Cell-Free DNA Screening for Aneuploidy and Microdeletion Syndromes

Evaluation of the clinical effects of non-invasive prenatal screening for diseases associated with aneuploidy and copy number variation

BACKGROUND

To explore and compare the clinical effects of high-resolution non-invasive prenatal screening (NIPS-Plus) for common/uncommon chromosomal aneuploidy and microdeletion/microduplication syndromes (MMS).

METHODS

The current prospective study included a total of 25,380 pregnant women who performed NIPS-Plus, and amniocentesis was performed on women with MMS with the screening results to diagnose patients with suspected MMS.

RESULTS

There were 415 samples with positive results for NIPS-Plus, included 275 with aneuploidy and 140 with MMS. After diagnosis by amniocentesis, 188 cases were confirmed as true positive, included46 cases of T21, 9 cases of T18, 1 case of T13, 34 cases of SCA, 41 cases of other chromosomal euploidy and 57 cases of MMS. In addition, no false negative cases were found, MMS was classified with 5 Mb with the cutoff value, and the PPV of different fragment size was counted, respectively.

CONCLUSION

We found that the corresponding PPV was 44.66% with the fragment of copy number variation (CNV) being less than or equal to 5 Mb, and when it was greater than 5 Mb, the PPV was 29.73%, which suggested that NIPS-Plus was more suitable for screening the PPV of small fragment abnormalities. NIPS-Plus has a good application effect in routine aneuploidy screening and had the best detection effect for T21; moreover, it performed well in screening of MMS and had better detection effect on MMS with CNV fragment length less than 5 Mb. Based on the current results, we suggested that NIPS-Plus should be used as a comprehensive elementary prenatal screening method for all pregnant women, but for MMS caused by abnormal large fragment CNV, the detection method and efficiency still need to be improved.

Diagnosis of hydatidiform moles using circulating gestational trophoblasts isolated from maternal blood

INTRODUCTION

Identifying hydatidiform moles (HMs) is crucial due to the risk of gestational trophoblastic neoplasia. When a HM is suspected on clinical findings, surgical termination is recommended. However, in a substantial fraction of the cases, the conceptus is actually a non-molar miscarriage. If distinction between molar and non-molar gestations could be obtained before termination, surgical intervention could be minimized.

METHODS

Circulating gestational trophoblasts (cGTs) were isolated from blood from 15 consecutive women suspected of molar pregnancies in gestational week 6-13. The trophoblasts were individually sorted using fluorescence activated cell sorting. STR analysis targeting 24 loci was performed on DNA isolated from maternal and paternal leukocytes, chorionic villi, cGTs, and cfDNA.

RESULTS

With a gestational age above 10 weeks, cGTs were isolated in 87% of the cases. Two androgenetic HMs, three triploid diandric HMs, and six conceptuses with diploid biparental genome were diagnosed using cGTs. The STR profiles in cGTs were identical to the profiles in DNA from chorionic villi. Eight of the 15 women suspected to have a HM prior to termination had a conceptus with a diploid biparental genome, and thus most likely a non-molar miscarriage.

DISCUSSION

Genetic analysis of cGTs is superior to identify HMs, compared to analysis of cfDNA, as it is not hampered by the presence of maternal DNA. cGTs provide information about the full genome in single cells, facilitating estimation of ploidy. This may be a step towards differentiating HMs from non-HMs before termination.

Enrichment of circulating trophoblasts from maternal blood using filtration-based Metacell® technology

In a cell-based non-invasive prenatal test (cbNIPT), intact circulating trophoblasts (CTs) are isolated from maternal blood for subsequent genetic analysis. Enrichment of these CTs from maternal blood is the most challenging step in the cbNIPT workflow. This study aims to assess the suitability of the filtration-based Metacell® technology to enrich CTs from maternal blood at week 10 to 13 of gestation. The Metacell® technology is a novel size-based enrichment technology that combines blood filtration through 8 μm pores with an in vitro culture method. Three protocols were evaluated. First, 8 mL or 16 mL of maternal blood was filtered and subsequently cultured in vitro on the separation membrane for 3 days in RPMI 1640. In addition, 16 mL of maternal blood was filtered, and immediately processed without further culturing. Y-chromosome-specific qPCR or STR analysis was performed to evaluate the enrichment of CTs. A total of 44 samples from pregnant women, out of which 26 were carrying a male fetus, were processed. Although five enriched male fetus samples show detectable male DNA quantities, it cannot be excluded that the obtained positive signal is caused by cell-free fetal DNA sticking to the Metacell® separation membrane. In conclusion, the Metacell® technology, tested as described, is not suitable for consistent enrichment of CTs.

Validity and Utility of Non-Invasive Prenatal Testing for Copy Number Variations and Microdeletions: A Systematic Review

Valid data on prenatal cell-free DNA-based screening tests for copy number variations and microdeletions are still insufficient. We aimed to compare different methodological approaches concerning the achieved diagnostic accuracy measurements and positive predictive values. For this systematic review, we searched the Scopus and PubMed databases and backward citations for studies published between 2013 and 4 February 2022 and included articles reporting the analytical and clinical performance of cfDNA screening tests for CNVs and microdeletions. Of the 1810 articles identified, 32 met the criteria. The reported sensitivity of the applied tests ranged from 20% to 100%, the specificity from 81.62% to 100%, and the PPV from 3% to 100% for cases with diagnostic or clinical follow-up information. No confirmatory analysis was available in the majority of cases with negative screening results, and, therefore, the NPVs could not be determined. NIPT for CNVs and microdeletions should be used with caution and any developments regarding new technologies should undergo strict evaluation before their implementation into clinical practice. Indications for testing should be in correlation with the application guidelines issued by international organizations in the field of prenatal diagnostics.

