screening results

The introduction of noninvasive prenatal testing has resulted in substantial reductions to previously accepted false-positive rates of prenatal screening. Despite this, the possibility of false-positive results remains a challenging consideration in clinical practice, particularly considering the increasing uptake of genome-wide noninvasive prenatal testing, and the subsequent increased proportion of high-risk results attributable to various biological events besides fetal aneuploidy. Confined placental mosaicism, whereby chromosome anomalies exclusively affect the placenta, is perhaps the most widely accepted cause of false-positive noninvasive prenatal testing. There remains, however, a substantial degree of ambiguity in the literature pertaining to the clinical ramifications of confined placental mosaicism and its potential association with placental insufficiency, and consequentially adverse pregnancy outcomes including fetal growth restriction. Other causes of false-positive noninvasive prenatal testing include vanishing twin syndrome, in which the cell-free DNA from a demised aneuploidy-affected twin triggers a high-risk result, technical failures, and maternal origins of abnormal cell-free DNA such as uterine fibroids or unrecognized mosaicisms. Most concerningly, maternal malignancies are also a documented cause of false-positive screening results. In this review, we compile what is currently known about the various causes of false-positive noninvasive prenatal testing.

The role of confined placental mosaicism in fetal growth restriction: A retrospective cohort study

OBJECTIVE

To evaluate which cytogenetic characteristics of confined placental mosaicism (CPM) detected in the first trimester chorionic villi and/or placentas in terms of chromosome aberration, cell lineage involved and trisomy origin will lead to fetal growth restriction and low birthweight.

METHODS

Cohort study using routinely collected perinatal data and cytogenetic data of non-invasive prenatal testing, the first trimester chorionic villi sampling and postnatal placentas.

RESULTS

215 CPM cases were found. Fetal growth restriction (FGR) and low birthweight below the 10th percentile (BW < p10) were seen in 34.0% and 23.1%, respectively. Excluding cases of trisomy 16, 29.1% showed FGR and 17.9% had a BW < p10. The highest rate of FGR and BW < p10 was found in CPM type 3, but differences with type 1 and 2 were not significant. FGR and BW < p10 were significantly more often observed in cases with meiotic trisomies.

CONCLUSION

There is an association between CPM and FGR and BW < p10. This association is not restricted to trisomy 16, neither to CPM type 3, nor to CPM involving a meiotic trisomy. Pregnancies with all CPM types and origins should be considered to be at increased risk of FGR and low BW < p10. A close prenatal fetal monitoring is indicated in all cases of CPM.

Psychological impact of additional findings detected by genome-wide Non-Invasive Prenatal Testing (NIPT): TRIDENT-2 study

In the Netherlands, genome-wide non-invasive prenatal testing (NIPT) is offered to all pregnant women as part of the nationwide TRIDENT-2 study. Findings other than trisomy 21, 18, or 13, which are called "additional findings", are reported only on request of the pregnant woman. This study examined: (1) women's pre-test perceptions and reasons to opt for additional findings and (2) women's experiences with- and the psychological impact of being informed about an additional finding. A questionnaire, consisting of the anxiety measure State-Trait Anxiety Inventory (STAI), distress measure Impact of Event Scale (IES) and questions developed specifically for this study, was retrospectively administered to 402 women who received an additional finding. A total of 227 (56.5%) women completed the questionnaire. Most (60.2%) chose to know additional findings because they wanted as much information as possible about the health of their fetus. Almost all (92%) stated that receiving the additional finding was unexpected, a shock, and/or they were in disbelief, for 85% it caused a lot of worry. Post-test, high anxiety (STAI) levels were reported in 15.5% of women, and 7.5% reported severe distress (IES). Women who gave birth to an affected child (n = 10) experienced most psychological impact (STAI and IES). Eighty-six percent of women with a fetal aberration would opt for additional findings again, compared to 49.2% of women whose result was confined to the placenta. Pre-test counseling should focus on explaining the different results NIPT can generate. Post-test counseling should focus on guiding pregnant women through this uncertain and anxious time.

A high Z-score might increase the positive predictive value of cell-free noninvasive prenatal testing for singleton-pregnant women

OBJECTIVE

To explore the positive predictive value (PPV) in noninvasive prenatal testing (NIPT)-positive cases and analyze the effect of the Z-score intervals on PPV performance.

METHODS

In this retrospective study, 26,667 pregnant women underwent NIPT from November 2014 to August 2022, of which 169 were NIPT-positive cases. NIPT-positive cases were divided into three groups according to the Z-score: 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10.

RESULTS

The PPVs of NIPT were 91.26% (94/103) for trisomy (T) 21, 80.65% (25/31) for T18, and 36.84% (7/19) for T13. The PPVs for the 3 ≤ Z < 6, 6 ≤ Z < 10, and Z ≥ 10 groups were 50%, 84.62%, and 87.95%, respectively. A higher PPV was found in the NIPT results when the Z-score was larger, with significant differences. The PPVs for T21/T18/T13 were 71.43%/42.86%/25% for 3 ≤ Z < 6, 90.32%/85.71%/57.14% for 6 ≤ Z < 10, and 93.85%/100%/25% for Z ≥ 10. For T21, T18, and T13, the correlations between the Z-score and fetal fraction concentration in true positives were r = 0.85, r = 0.59, and r = 0.71 (all p < .001), respectively.

CONCLUSION

Z-score is associated with the PPV performance of NIPT in fetal T13, T18, and T21. The possibility of false positives caused by placental chimerism should be considered when determining whether high Z-values lead to high PPVs.

Clinical Potential of Expanded Noninvasive Prenatal Testing for Detection of Aneuploidies and Microdeletion/Microduplication Syndromes

OBJECTIVE

We aimed to evaluate the clinical performance of expanded noninvasive prenatal testing (NIPT-Plus) for the detection of aneuploidies and microdeletion/microduplication syndromes.

METHODS

A total of 7177 pregnant women were enrolled in the study from June 2020 to March 2022 at Xijing Hospital, China. Cases with NIPT-Plus-positive results were further confirmed by chromosomal karyotyping and a chromosomal microarray analysis.

