Clinical value of positive CNVs results by NIPT without fetal ultrasonography-identified structural anomalies

OBJECTIVE

To evaluate the clinical value of positive copy number variations (CNVs) results by non-invasive prenatal testing (NIPT) without fetal ultrasonography-identified structural anomalies, especially with several known CNVs results.

METHODS

A total of 135,981 results of NIPT performed between April 1, 2017, and March 31, 2020, enrolled in the free NIPT service program implemented by the local government were retrospectively analyzed. Of these, 87 cases with positive NIPT screens for CNVs and no fetal ultrasonography-identified anomalies were recalled and provided genetic counseling. After obtaining full informed consent, these cases were provided invasive prenatal diagnosis by karyotyping and chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq) with follow-up. One case was lost, while 86 cases were successfully followed up.

RESULTS

A total of 44 (50.6%) cases underwent invasive prenatal diagnosis, of which six cases were detected with abnormal karyotype. CMA/CNV-Seq revealed 11 fetuses with positive results for CNVs, among whom eight were consistent with NIPT results, two were partially consistent, one was inconsistent, and positive predictive value (PPV) was 22.7% (10/44). For known CNVs, PPVs were 20% (15q11.2-q13 microdeletion) and 33.3% (5p end deletions). Among 11 pregnant women with positive prenatal diagnosis, seven were confirmed to have pathogenic CNVs in their fetuses; four had CNVs of unknown clinical significance.

CONCLUSIONS

Even in pregnancies without ultrasonography-identified anomalies, a positive NIPT screen for CNVs must be interpreted with caution and validated by additional diagnostic study.

Evaluation of pre-test counselling offered for non-invasive prenatal testing (NIPT) as a primary screening tool

The increasing popularity and expansion of non-invasive prenatal testing (NIPT) to screen for rare conditions beyond common trisomies prompts evaluation of pre-test counselling currently offered. We conducted a prospective survey to assess women's knowledge of NIPT in those who had undergone NIPT (study group) and those who were planning to have NIPT (control group). Out of the 189 questionnaires analysed, the study group did not show a higher knowledge score compared to the control group (P = 0.097). 44% misunderstood that NIPT can identify more conditions than invasive testing, 69.8% were unaware of the recommended need for nuchal translucency measurement and 52.6% were unaware of the possibility of incidental findings. 31% even considered discussing termination of pregnancy as one of the next steps if NIPT shows high risk for Down syndrome. This study shows that current pre-test counselling is inadequate. Service providers should address these knowledge gaps and assist women to make informed choices.Impact StatementWhat is already known on this subject? Pre-test counselling for non-invasive prenatal testing (NIPT) should be conducted to assist women in making an informed consent.What do the results of this study add? Our results show that a significant proportion of women are unaware of the limitations of NIPT.What are the implications of these findings for clinical practice and/or further research? Service providers should improve their pre-test counselling focusing on areas of knowledge deficiencies and misunderstanding on NIPT identified in this study.

Invasive prenatal diagnosis in the era of cell-free fetal DNA: experience at a single center

BACKGROUND

We aimed to assess procedure-related risk of fetal loss associated with amniocentesis and chorionic villus sampling and compare amniocentesis and chorionic villus sampling with cell-free fetal DNA in identifying chromosomal abnormalities.

METHODS

A retrospective observational study on 4712 women with singleton pregnancy who underwent invasive prenatal diagnosis, from January 2010 to December 2019. Postprocedural miscarriage rate (before 24+0 weeks gestation) was determined for the whole population and for the group of women aged ≥35 years who underwent the procedure for the sole maternal age.

RESULTS

Miscarriage rate following amniocentesis and chorionic villus sampling were 0.50% and 1.25%, respectively. In our population of women undergoing invasive procedure for advanced maternal age cell-free fetal DNA would have identified only the 49 cases of trisomy 21, 13 and 18, whereas the other 21 more subtle chromosomal anomalies, diagnosed by amniocentesis and chorionic villus sampling, would have been missed.

CONCLUSIONS

Patients who opt for cell-free fetal DNA test should be informed of the screening nature of the test and the possibility of false positive results. Invasive prenatal testing has probably lower risks than previously reported and has unquestionable advantages such as the certainty of diagnosis and the ability to detect a higher number of chromosomal abnormalities, when compared with cell-free fetal DNA.