RESULTS

A total of 112 positive cases (1.56%) were identified by NIPT-Plus, including 60 chromosome aneuploidies and 52 microdeletion/microduplication syndromes. Ninety-five cases were validated by amniocentesis, and 57 were confirmed with true-positive results, comprising 18 trisomy 21, 4 trisomy 18, 1 trisomy 13, 17 sex chromosome aneuploidies, 1 other aneuploidy, and 16 microdeletion/microduplication syndromes. The positive predictive value of total chromosomal abnormalities was 60% (57/95). For trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, other aneuploidies and microdeletion/microduplication syndromes, the sensitivity was all 100%, the specificity was 100, 99.986, 100, 99.888, 99.958, and 99.636%, and the positive predictive value was 100, 80, 100, 68, 25, and 38.10%, respectively. For all clinical characteristics, the abnormal maternal serum screening group was found to have the highest prevalence of chromosomal abnormalities (1.54%), and the ultrasound abnormality group presented the highest positive predictive value (73.33%).

CONCLUSIONS

NIPT-Plus has great potential for the detection of aneuploidies and microdeletion/microduplication syndromes owing to its high sensitivity, safety, and specificity, which greatly reduces unnecessary invasive procedures and the risk of miscarriage and allows informed maternal choice.

Assessment of Amniotic Fluid Volume in Pregnancy

Amniotic fluid (AF) is an integral part of the fetal environment and is essential for fetal growth and development. Pathways of AF recirculation include the fetal lungs, swallowing, absorption through the fetal gastrointestinal tract, excretion through fetal urine production, and movement. In addition to being a marker for fetal health, adequate AF is necessary for fetal lung development, growth, and movement. The role of diagnostic imaging is to provide a detailed fetal survey, placental evaluation, and clinical correlation with maternal conditions to help identify causes of AF abnormalities and thereby enable specific therapy. Oligohydramnios prompts evaluation for fetal growth restriction as well as genitourinary issues, including renal agenesis, multicystic dysplastic kidneys, ureteropelvic junction obstruction, and bladder outlet obstruction. Premature preterm rupture of membranes should also be clinically excluded as a cause of oligohydramnios. Clinical trials evaluating amnioinfusion are underway as a potential intervention for renal causes of oligohydramnios. Most cases of polyhydramnios are idiopathic, with maternal diabetes being a common cause. Polyhydramnios prompts evaluation for fetal gastrointestinal obstruction and oropharyngeal or thoracic masses, as well as neurologic or musculoskeletal anomalies. Amnioreduction is performed only for maternal indications such as symptomatic polyhydramnios causing maternal respiratory distress. Polyhydramnios with fetal growth restriction is paradoxical and can occur with maternal diabetes and hypertension. When these maternal conditions are absent, this raises concern for aneuploidy. The authors describe the pathways of AF production and circulation, US and MRI assessment of AF, disease-specific disruption of AF pathways, and an algorithmic approach to AF abnormalities. ^©RSNA, 2023 Online supplemental material is available for this article. Quiz questions for this article are available through the Online Learning Center.

Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing

The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing.

Performance of a cell-free DNA prenatal screening test, choice of prenatal procedure, and chromosome conditions identified during pregnancy after low-risk cell-free DNA screening

OBJECTIVES

To evaluate the performance of cell-free DNA (cfDNA) screening for common fetal aneuploidies, choice of prenatal procedure, and chromosome conditions identified during pregnancy after low-risk cfDNA screening.

METHOD

A single-center prenatal cfDNA screening test was employed to detect trisomies 21, 18, and 13 (T21, T18, T13) and sex chromosome aneuploidies (SCAs). Test performance, choice of prenatal procedure, and cytogenetic results in pregnancies with low-risk cfDNA screening were reviewed.

RESULTS

CfDNA screening of 38,289 consecutive samples identified 720 (1.9%) pregnancies at increased risk for aneuploidy. Positive predictive values (PPVs) for high-risk singleton pregnancies were 98.5% (T21), 92.5% (T18) and 55.2% (T13). PPVs for SCAs ranged from 30.6% to 95.2%. Most women elected chorionic villus sampling for prenatal diagnosis of T21, T18 and T13; amniocentesis and/or postnatal testing were commonly chosen for SCAs. Cytogenetic tests from 616 screen-negative pregnancies identified 64 cases (12.7%) with chromosome conditions not detected by cfDNA screening, including triploidy (n = 30) and pathogenic and likely pathogenic copy number variants (n = 34). A further 15 (0.04%) false-negative common aneuploidy results were identified.

CONCLUSIONS

CfDNA screening was highly accurate for detecting fetal aneuploidy in this general-risk obstetric population. Fetal ultrasound and prenatal diagnostic testing were important in identifying chromosome conditions in pregnancies screened as low-risk.

Clinical, Cytogenetic and Molecular Cytogenetic Outcomes of Cell-Free DNA Testing for Rare Chromosomal Anomalies

The scope of cell-free DNA (cfDNA) testing was expanded to the genome, which allowed screening for rare chromosome anomalies (RCAs). Since the efficiency of the test for RCAs remains below the common aneuploidies, there is a debate on the usage of expanded tests. This study focuses on the confirmatory and follow-up data of cases with positive cfDNA testing for RCAs and cases with screen-negative results in a series of 912 consecutive cases that underwent invasive testing following cfDNA testing. Chorion villus sampling (CVS), amniocentesis (AS), fetal blood sampling, and term placenta samples were investigated using classical cytogenetic and molecular cytogenetic techniques. Out of 593 screen-positive results, 504 (85%) were for common aneuploidies, 40 (6.7%) for rare autosomal trisomies (RATs), and 49 (8.3%) for structural chromosome anomalies (SAs). Of the screen-positives for RATs, 20 cases were evaluated only in fetal tissue, and confined placental mosaicism (CPM) could not be excluded. Among cases with definitive results (n = 20), the rates of true positives, placental mosaics, and false positives were 35%, 45%, and 10%, respectively. Among screen-positives for SAs, 32.7% were true positives. The confirmation rate was higher for duplications than deletions (58.3% vs. 29.4%). The rate of chromosomal abnormality was 10.9% in the group of 256 screen-negatives with pathological ultrasound findings. This study provides further data to assess the efficiency of expanded cfDNA testing for RATs and SAs. The test efficiency for cfDNA seems to be higher for duplications than for deletions, which is evidence of the role of expert ultrasound in identifying pregnancies at increased risk for chromosome anomalies, even in pregnancies with screen-negatives. Furthermore, we discussed the efficiency of CVS vs. AC in screen-positives for RATs.