Prenatal Screening for Microdeletions and Rare Autosomal Aneuploidies

Noninvasive prenatal screening with cell-free DNA is now considered a first-line screening for common aneuploidies. Advancements in existing laboratory techniques now allow to interrogate the entirety of the fetal genome, and many commercial laboratories have expanded their screening panels to include screening for rare autosomal aneuploidies and copy number variants. Here, we review the currently available data on the performance of fetal cell-free DNA to detect rare autosomal aneuploidies and copy number variants that are associated with clinically significant microdeletion and microduplication syndromes and the current position of medical societies on routine screening for these syndromes.

Expanded Non-invasive Prenatal Testing (NIPT) : Can the Child's Right to an Open Future Help Set the Scope?

Expanded non-invasive prenatal testing (NIPT) has provoked ethical concerns about its justifiable scope. In this paper, we evaluate the role of the child's right to an open future in setting the scope of NIPT. This 'open future principle' has been cited in arguments both limiting and expanding parental freedoms. This moral right holds that adult autonomy rights which children cannot yet exercise should nonetheless be protected until they can. Its purpose is to protect the future autonomy of the child as a future adult. Several authors have extended this rationale from child to fetus. However, the right was not anticipated to apply to the fetus, a non-legal entity in many jurisdictions. The aim of this paper is to reconsider whether this principle is useful to help deliberate the scope of NIPT. We find that extending the open future principle to delineate the scope of NIPT is theoretically flawed. We contend that in the prenatal context its value primarily lies with counselling for prenatal screening where it can be used to encourage parents' reflection on the implications of knowing for the sake of knowing on their future children and their relationship with them.

Performance of expanded non-invasive prenatal testing for fetal aneuploidies and copy number variations: A prospective study from a single center in Jiangxi province, China

To evaluate the performance of expanded non-invasive prenatal testing (expanded noninvasive prenatal testing, NIPT-Plus) in screening for fetal chromosomal abnormalities includes aneuploidies and copy number variations, a total of 23,116 pregnant women with a singleton pregnancy were recruited for NIPT-Plus. Screening positive results were verified by karyotype analysis and chromosomal microarray analysis after amniocentesis. A total of 264 pregnancies (1.14%) were positive results as predicted by NIPT-Plus, including 233 aneuploidies and 31 copy number variations. Following genetic counseling, 233 (88.26%) pregnant women underwent invasive prenatal diagnosis and 136 were verified as true positives, comprising 72 common trisomies (T21, T18, T13), 47 sex chromosomal abnormalities two rare autosomal aneuploidies (RATs) and 15 copy number variations The positive predictive value for common trisomies, SCAs, RATs and CNVs were 68.57%, 68.12%, 6.67% and 51.72%, respectively. Pregnant women with screen-positive results for common trisomies have higher rates of invasive prenatal diagnosis and pregnancy termination than those with positive results for SCAs, RATs, and CNVs. NIPT-Plus showed a good performance in detecting common trisomies, SCAs and also contributed to detecting pathogenic CNVs, but higher accuracy was required in the detection of RATs. In summary, this study provides a reference for the clinical application of NIPT-Plus for screening fetal chromosomal abnormalities in this region. Therefore, we suggest that NIPT-Plus could be widely used in clinical screening for fetal chromosomal abnormalities in combination with prenatal diagnosis and genetic counseling.

Experiences of pregnant women with genome-wide non-invasive prenatal testing in a national screening program

Pregnant women’s perspectives should be included in the dialogue surrounding the expanding offers of non-invasive prenatal testing (NIPT), especially now that technological possibilities are rapidly increasing. This study evaluated women’s experiences with the offer of genome-wide (GW) first-tier NIPT in a national screening program. A nationwide pre-and post-test questionnaire was completed by 473 pregnant women choosing between targeted NIPT (trisomies 21, 18 and 13 only) and GW-NIPT (also other findings) within the Dutch TRIDENT-2 study. Measures included satisfaction, reasons for or against choosing GW-NIPT, anxiety, and opinion on the future scope of NIPT. Most respondents (90.4%) were glad to have been offered the choice between GW-NIPT and targeted NIPT; 76.5% chose GW-NIPT. Main reasons to choose GW-NIPT were ‘wanting as much information as possible regarding the child’s health’ (38.6%) and ‘to be prepared for everything’ (23.8%). Main reasons to choose targeted NIPT were ‘avoiding uncertain results/outcomes’ (33.7%) and ‘not wanting to unnecessarily worry’ (32.6%). Nearly all respondents received a low-risk NIPT result (98.7%). No differences were found in anxiety between women choosing GW-NIPT and targeted NIPT. Most respondents were favorable toward future prenatal screening for a range of conditions, including life-threatening disorders, mental disabilities, disorders treatable in pregnancy and severe physical disabilities, regardless of their choice for GW-NIPT or targeted NIPT. In conclusion, women who chose first-tier NIPT were satisfied with the choice between GW-NIPT and targeted NIPT, and most women were favorable toward a broader future screening offer. Our results contribute to the debate concerning the expansion of NIPT.

Clinical experience of noninvasive prenatal testing for rare chromosome abnormalities in singleton pregnancies

Objectives: The study aimed to investigate the clinical use of noninvasive prenatal testing (NIPT) for common fetal aneuploidies as a prenatal screening tool for the detection of rare chromosomal abnormalities (RCAs).

Methods: Gravidas with positive NIPT results for RCAs who subsequently underwent amniocentesis for a single nucleotide polymorphism array (SNP array) were recruited. The degrees of concordance between the NIPT and SNP array were classified into full concordance, partial concordance, and discordance. The positive predictive value (PPV) was used to evaluate the performance of NIPT.

Results: The screen-positivity rate of NIPT for RCAs was 0.5% (842/158,824). Of the 528 gravidas who underwent amniocentesis, 29.2% (154/528) were confirmed to have positive prenatal SNP array results. PPVs for rare autosomal trisomies (RATs) and segmental imbalances were 6.1% (7/115) and 21.1% (87/413), respectively. Regions of homozygosity/uniparental disomy (ROH/UPD) were identified in 9.5% (50/528) of gravidas. The PPV for clinically significant findings was 8.0% (42/528), including 7 cases with mosaic RATs, 30 with pathogenic/likely pathogenic copy number variants, and 5 with imprinting disorders.

Conclusion: NIPT for common fetal aneuploidies yielded low PPVs for RATs, moderate PPVs for segmental imbalances, and incidental findings for ROH/UPD. Due to the low PPV for clinically significant findings, NIPT for common fetal aneuploidies need to be noticed for RCAs.

Video education about genetic privacy and patient perspectives about sharing prenatal genetic data: a randomized trial

BACKGROUND

Laboratories offering cell-free DNA often reserve the right to share prenatal genetic data for research or even commercial purposes, and obtain this permission on the patient consent form. Although it is known that nonpregnant patients are often reluctant to share their genetic data for research, pregnant patients' knowledge of, and opinions about, genetic data privacy are unknown.

OBJECTIVE

We investigated whether pregnant patients who had already undergone cell-free DNA screening were aware that genetic data derived from cell-free DNA may be shared for research. Furthermore, we examined whether pregnant patients exposed to video education about the Genetic Information Nondiscrimination Act-a federal law that mandates workplace and health insurance protections against genetic discrimination-were more willing to share cell-free DNA-related genetic data for research than pregnant patients who were unexposed.

STUDY DESIGN

In this randomized controlled trial (ClinicalTrials.gov Identifier: NCT04420858), English-speaking patients with singleton pregnancies who underwent cell-free DNA and subsequently presented at 17 0/7 to 23 6/7 weeks of gestation for a detailed anatomy scan were randomized 1:1 to a control or intervention group. Both groups viewed an infographic about cell-free DNA. In addition, the intervention group viewed an educational video about the Genetic Information Nondiscrimination Act. The primary outcomes were knowledge about, and willingness to share, prenatal genetic data from cell-free DNA by commercial laboratories for nonclinical purposes, such as research. The secondary outcomes included knowledge about existing genetic privacy laws, knowledge about the potential for reidentification of anonymized genetic data, and acceptability of various use and sharing scenarios for prenatal genetic data. Eighty-one participants per group were required for 80% power to detect an increase in willingness to share data from 60% to 80% (α=0.05).