Rare autosomal trisomies detected by non-invasive prenatal testing: an overview of current knowledge

Non-invasive prenatal testing has been introduced for the detection of Trisomy 13, 18, and 21. Using genome-wide screening also other "rare" autosomal trisomies (RATs) can be detected with a frequency about half the frequency of the common trisomies in the large population-based studies. Large prospective studies and clear clinical guidelines are lacking to provide adequate counseling and management to those who are confronted with a RAT as a healthcare professional or patient. In this review we reviewed the current knowledge of the most common RATs. We compiled clinical relevant parameters such as incidence, meiotic or mitotic origin, the risk of fetal (mosaic) aneuploidy, clinical manifestations of fetal mosaicism for a RAT, the effect of confined placental mosaicism on placental function and the risk of uniparental disomy (UPD). Finally, we identified gaps in the knowledge on RATs and highlight areas of future research. This overview may serve as a first guide for prenatal management for each of these RATs.

Cell-free DNA screening for rare autosomal trisomies and segmental chromosome imbalances

OBJECTIVE

To assess the outcomes of pregnancies at high-risk for rare autosomal trisomies (RATs) and segmental imbalances (SIs) on cell-free DNA (cfDNA) screening.

METHOD

A retrospective study of women who underwent cfDNA screening between September 2019 and July 2021 at three ultrasound services in Australia. Positive predictive values (PPVs) were calculated using fetal chromosomal analysis.

RESULTS

Among 23,857 women screened, there were 93 high-risk results for RATs (0.39%) and 82 for SIs (0.34%). The PPVs were 3.8% (3/78, 95% CI 0.8%-10.8%) for RATs and 19.1% (13/68, 95% CI 10.6%-30.5%) for SIs. If fetuses with structural anomalies were also counted as true-positive cases, the PPV for RATS increased to 8.5% (7/82, 95% CI 3.5%-16.8%). Among 85 discordant cases with birth outcomes available (65.4%), discordant positive RATs had a significantly higher proportion of infants born below the 10th and 3rd birthweight percentiles than expected (19.6% (p = 0.022) and 9.8% (p = 0.004), respectively), which was not observed in the SI group (2.9% < 10th (p = 0.168) and 0.0% <3rd (p = 0.305)).

CONCLUSION

The PPVs for SI and RAT results are low, except when a structural abnormality is also present. Discordant positive RATs are associated with growth restriction.

A retrospective single-center analysis of prenatal diagnosis and follow-up of 626 chinese patients with positive non-invasive prenatal screening results

This study explored the diagnostic efficiency of different prenatal diagnostic approaches for women with positive non-invasive prenatal screening (NIPS) results by analyzing their clinical information and pregnancy outcomes. We collected data on 626 NIPS-positive pregnant women from January 2017 to June 2021 and arranged subsequent prenatal diagnostic operations for them after genetic counseling, along with long-term intensive follow-up. A total of 567 women accepted invasive prenatal diagnosis (IPD) (90.58%), and 262 cases were confirmed as true positives for NIPS. The positive predictive values for trisomies 21 (T21), 18 (T18), and 13 (T13); sex chromosome aneuploidies (SCAs); rare autosomal trisomies (RATs); and microdeletion and microduplication syndromes (MMS) were 81.13%, 37.93%, 18.42%, 48.83%, 18.37%, and 41.67%, respectively. Discordant results between NIPS and IPD were observed in 48 cases, with the discordance rate being 8.47%. Additionally, there were 43 cases with discordant results between karyotyping and chromosomal microarray analysis (CMA)/copy number variation sequencing. Additional reporting of RATs and MMS with routine NIPS that only detects T21/T18/T13 and SCAs can yield more accurate diagnoses. However, NIPS cannot be used as a substitute for IPD owing to its high false positive rate and discordance with other diagnostic methods. Therefore, we recommend CMA combined with karyotyping as the preferred method for accurately diagnosing NIPS-positive women.

Clinical impact of additional findings detected by genome-wide non-invasive prenatal testing: Follow-up results of the TRIDENT-2 study

In the TRIDENT-2 study, all pregnant women in the Netherlands are offered genome-wide non-invasive prenatal testing (GW-NIPT) with a choice of receiving either full screening or screening solely for common trisomies. Previous data showed that GW-NIPT can reliably detect common trisomies in the general obstetric population and that this test can also detect other chromosomal abnormalities (additional findings). However, evidence regarding the clinical impact of screening for additional findings is lacking. Therefore, we present follow-up results of the TRIDENT-2 study to determine this clinical impact based on the laboratory and perinatal outcomes of cases with additional findings. Between April 2017 and April 2019, additional findings were detected in 402/110,739 pregnancies (0.36%). For 358 cases, the origin was proven to be either fetal (n = 79; 22.1%), (assumed) confined placental mosaicism (CPM) (n = 189; 52.8%), or maternal (n = 90; 25.1%). For the remaining 44 (10.9%), the origin of the aberration could not be determined. Most fetal chromosomal aberrations were pathogenic and associated with severe clinical phenotypes (61/79; 77.2%). For CPM cases, occurrence of pre-eclampsia (8.5% [16/189] vs 0.5% [754/159,924]; RR 18.5), and birth weight <2.3rd percentile (13.6% [24/177] vs 2.5% [3,892/155,491]; RR 5.5) were significantly increased compared to the general obstetric population. Of the 90 maternal findings, 12 (13.3%) were malignancies and 32 (35.6%) (mosaic) pathogenic copy number variants, mostly associated with mild or no clinical phenotypes. Data from this large cohort study provide crucial information for deciding if and how to implement GW-NIPT in screening programs. Additionally, these data can inform the challenging interpretation, counseling, and follow-up of additional findings.