RESULTS

A total of 747 pregnant patients were screened, and 213 patients were deemed eligible and approached for potential study participation. Of these patients, 163 (76.5%) consented and were randomized; one participant discontinued the intervention, and two participants were excluded from analysis after the intervention when it was discovered that they did not fulfill all eligibility criteria. Overall, 160 (75.1%) of those approached were included in the final analysis. Most patients in the control group (72 [90.0%]) and intervention (76 [97.4%]) group were either unsure about or incorrectly thought that cell-free DNA companies could not share prenatal genetic data for research. Participants in the intervention group were more likely to incorrectly believe that their prenatal genetic data would not be shared for nonclinical purposes than participants in the control group (28.8% in the control group vs 46.2% in the intervention; P=.03). However, video education did not increase participant willingness to share genetic data in multiple scenarios. Non-White participants were less willing than White participants to allow sharing of genetic data specifically for academic research (P<.001).

CONCLUSION

Most participants were unaware that their prenatal genetic data may be used for nonclinical purposes. Pregnant patients who were educated about the Genetic Information Nondiscrimination Act were not more willing to share genetic data than those who did not receive this education. Surprisingly, video education about the Genetic Information Nondiscrimination Act led patients to falsely believe that their data would not be shared for research, and participants who identified as racial minorities were less willing to share genetic data. New strategies are needed to improve pregnant patients' understanding of genetic privacy.

Pregnancy outcomes of rare autosomal trisomies results in non-invasive prenatal screening: clinical follow-up data from a single tertiary centre

This study was performed to assess the association between detection of rare autosomal trisomies (RATs) by non-invasive prenatal screening (NIPS) and adverse pregnancy outcomes. We retrospectively analyzed women with high-risk RATs results from January 2014 to December 2020. The women's clinical information was collected, and their pregnancy outcomes were compared with those of women with low-risk results. In total, 151 (0.24%) RATs results were reported among 62,752 NIPS examinations. Sixty-five women chose to undergo amniocentesis for confirmation, which revealed 3 cases of true fetal mosaicism for RATs and a positive predictive value of 4.6% (3/65). Among the 139 women with available outcomes, 26 (18.7%) had a preterm birth, 10 (7.2%) underwent pregnancy termination because of fetal defects and 5 (3.6%) had miscarriages. Interestingly, compared with the control group, pregnancies in which NIPS revealed trisomy 16 (T16), T22, T9 and T2 were at higher risk of adverse outcomes, including preterm birth, miscarriage and ultrasound abnormalities. However, the risk of adverse outcomes was comparable between the control group and pregnancies with positive results of T7, T3, T8 and T20. In summary, the risk of adverse pregnancy outcomes was higher in women with specific RATs-positive NIPS results. Pregnancies with T16, T22, T9 and T2 results, even if false-positive, should be considered high-risk pregnancies.

Cell-free DNA screening for prenatal detection of 22q11.2 deletion syndrome

BACKGROUND

Historically, prenatal screening has focused primarily on the detection of fetal aneuploidies. Cell-free DNA now enables noninvasive screening for subchromosomal copy number variants, including 22q11.2 deletion syndrome (or DiGeorge syndrome), which is the most common microdeletion and a leading cause of congenital heart defects and neurodevelopmental delay. Although smaller studies have demonstrated the feasibility of screening for 22q11.2 deletion syndrome, large cohort studies with confirmatory postnatal testing to assess test performance have not been reported.

OBJECTIVE

This study aimed to assess the performance of single-nucleotide polymorphism-based, prenatal cell-free DNA screening for detection of 22q11.2 deletion syndrome.

STUDY DESIGN

Patients who underwent single-nucleotide polymorphism-based prenatal cell-free DNA screening for 22q11.2 deletion syndrome were prospectively enrolled at 21 centers in 6 countries. Prenatal or newborn DNA samples were requested in all cases for genetic confirmation using chromosomal microarrays. The primary outcome was sensitivity, specificity, positive predictive value, and negative predictive value of cell-free DNA screening for the detection of all deletions, including the classical deletion and nested deletions that are ≥500 kb, in the 22q11.2 low-copy repeat A-D region. Secondary outcomes included the prevalence of 22q11.2 deletion syndrome and performance of an updated cell-free DNA algorithm that was evaluated with blinding to the pregnancy outcome.