Tetrasomy 9p, a Prenatal Challenge: Two Novel Cases

Tetrasomy 9p is a chromosomal disorder characterized by the presence of a supernumerary chromosome. This rare abnormality exhibits a broad phenotypic variability and is not clearly distinguishable from other more frequent aneuploidies in the prenatal setting. We present two prenatal cases with dissimilar phenotypes, one with solely increased fetal nuchal translucency and one with multiple congenital anomalies, and discuss prior studies. These cases illustrate the difficulty of prenatally diagnosing this condition based on phenotypic information alone. We conclude that invasive prenatal diagnosis with (molecular) karyotyping is the best choice for the prenatal detection of tetrasomy 9p.

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.

What’s already known about this topic?

Cell‐free fetal DNA originates from placental tissues and circulates in maternal plasma as a minor population in the form of short fragments which disappears from maternal circulation rapidly after delivery.

What does this study add?

Cell‐free DNA studies at the per molecule per nucleotide level documented the detailed genomic distributions, fragment end characteristics and physical forms of cell‐free DNA unveiling the fine feature differences between maternal and fetal DNA as well as their intricate relationships with the chromatin structure of the cells‐of‐origin. These studies have substantially bridged the knowledge gaps in the biology of cell‐free fetal DNA and may provide insights on how to enhance prenatal tests based on their analyses.

Performance of cell-free DNA sequencing-based non-invasive prenatal testing: experience on 36,456 singleton and multiple pregnancies

BACKGROUND

This paper describes the clinical practice and performance of cell-free DNA sequencing-based non-invasive prenatal testing (NIPT) as a screening method for fetal trisomy 21, 18, and 13 (T21, T18, and T13) and sex chromosome aneuploidies (SCA) in a general Italian pregnancy population.

METHODS

The AMES-accredited laboratory offers NIPT in maternal blood as a screening test for fetal T21, T18, T13 and SCA. Samples were sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay.

RESULTS

A retrospective analysis was performed on 36,456 consecutive maternal blood samples, including 35,650 singleton pregnancies, 800 twin pregnancies, and 6 triplet pregnancies. Samples were tested between April 2017 and September 2019. The cohort included 46% elevated-risk and 54% low-risk patients. A result indicative of a classic trisomy was found in 356 (1%) of singleton or twin samples: 254 T21, 69 T18, and 33 T13. In addition, 145 results (0.4%) were indicative of a SCA. Of the combined 501 screen-positive cases, 484 had confirmatory diagnostic testing. NIPT results were confirmed in 99.2% (247/249) of T21 cases, 91.2% (62/68) of T18 cases, 84.4% (27/32) of T13 cases, and 86.7% (117/135) of SCA cases. In the 35,955 cases reported as unaffected by a classic trisomy or SCA, no false negative cases were reported. Assuming that false negative results would be reported, the sensitivity of NIPT was 100.00% for T21 (95% Cl 98.47-100.0), T18 (95% Cl 94.17-100.0), and T13 (95% Cl 87.54-100.0). The specificities were 99.99% (95% Cl 99.98-100.0), 99.98% (95% Cl 99.96-100.0), 99.99% (95% Cl 99.97-100.0), and 99.95% (95% Cl 99.92-99.97) for T21, T18, T13, and SCA, respectively.

CONCLUSION

This retrospective analysis of a large cohort of consecutive patients who had whole-genome sequencing-based NIPT for classic trisomies and SCA shows excellent detection rates and low false positive rates.

Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses

Global medical associations (ACOG, ISUOG, ACMG) recommend diagnostic prenatal testing for the detection and prevention of genetic disorders. Historically, cytogenetic methods such as karyotype analysis, fluorescent in situ hybridization (FISH) and chromosomal microarray (CMA) are utilized worldwide to diagnose common syndromes. However, the limitations of each of these methods, either performed in tandem or simultaneously, demonstrates the need of a revolutionary technology that can alleviate the need for multiple technologies. Optical genome mapping (OGM) is a novel method that fills this void by being able to detect all classes of structural variations (SVs), including copy number variations (CNVs). OGM is being adopted by laboratories as a tool for both postnatal constitutional genetic disorders and hematological malignancies. This commentary highlights the potential for OGM to become a standard of care in prenatal genetic testing based on its capability to comprehensively identify large balanced and unbalanced SVs (currently the strength of karyotyping and metaphase FISH), CNVs (by CMA), repeat contraction disorders (by Southern blotting) and multiple repeat expansion disorders (by PCR-based methods or Southern blotting). Next-generation sequencing (NGS) methods are excellent at detecting sequence variants, but they are unable to accurately resolve repeat regions of the genome, which limits their ability to detect all classes of SVs. Notably, multiple molecular methods are used to identify repeat expansion and contraction disorders in routine clinical laboratories around the world. With non-invasive prenatal testing (NIPT) becoming the standard of care screening assay for all global pregnancies, we anticipate that OGM can provide a high-resolution, cytogenomic assay to be employed following a positive NIPT screen or for high-risk pregnancies with an abnormal ultrasound. Accurate detection of all types of genetic disorders by OGM, such as liveborn aneuploidies, sex chromosome anomalies, microdeletion/microduplication syndromes, repeat expansion/contraction disorders is key to reducing the global burden of genetic disorders.

Detection of cell-free fetal DNA in maternal plasma using two types of compound markers

With the discovery of circulating cell-free fetal DNA (cffDNA) in maternal plasma, noninvasive prenatal testing became possible. However, analysis of low-level cffDNA against high background maternal DNA remains complicated and challenging. To circumvent this limitation, selective amplification of cffDNA was used in this study. Two kinds of compound markers (namely DIP-STR and SNP-STR), both based on selective amplification, were used here for targeting fetal DNA. By designing two allele-specific forward primers for DIP-STR and SNP-STR, DNA fragments with different DIP/SNP alleles can be selectively amplified. When analyzing maternal plasma DNA, these markers can selectively target paternally inherited fetal alleles whose DIP/SNP allele was not shared with the mother. In this study, 21 families were studied with six DIP-STRs and 11 SNP-STRs. Fetal DNA was successfully detected across plasma samples for at least one marker. Detection rate varied between DIP-STR and SNP-STR markers, and DIP-STR outperforms SNP-STR. Fetal alleles obtained from maternal plasma were double confirmed by genotyping paternal genomic DNA and fetal genomic DNA from amniocentesis. This study demonstrated that selective amplification strategy can be used to target cffDNA in maternal plasma, which will be a promising method for noninvasive prenatal paternity testing.