RESULTS

Of the 20,887 women enrolled, a genetic outcome was available for 18,289 (87.6%). A total of 12 22q11.2 deletion syndrome cases were confirmed in the cohort, including 5 (41.7%) nested deletions, yielding a prevalence of 1 in 1524. In the total cohort, cell-free DNA screening identified 17,976 (98.3%) cases as low risk for 22q11.2 deletion syndrome and 38 (0.2%) cases as high risk; 275 (1.5%) cases were nonreportable. Overall, 9 of 12 cases of 22q11.2 were detected, yielding a sensitivity of 75.0% (95% confidence interval, 42.8-94.5); specificity of 99.84% (95% confidence interval, 99.77-99.89); positive predictive value of 23.7% (95% confidence interval, 11.44-40.24), and negative predictive value of 99.98% (95% confidence interval, 99.95-100). None of the cases with a nonreportable result was diagnosed with 22q11.2 deletion syndrome. The updated algorithm detected 10 of 12 cases (83.3%; 95% confidence interval, 51.6-97.9) with a lower false positive rate (0.05% vs 0.16%; P<.001) and a positive predictive value of 52.6% (10/19; 95% confidence interval, 28.9-75.6).

CONCLUSION

Noninvasive cell-free DNA prenatal screening for 22q11.2 deletion syndrome can detect most affected cases, including smaller nested deletions, with a low false positive rate.

The application of expanded noninvasive prenatal screening for genome-wide chromosomal abnormalities and genetic counseling

OBJECTIVE

To evaluate the clinical application of expanded noninvasive prenatal screening (eNIPS) for genome-wide large copy number variation (CNV), i.e. chromosomal deletion/duplication >5 Mb, and aneuploidy; also to provide practical information for counseling eNIPS positive cases.

METHOD

We recruited 34,620 women with singleton pregnancy for genome-wide cell-free plasma DNA sequencing. Screening positive cases were verified by karyotyping and/or SNP array.

RESULT

A total of 461 (1.33%) positive cases were identified through our cfDNA screening including 209 cases of common trisomies (0.60%), 124 cases of sex chromosomal abnormalities (SCA) (0.36%), 71 cases of other autosomal anueploidies (OAA) (0.21%), and 57 CNVs larger than 5 Mb (0.16%). The predictive positive values (PPV) were 70.06% in general for common trisomies with as high as 91.67% for Trisomy21 (T21), 40.22% in general for SCAs with as high as 100% for Jacob Syndrome (XYY). The PPV for OAAs was 5.45%, and T7/T8/T16/T22 were the most frequent OAAs (n = 15, 9, 9, 8, respectively). The PPV for CNVs larger than 5 Mb was 51.22% (n = 57) with the CNV mostly detected on Chr5/Chr4/Chr2/Chr7 (n = 10, 8, 5, 5, respectively).

CONCLUSION

The expanded NIPS had shown promising PPVs for CNVs (large than 5 Mb), SCAs and common trisomies, yet this method required higher efficacy in screening for OAAs. The post-test genetic counseling for expanded NIPS should be tailored to the types of positive cases and also address the origin of abnormal signals (fetal vs. maternal).

Current controversies in prenatal diagnosis: Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered

Non-invasive prenatal testing (NIPT) based on analysis of cell free DNA circulating in the maternal plasma has been available clinically to screen for chromosomal abnormalities since 2011. There is significant evidence to suggest that NIPT has revolutionised prenatal screening for the common trisomies 13, 18, and 21. However, the evidence in favour of its extended use to screen for conditions other than these trisomies remains a topic of debate with no national or international organisation supporting clinical implementation for these indications. In the debate presented here - "Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered" - we will see the pros and cons of screening for a wider range of chromosomal problems. The discussion presented swung the vote from 65% in favour and 35% against before the arguments were voiced to 41% in favour and 59% against. This significant swing in the vote indicates that the majority of our community feel more evidence is required before clinical implementation of extended NIPT.

The Setup and Application of Reference Material in Sequencing-Based Noninvasive Prenatal Testing

INTRODUCTION

The sequencing-based noninvasive prenatal testing (NIPT) has been successfully integrated into clinical practice and facilitated the early detection of fetal chromosomal anomalies. However, a comprehensive reference material to evaluate and quality control NIPT services from different NIPT providers remains unavailable.

METHODS

In this study, we established a set of NIPT reference material consisting of 192 simulated samples. Most of the potential factors influencing the accuracy of NIPT, such as fetal fraction, mosaicism, and interfering substances, were included in the reference material. We compared the performance of chromosomal abnormalities detection on 3 widely used sequencers (NextSeq 500, BGISEQ-500, and Ion Proton) based on the reference material.

RESULTS

All 3 sequencers provided highly accurate and reliable results to samples with ≥3.5% fetal fractions and high percentage of mosaicism.

CONCLUSIONS

The established reference material can serve as a universal standard quality control for the current and new-coming NIPT providers based on various sequencers.

Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy

OBJECTIVE

To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies.

METHODS

This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results.

RESULTS

Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result.

CONCLUSION

CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.

Analyzing false-negative results detected in low-risk non-invasive prenatal screening cases

Background

The non‐invasive prenatal screening (NIPS) has been introduced into clinical practice with a high sensitivity and specificity. Although the false‐negative results are inevitable and important, limited false‐negative NIPS results have been reported and studied previously. In this study, we aim to report and analyze false‐negative results detected in the NIPS cases with a low‐risk result.

Methods

NIPS was performed using whole‐genome massively parallel shotgun sequencing for screening common trisomies, rare autosomal aneuploidies, and subchromosome copy number variants. All the NIPS cases with a low‐risk result performed in our center in 2017 were followed‐up using medical records and telephone interview at 3 months after delivery. Fetal ultrasound results and available genetic diagnostic testing results were collected for pregnancies with adverse outcomes. The genetic diagnostic testing referred to chromosomal microarray analysis or fluorescent in situ hybridization on amniotic fluid cells, fetal skin tissue, neonatal peripheral blood, or available placental biopsies.

Results

By following‐up 10,975 low‐risk results, we found 166 NIPS cases with adverse pregnancy outcomes, in which eight cases had diagnostic testing. Among them, four false‐negative cases were confirmed, including one trisomy 18 caused by placental mosaicism, one mosaic tetrasomy 12p, and 2 microdeletion/microduplication cases.

Conclusion

Our results revealed that mosaicism contributes to a major cause of false negative in NIPS, and highlighted the importance of ultrasound in identifying these false‐negative results.

Non-Invasive Prenatal Testing beyond Trisomies

The last decade has seen incredible advances in the genetic era, in next-generation sequencing of cell-free DNA in the maternal plasma, detecting abnormal fetal chromosomes. Non-invasive prenatal testing (NIPT) has showed increased sensitivity and specificity for Down syndrome superior to any other screening test. Technical advances have made possible the detection of other conditions which does not necessarily mean clinical benefit for the patient. Private laboratories have added multiple conditions in the panel of NIPT, but some of these abnormalities are so rare, that their prevalence is not even clear. Data regarding clinical performance of extended NIPT is lacking. Implementation of such a test has to be carefully weighed, and not only the benefits but also the harm should be taken into account.

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.

Characteristics and mode of inheritance of pathogenic copy number variants in prenatal diagnosis

BACKGROUND

Microdeletions and microduplications can occur in any pregnancy independent of maternal age. The spectrum and features of pathogenic copy number variants including the size, genomic distribution, and mode of inheritance are not well studied. These characteristics have important clinical implications regarding expanding noninvasive prenatal screening for microdeletions and microduplications.

OBJECTIVES

The aim was to investigate the spectrum and characteristics of pathogenic copy number variants in prenatal genetic diagnosis and to provide recommendations for expanding the scope of noninvasive prenatal screening for microdeletions and microduplications.

STUDY DESIGN

This was a retrospective study of 1510 pregnant women who underwent invasive prenatal diagnostic testing by chromosomal microarray analysis. Prenatal samples were retrieved by amniocentesis or chorionic villus sampling and sent to our prenatal genetic diagnosis laboratory for chromosomal microarray analysis. The risk of carrying a fetus with pathogenic copy number variants is stratified by the patients' primary indication for invasive testing. We searched the literature for published prenatal chromosomal microarray data to generate a large cohort of 23,865 fetuses. The characteristics and spectrum of pathogenic copy number variants including the type of aberrations (gains or losses), genomic loci, sizes, and the mode of inheritance were studied.