Patient-friendly integrated first trimester screening by NIPT and fetal anomaly scan

Many major structural fetal anomalies can be diagnosed by first trimester fetal anomaly scan. NIPT can accurately detect aneuploidies and large chromosomal aberrations in cfDNA in maternal blood plasma. This study shows how a patient-friendly first trimester screening for both chromosomal and structural fetal anomalies in only two outpatient visits can be provided. Genotype-first approach assures not only the earliest diagnosis of trisomy 21 (the most prevalent chromosome aberration), but also completion of the screening at 12–14 weeks. To ensure proper management and avoid unnecessary anxiety abnormal NIPT different from trisomy 21, 18 and 13 should be referred for genetic counseling.

Impact of Emerging Technologies in Prenatal Genetic Counseling

For decades, prenatal testing has been offered to evaluate pregnancies for genetic conditions. In recent years, the number of testing options and range of testing capabilities has dramatically increased. Because of the risks associated with invasive diagnostic testing, research has focused on the detection of genetic conditions through screening technologies such as cell-free DNA. Screening for aneuploidy, copy number variants, and monogenic disorders is clinically available using a sample of maternal blood, but limited data exist on the accuracy of some of these testing options. Additional research is needed to examine the accuracy and utility of screening for increasingly rare conditions. As the breadth of prenatal genetic testing options continues to expand, patients, clinical providers, laboratories, and researchers need to find collaborative means to validate and introduce new testing technologies responsibly. Adequate validation of prenatal tests and effective integration of emerging technologies into prenatal care will become even more important once prenatal treatments for genetic conditions become available.

Discordant fetal sex on NIPT and ultrasound

Prenatal diagnosis of sex discordance is a relatively new phenomenon. Prior to cell-free DNA testing, the diagnosis of a disorder of sexual differentiation was serendipitous, either through identification of ambiguous genitalia at the midtrimester morphology ultrasound or discovery of genotype-phenotype discordance in cases where preimplantation genetic diagnosis or invasive prenatal testing had occurred. The widespread integration of cfDNA testing into modern antenatal screening has made sex chromosome assessment possible from 10 weeks of gestation, and discordant fetal sex is now more commonly diagnosed prenatally, with a prevalence of approximately 1 in 1500-2000 pregnancies. Early detection of phenotype-genotype sex discordance is important as it may indicate an underlying genetic, chromosomal or biochemical condition and it also allows for time-critical postnatal treatment. The aim of this article is to review cfDNA and ultrasound diagnosis of fetal sex, identify possible causes of phenotype-genotype discordance and provide a systematic approach for clinicians when counseling and managing couples in this circumstance.

TRIDENT-2: National Implementation of Genome-wide Non-invasive Prenatal Testing as a First-Tier Screening Test in the Netherlands

The Netherlands launched a nationwide implementation study on non-invasive prenatal testing (NIPT) as a first-tier test offered to all pregnant women. This started on April 1, 2017 as the TRIDENT-2 study, licensed by the Dutch Ministry of Health. In the first year, NIPT was performed in 73,239 pregnancies (42% of all pregnancies), 7,239 (4%) chose first-trimester combined testing, and 54% did not participate. The number of trisomies 21 (239, 0.33%), 18 (49, 0.07%), and 13 (55, 0.08%) found in this study is comparable to earlier studies, but the Positive Predictive Values (PPV)-96% for trisomy 21, 98% for trisomy 18, and 53% for trisomy 13-were higher than expected. Findings other than trisomy 21, 18, or 13 were reported on request of the pregnant women; 78% of women chose to have these reported. The number of additional findings was 207 (0.36%); these included other trisomies (101, 0.18%, PPV 6%, many of the remaining 94% of cases are likely confined placental mosaics and possibly clinically significant), structural chromosomal aberrations (95, 0.16%, PPV 32%,) and complex abnormal profiles indicative of maternal malignancies (11, 0.02%, PPV 64%). The implementation of genome-wide NIPT is under debate because the benefits of detecting other fetal chromosomal aberrations must be balanced against the risks of discordant positives, parental anxiety, and a potential increase in (invasive) diagnostic procedures. Our first-year data, including clinical data and laboratory follow-up data, will fuel this debate. Furthermore, we describe how NIPT can successfully be embedded into a national screening program with a single chain for prenatal care including counseling, testing, and follow-up.

Multilevel regression modeling for aneuploidy classification and physical separation of maternal cell contamination facilitates the QF-PCR based analysis of common fetal aneuploidies

Background

The quantitative fluorescent polymerase chain reaction (QF-PCR) has proven to be a reliable method for detection of common fetal chromosomal aneuploidies. However, there are some technical shortcomings, such as uncertainty of aneuploidy determination when the short tandem repeats (STR) height ratio is unusual due to a large size difference between alleles or failure due to the presence of maternal cell contamination (MCC). The aim of our study is to facilitate the implementation of the QF-PCR as a rapid diagnostic test for common fetal aneuploidies.

Methods

Here, we describe an in-house one-tube multiplex QF-PCR method including 20 PCR markers (15 STR markers and 5 fixed size) for rapid prenatal diagnosis of chromosome 13, 18, 21, X and Y aneuploidies. In order to improve the aneuploidy classification of a given diallelic STR marker, we have employed a multilevel logistic regression analysis using "height-ratio" and "allele-size-difference" as fixed effects and "marker" as a random effect. We employed two regression models, one for the 2:1 height ratio (n = 48 genotypes) and another for the 1:2 height ratio (n = 41 genotypes) of the trisomic diallelic markers while using the same 9015 genotypes with normal 1:1 height ratio in both models. Furthermore, we have described a simple procedure for the treatment of the MCC, prior DNA isolation and QF-PCR analysis.

Results

For both models, we have achieved 100% specificity for the marker aneuploidy classification as compared to 98.60% (2:1 ratio) and 98.04% (1:2 ratio) specificity when using only the height ratio for classification. Treatment of the MCC enables a successful diagnosis rate of 76% among truly contaminated amniotic fluids.

Conclusions

Adjustment for the allele size difference and marker type improves the STR aneuploidy classification, which, complemented with appropriate treatment of contaminated amniotic fluids, eliminates sample re-testing and reinforces the robustness of the QF-PCR method for prenatal testing.

The importance of pre- and post-test counseling for prenatal cell-free DNA screening for common fetal aneuploidies

INTRODUCTION

Prenatal cell-free DNA screening for common fetal aneuploidies has rapidly changed the paradigm of prenatal care. Despite its advantages compared to conventional screening methods, its unexpectedly rapid implementation in clinical practice has generated several ethical and medical issues and misconceptions. Aggressive commercial marketing of cell-free DNA screening and media dissemination of misleading information have added confusion. Areas covered: This review provides an extensive update and will focus on the importance of pre-and post-test counseling for prenatal cell-free DNA screening not previously discussed extensively in the available literature. Additionally, we report cell-free DNA screening implementation in the largest obstetrical tertiary unit in Finland which is one of few countries that provides all prenatal screening methods free of charge for all women and has a very high uptake of first-trimester screening. This is not a systematical review, but rather a narrative overview which includes the most relevant and recent original publications and reviews covering this issue. Expert opinion: Despite being the most accurate method for screening of common fetal aneuploidies, the knowledge and counseling should be substantially improved. Cell-free DNA screening is not a replacement for diagnostic testing and its use in prenatal testing is complex and limited.

Limits to the scope of non-invasive prenatal testing (NIPT): an analysis of the international ethical framework for prenatal screening and an interview study with Dutch professionals

Background

The introduction of non-invasive prenatal testing (NIPT) for foetal aneuploidies is currently changing the field of prenatal screening in many countries. As it is non-invasive, safe and accurate, this technique allows for a broad implementation of first-trimester prenatal screening, which raises ethical issues, related, for instance, to informed choice and adverse societal consequences. This article offers an account of a leading international ethical framework for prenatal screening, examines how this framework is used by professionals working in the field of NIPT, and presents ethical guidance for the expansion of the scope of prenatal screening in practice.

Methods

A comparative analysis of authoritative documents is combined with 15 semi-structured interviews with professionals in the field of prenatal screening in the Netherlands. Data were recorded, transcribed verbatim and analysed using thematic analysis.

Results

The current ethical framework consists of four pillars: the aim of screening, the proportionality of the test, justice, and societal aspects. Respondents recognised and supported this framework in practice, but expressed some concerns. Professionals felt that pregnant women do not always make informed choices, while this is seen as central to reproductive autonomy (the aim of screening), and that pre-test counselling practices stand in need of improvement. Respondents believed that the benefits of NIPT, and of an expansion of its scope, outweigh the harms (proportionality), which are thought to be acceptable. They felt that the out-of-pocket financial contribution currently required by pregnant women constitutes a barrier to access to NIPT, which disproportionally affects those of a lower socioeconomic status (justice). Finally, professionals recognised but did not share concerns about a rising pressure to test or discrimination of disabled persons (societal aspects).

Conclusions

Four types of limits to the scope of NIPT are proposed: NIPT should generate only test outcomes that are relevant to reproductive decision-making, informed choice should be (made) possible through adequate pre-test counselling, the rights of future children should be respected, and equal access should be guaranteed. Although the focus of the interview study is on the Dutch healthcare setting, insights and conclusions can be applied internationally and to other healthcare systems.

Unexpected finding of uniparental disomy mosaicism in term placentas: Is it a common feature in trisomic placentas?

Objective

Non‐invasive prenatal testing (NIPT) detects placental chromosome aberrations. When amniocentesis reveals a normal karyotype, confined placental mosaicism (CPM) may be assumed. In order to confirm this, placental cytogenetic studies were performed.

Method

NIPT was conducted in the course of the Dutch TRIDENT study. Placentas of 10 cases with NIPT results indicating an autosomal trisomy and showing a normal (N = 9) or low mosaic karyotype (N = 1) in amniotic fluid (AF) were investigated. The cytotrophoblast as well as the mesenchymal core of two to four placental chorionic villi biopsies were studied with single nucleotide polymorphism (SNP) array. Clinical outcome data were collected.

Results

In 10/10 cases, CPM was proven. In 3/10 cases trisomy/uniparental disomy (UPD)/biparental disomy (BPD) mosaicism was discovered. In 2/3 cases, all three cell lines were present in the placenta, whereas BPD was found in AF. In 1/3 cases trisomy 22/UPD22 was present in AF while trisomy 22/BPD22 mosaicism was found in the placenta. Five of 10 pregnancies were affected with pre‐eclampsia, low birth weight, preterm delivery, and/or congenital malformations.

Conclusion

The presence of trisomy/UPD/BPD mosaicism in 3/10 cases that we investigated proves that trisomic zygote rescue may involve multiple rescue events during early embryogenesis. UPD mosaicism, when present in crucial fetal tissues, may explain the abnormal phenotype in undiagnosed cases.

What's already known about this topic?

Trisomic zygote rescue is the main mechanism for uniparental disomy (UPD) formation.

Confined placental mosaicism (CPM) is the major source of discordant NIPT results.

CPM is associated with a risk for adverse pregnancy outcome.

What does this study add?

Trisomic zygote rescue may involve multiple rescue events based on the co‐occurrence of a trisomy‐, UPD‐, and BPD‐cell line in half of the rescued cases as revealed by placental studies.

Confined placental mosaicism revisited: Impact on pregnancy characteristics and outcome

OBJECTIVES

We wanted to re-evaluate the influence of confined placental mosaicism subtypes (type 2 and type 3) on pregnancy characteristics and outcome.

MATERIAL AND METHODS

From July 2009 to December 2015, 5512 chorionic villus samplings were performed in our Fetal Medicine Center. Conventional karyotyping was performed after long-term and short-term cultured villi to define type 2 or type 3 confined placental mosaicisms. Karyotype after amniocentesis was performed to exclude true fetal mosaicism, when appropriate. Pregnancy characteristics and outcomes were collected and compared to a control population.