RESULTS

Overall, 375 of 23,865 fetuses (1.6%) carried pathogenic copy number variants for any indication for invasive testing, and 44 of them (11.7%) involve 2 or more pathogenic copy number variants. A total of 428 pathogenic copy number variants were detected in these fetuses, of which 280 were deletions and 148 were duplications. Three hundred sixty (84.1%) were less than 5 Mb in size and 68 (15.9%) were between 5 and 10 Mb. The incidence of carrying a pathogenic copy number variant in the high-risk group is 1 in 36 and the low-risk group is 1 in 125. Parental inheritance study results were available for 311 pathogenic copy number variants, 71 (22.8%) were maternally inherited, 36 (11.6%) were paternally inherited, and 204 (65.6%) occurred de novo.

CONCLUSION

Collectively, pathogenic copy number variants are common in pregnancies. High-risk pregnancies should be offered invasive testing with chromosomal microarray analysis for the most comprehensive investigation. Detection limits on size, parental inheritance, and genomic distribution should be carefully considered before implementing copy number variant screening in expanded noninvasive prenatal screening.

Profile of women choosing the Harmony® Prenatal Test

INTRODUCTION

The Harmony® Prenatal Test, a noninvasive cell-free DNA (cfDNA) method for major trisomies has been available since January 2013 at our unit, and tests were sent to the Ariosa Clinical Laboratory Improvement Amendments (CLIA) laboratory in California. From July 2017 onward, prenatal cfDNA has been reimbursed in Belgium for all pregnancies; however, since then samples are sent to a local laboratory. Little data are available on patient's profile and choices toward cfDNA and on the performance of local technology transfer centers. Areas covered: The profiles and choices of women regarding this test were evaluated. Further, the performance of cfDNA at the local laboratory was compared to the one in California. Our results showed that women from the Netherlands, as compared to Belgium, were more likely to undergo cfDNA testing for maternal request and would be less likely to undergo karyotyping if cfDNA were unavailable, therefore are better candidates for cfDNA testing, when this is used as first-line screening. Expert commentary: Our findings highlight the importance of conducting these types of studies, before decisions about clinical implementation are made by national governments and ministries of health.

The consequences of implementing non-invasive prenatal testing with cell-free foetal DNA for the detection of Down syndrome in the Spanish National Health Service: a cost-effectiveness analysis

Background

DNA-based non-invasive prenatal testing (NIPT) using maternal blood constitutes an emerging technology for the detection of Down syndrome (DS). The aim of the study was to conduct a cost-effectiveness analysis to evaluate the economic costs and health implications of the introduction of NIPT based on cell-free foetal DNA analysis through different screening strategies for the detection of DS.

Methods

An analytical short-term decision model was developed, from the payer´s perspective (Spanish National Health Service). The main outcome measure was the number of DS cases detected. Secondary measures included associated miscarriages, women undergoing current screening, women undergoing NIPT, positive NIPT and invasive procedures performed. The study setting was the Spanish National Health Service. Three strategies were compared: (a) first- and second-trimester screening (current screening); (b) NIPT as contingent testing; and (c) NIPT as first-line testing. Modelling was based on a hypothetical cohort of 100,000 Spanish pregnant women. Population data were obtained from the database of the Basque Antenatal Screening Programme. Deterministic sensitivity analyses were performed to assess variations in the cost of NIPT, screening risk cut-off, screening uptake-rate and rate of failure of NIPT.

Results

NIPT as contingent testing (strategy b) led to fewer miscarriages following invasive procedures and a slight reduction in the number of DS cases detected compared to current screening. However, lowering the screening cut-off to ≥ 1:500 would improve the overall effectiveness of NIPT as contingent testing, increasing the number of DS cases detected and decreasing foetal losses as compared to the current screening, despite there would be an extra-cost of 3.5%. When NIPT was used as first-line testing (strategy c), the screening would be more effective but also more expensive, with incremental cost-effectiveness ratios (ICERs) per additional case of DS detected of €1,299,763 and €1,232,763, compared with strategies a and b, respectively. Results were sensitive to the different parameters considered in the analysis.

Conclusions

Both, as first-line testing and as contingent testing when screening cut-off was lowered ≥ 1:500, NIPT would lead to more favourable outcomes as compared to the current screening (both in terms of DS cases detected and miscarriages avoided), but at a greater cost.