RESULTS

Thirty-six (0.65%) confined placental mosaicisms were observed (13 type 2 and 23 type 3). Nuchal translucency was not increased for type 2 and type 3 confined placental mosaicisms. Pregnancy characteristics and outcomes were comparable between type 2 confined placental mosaicisms and the control population. In type 3 confined placental mosaicisms, median first trimester serum pregnancy-associated plasma protein A was lower than for the control population (p<0.001), preterm births were noticed in 56% (p<0.001), small for gestational age newborns in 74% (p<0.001), and adverse pregnancy outcome was reported in 35% (p<0.01).

CONCLUSION

Although type 2 confined placental mosaicisms appeared to have no influence on pregnancy characteristics and outcome, type 3 confined placental mosaicisms were associated with low levels of first trimester serum pregnancy-associated plasma protein A, preterm birth, small for gestational age newborns, and adverse pregnancy outcomes.

Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies

Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.

Origin and clinical relevance of chromosomal aberrations other than the common trisomies detected by genome-wide NIPS: results of the TRIDENT study

PurposeNoninvasive prenatal screening (NIPS) using cell-free DNA in maternal blood is highly sensitive for detecting fetal trisomies 21, 18, and 13. Using a genome-wide approach, other chromosome anomalies can also be detected. We report on the origin, frequency, and clinical significance of these other chromosome aberrations found in pregnancies at risk for trisomy 21, 18, or 13.MethodsWhole-genome shallow massively parallel sequencing was used and all autosomes were analyzed.ResultsIn 78 of 2,527 cases (3.1%) NIPS was indicative of trisomy 21, 18, or 13, and in 41 (1.6%) of other chromosome aberrations. The latter were of fetal (n = 10), placental (n = 22), maternal (n = 1) or unknown (n = 7). One case lacked cytogenetic follow-up. Nine of the 10 fetal cases were associated with an abnormal phenotype. Thirteen of the 22 (59%) placental aberrations were associated with fetal congenital anomalies and/or poor fetal growth ( Collapse

Key Words

• confined placental mosaicism; genome-wide nips
• noninvasive testing
• prenatal screening
• trisomy 21

Collapse

MESH Headings

• Chromosome Aberrations
• Chromosome Disorders/diagnosis
• Chromosome Disorders/genetics
• DNA Copy Number Variations
• Female
• Genetic Testing/methods
• Genomics/methods
• Humans
• Placenta/metabolism
• Pregnancy
• Pregnancy Outcome
• Prenatal Diagnosis/methods
• Trisomy
• Whole Genome Sequencing

Collapse

Grants Collapse

Affiliation(s)

Diane Van Opstal Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
Merel C van Maarle Department of Clinical Genetics, Academic Medical Center, Amsterdam, Amsterdam, The Netherlands
Klaske Lichtenbelt Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
Marjan M Weiss Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
Heleen Schuring-Blom Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
Shama L Bhola Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
Mariette J V Hoffer Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Karin Huijsdens-van Amsterdam Department of Clinical Genetics, Academic Medical Center, Amsterdam, Amsterdam, The Netherlands
Merryn V Macville Department of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
Angelique J A Kooper Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
Brigitte H W Faas Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
Lutgarde Govaerts Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
Gita M Tan-Sindhunata Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
Nicolette den Hollander Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Ilse Feenstra Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
Robert-Jan H Galjaard Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
Dick Oepkes Department of Obstetrics, Leiden University Medical Center, Leiden, The Netherlands
Stijn Ghesquiere Department of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
Rutger W W Brouwer Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
Lean Beulen Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
Sander Bollen Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
Martin G Elferink Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
Roy Straver Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
Lidewij Henneman Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
Godelieve C Page-Christiaens Department of Obstetrics and Gynaecology, University Medical Center Utrecht, Utrecht, The Netherlands
Erik A Sistermans Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands

Collapse

Recent developments in genetics and medically assisted reproduction: from research to clinical applications

Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.

Recent developments in genetics and medically-assisted reproduction: from research to clinical applications†‡

Two leading European professional societies, the European Society of Human Genetics and the European Society for Human Reproduction and Embryology, have worked together since 2004 to evaluate the impact of fast research advances at the interface of assisted reproduction and genetics, including their application into clinical practice. In September 2016, the expert panel met for the third time. The topics discussed highlighted important issues covering the impacts of expanded carrier screening, direct-to-consumer genetic testing, voiding of the presumed anonymity of gamete donors by advanced genetic testing, advances in the research of genetic causes underlying male and female infertility, utilisation of massively-parallel sequencing in preimplantation genetic testing and non-invasive prenatal screening, mitochondrial replacement in human oocytes, and additionally, issues related to cross-generational epigenetic inheritance following IVF and germline genome editing. The resulting paper represents a consensus of both professional societies involved.

Combined detection of α-fetoprotein and free β-human chorionic gonadotropin in screening for trisomy 21 and management of cases in the moderate risk value range

Down syndrome is the most common cause of prenatal chromosomal abnormalities, and prenatal serum screening is an effective method for decreasing the birth prevalence of children with Down syndrome. The aim of the present study was to observe the effect of duplex screening and investigate the treatment of cases under specific conditions. The medians of free β-human chorionic gonadotropin (HCG) and α-fetoprotein (AFP) were calculated and compared with those embedded in the 2T software. The detection and false-positive rates were analyzed under different conditions, and the distribution of Down syndrome cases was investigated in different risk ranges. Finally, suitable recommendations for further diagnostic investigation were provided according to the status of each individual. The medians of free β-HCG and AFP were found to differ from the corresponding medians embedded in the 2T software (P<0.01), and on the basis of a 5% false-positive rate, the detection rate would increase from 63.6 to 67.8% when compared with medians embedded in the 2T software, indicating we should establish our own medians of free β-HCG and AFP. In addition, residual cases (risk value <1/300) with relevant Down syndrome indications mainly concentrated at risk values between 1/1,000 and 1/300, and partial residual screening cases were verified through diverse methods. These findings indicated that different laboratories should establish their own medians; furthermore, what is classed as moderate risk is extremely important in screening for Down syndrome and reasonable recommendations may be offered under different conditions.

Confined placental mosaicism for 22q11.2 deletion as the etiology for discordant positive NIPT results

22q11.2 deletion, the most common microdeletion syndrome within the general population, is estimated to have a prevalence of 1 in 3000 to 6000. Non-invasive prenatal testing has recently expanded to include screening for several microdeletions including 22q11.2. Given the expansion of prenatal screening options to include microdeletions, it is important to understand the limits of this technology and the variety of reasons that a discordant positive result can occur. Here, we describe a case of a pregnant woman who received a positive non-invasive prenatal maternal plasma screen for 22q11.2 deletion. Maternal and postnatal neonatal peripheral blood cytogenetic, PCR, and fluorescence in situ hybridization studies were normal, but the placenta was mosaic for 22q11.2 deletion in two of three biopsy sites. This case illustrates both the complexities of pre- and post-test counseling for microdeletion screening and the potential for a discordant positive microdeletion result because of confined placental mosaicism. © 2017 John Wiley & Sons, Ltd.

Revisiting the challenges of training Maternal Fetal Medicine fellows in chorionic villus sampling

BACKGROUND

More than a decade ago, researchers described a survey of Maternal Fetal Medicine fellows that showed that chorionic villus sampling training was limited for Maternal Fetal Medicine fellows in the United States. Prenatal screening and diagnosis have rapidly evolved since then and include the introduction of noninvasive aneuploidy screening that uses cell-free fetal DNA. Yet, chorionic villus sampling remains the only method available for first-trimester genetic diagnosis.

OBJECTIVE

This study evaluated the chorionic villus sampling training of Maternal Fetal Medicine fellows with respect to availability, competency standards, and education methods.

STUDY DESIGN

In November 2015, an electronic survey was sent to Maternal Fetal Medicine fellows and fellowship directors of accredited Maternal Fetal Medicine fellowship programs in the United States.

RESULTS

Fifty-eight percent of fellows (179/310) and 46% of program directors (35/76) responded. Ninety-five percent of Maternal Fetal Medicine fellows think that invasive diagnostic testing is essential to their training; 100% of fellows have amniocentesis training; and 65% have chorionic villus sampling training. The median number of chorionic villus sampling procedures that are expected during a fellowship in those who trained was 10. Eighty-eight percent of fellows and 89% of program directors state that chorionic villus sampling training could be better; 89% of fellows and 97% of directors would like access to simulated models. Barriers to training included lack of patients (71%) and lack of proficient attending supervisors (43%).

CONCLUSION

Since the last survey, >10 years ago, chorionic villus sampling training has declined further. A decrease in the number of procedures that are performed is the leading barrier to this training.

Trial by Dutch laboratories for evaluation of non-invasive prenatal testing. Part I-clinical impact

Objective

To evaluate the clinical impact of nationwide implementation of genome‐wide non‐invasive prenatal testing (NIPT) in pregnancies at increased risk for fetal trisomies 21, 18 and 13 (TRIDENT study).

Method

Women with elevated risk based on first trimester combined testing (FCT ≥ 1:200) or medical history, not advanced maternal age alone, were offered NIPT as contingent screening test, performed by Dutch University Medical laboratories. We analyzed uptake, test performance, redraw/failure rate, turn‐around time and pregnancy outcome.

Results

Between 1 April and 1 September 2014, 1413/23 232 (6%) women received a high‐risk FCT result. Of these, 1211 (85.7%) chose NIPT. One hundred seventy‐nine women had NIPT based on medical history. In total, 1386/1390 (99.7%) women received a result, 6 (0.4%) after redraw. Mean turn‐around time was 14 days. Follow‐up was available in 1376 (99.0%) pregnancies. NIPT correctly predicted 37/38 (97.4%) trisomies 21, 18 or 13 (29/30, 4/4 and 4/4 respectively); 5/1376 (0.4%) cases proved to be false positives: trisomies 21 (n = 2), 18 (n = 1) and 13 (n = 2). Estimated reduction in invasive testing was 62%.

Conclusion

Introduction of NIPT in the Dutch National healthcare‐funded Prenatal Screening Program resulted in high uptake and a vast reduction of invasive testing. Our study supports offering NIPT to pregnant women at increased risk for fetal trisomy. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.

What's already known about this topic?

Non‐invasive prenatal testing (NIPT) for trisomies 21, 18 and 13 is mainly offered in a commercial setting.

Offering NIPT to pregnant women at increased risk for fetal trisomy leads to a reduction in invasive testing.

What does this study adds?

NIPT implemented as a contingent test under the umbrella of a national health authority‐supported fetal trisomy screening program facilitates optimal counseling with close to 100% follow‐up, results in 86% uptake and confirms a major reduction of invasive tests.

Enlarged NT (≥3.5 mm) in the first trimester - not all chromosome aberrations can be detected by NIPT

BACKGROUND

Since non-invasive prenatal testing (NIPT) in maternal blood became available, we evaluated which chromosome aberrations found in our cohort of fetuses with an enlarged NT in the first trimester of pregnancy (tested with SNP microarray) could be detected by NIPT as well.

METHOD

362 fetuses were referred for cytogenetic testing due to an enlarged NT (≥3.5 mm). Chromosome aberrations were investigated using QF-PCR, karyotyping and whole genome SNP array.

RESULTS

After invasive testing a chromosomal abnormality was detected in 137/362 (38 %) fetuses. 100/362 (28 %) cases concerned trisomy 21, 18 or 13, 25/362 (7 %) an aneuploidy of sex chromosomes and 3/362 (0.8 %) triploidy. In 6/362 (1.6 %) a pathogenic structural unbalanced chromosome aberration was seen and in 3/362 (0.8 %) a susceptibility locus for neurodevelopmental disorders was found. We estimated that in 2-10 % of fetuses with enlarged NT a chromosome aberration would be missed by current NIPT approaches.

CONCLUSION

Based on our cohort of fetuses with enlarged NT we may conclude that NIPT, depending on the approach, will miss chromosome aberrations in a significant percentage of pregnancies. Moreover all abnormal NIPT results require confirmatory studies with invasive testing, which will delay definitive diagnosis in ca. 30 % of patients. These figures are important for pretest counseling enabling pregnant women to make informed choices on the prenatal test. Larger cohorts of fetuses with an enlarged NT should be investigated to assess the additional diagnostic value of high resolution array testing for this indication.