Análisis de concordancia entre la prueba prenatal no invasiva (NIPT) y el cariotipo prenatal para la detección de aneuploidías fetales

Introducción. La prueba prenatal no invasiva (NIPT, por su sigla en inglés) es una prueba de tamización de aneuploidías fetales con una mayor sensibilidad y especificidad que la tamización bioquímica prenatal tradicional. Objetivo. Evaluar la concordancia entre la NIPT y el cariotipo prenatal para la detección de aneuploidías fetales en embarazos de alto riesgo de dichas anomalías Materiales y métodos. Estudio piloto prospectivo realizado entre septiembre de 2019 y diciembre de 2020 en 20 pacientes con gestaciones clasificadas como de alto riesgo para aneuploidías fetales con base en los hallazgos ecográficos y atendidas en Bogotá y Medellín, Colombia. A cada paciente se le realizó una NIPT y una prueba invasiva confirmatoria (cariotipo prenatal). La concordancia entre ambos métodos se determinó mediante el coeficiente kappa de Cohen (nivel de significancia p<0.05), donde valores >0.7 se consideraron como un buen nivel de concordancia. Resultados. En 3 de las 20 gestaciones (15%) se detectaron aneuploidías mediante estudio citogenético invasivo: trisomía 21, trisomía 18 y monosomía X. La NIPT detectó la trisomía 21 y la monosomía X, pero falló en detectar la trisomía 18. Respecto al análisis de concordancia, el coeficiente de kappa de Cohen entre la NIPT y cariotipo prenatal fue 0.77, 1.0 y 0 para trisomía 21, monosomía X, trisomía 18, respectivamente. Además, la NIPT detectó 67% de las aneuploidías. Conclusión. En el presente estudio, primero en realizarse en Colombia, se observó una buena concordancia entre la NIPT y la prueba invasiva (cariotipo prenatal) para la detección de aneuploidías. Sin embargo, los resultados aquí reportados enfatizan la recomendación de utilizar la NIPT como prueba de tamización y no como prueba diagnóstica.

The potential of expanded noninvasive prenatal screening for detection of microdeletion and microduplication syndromes

OBJECTIVES

To evaluate the clinical potential of a higher resolution noninvasive prenatal screening (NIPS-Plus) test for detection of microdeletion/microduplication syndromes (MMS) in addition to common aneuploidies.

METHODS

In a multicenter prospective study, 37,002 pregnant women with unremarkable first-trimester ultrasound scans had a NIPS-Plus test. Ultrasound screen positive women were not included in this study.

RESULTS

Of 36,970 ultrasound negative women there were 291 NIPS-Plus screen positive results indicating 237 aneuploidies and 54 MMS. Following amniocentesis, 171 (72%) were confirmed as genuine, comprising 3 T13s, 10 T18s, 61 T21s, 70 SCAs and 27 MMS. The PPV for MMS with unremarkable ultrasound findings was 50%. Routine clinical examination of children born from NIPS-Plus negative pregnancies revealed no obvious signs of chromosome disease syndromes at one year of age.

CONCLUSIONS

NIPS-Plus has the potential for clinical utility not only for routine aneuploid screening but also for MMS that do not show overt signs during early pregnancy ultrasound screening. We suggest that ultrasound with NIPS-Plus in combination with appropriate counselling could be considered as a comprehensive first-tier prenatal screening approach for all pregnant women.

Optimizing Fetal Aneuploidy Screening in an Austere Military Clinical Environment: A Prenatal Cost Comparison

INTRODUCTION

Austere clinical settings, including remote military installations, face unique challenges in screening pregnant women for aneuploidy. The objective of this study was to compare the direct and indirect prenatal costs of traditional 2-part serum-based screening to cell-free DNA (cfDNA) for detection of trisomies 18 and 21 for a military treatment facility with limited in-house perinatal resources.

MATERIALS AND METHODS

We identified Naval Hospital Guantanamo Bay as a surrogate for an austere clinical environment. A prenatal cost of care analysis incorporating direct and indirect expenses was performed to compare the 2 aneuploidy screening strategies for a theoretical cohort of 100 patients for detection of trisomies 18 and 21. The baseline aneuploidy uptake rate was determined using a historical cohort. Test performance characteristics were obtained from the contracting laboratory. Aneuploidy rates and costs were calculated using previously published data.

RESULTS

Assuming a baseline screen uptake rate of 87%, initial screening using the traditional approach would directly cost $8,285.01 versus $44,140.32 with cfDNA. Considering indirect costs such as travel, consultative services, evaluation and follow-up testing of an abnormal screen result, and lost productivity, the cost difference narrows to $14,458.25 over a 5- to 6-year period. Cost equivalence is achieved when cfDNA is priced at $341.17 per test.

CONCLUSION

Cell-free DNA as an initial screening strategy offers enhanced detection rates for trisomies 18 and 21 but remains more costly than traditional screening when incorporating direct and indirect expenses. In a low volume setting with limited resources, the added cost may be justified given the implications of unrecognized aneuploidy.

Cell-based noninvasive prenatal testing (cbNIPT) detects pathogenic copy number variations

In two cases, cell-based noninvasive prenatal testing (cbNIPT) detected pathogenic copy number variations (CNVs) in the fetal genome. cbNIPT may potentially be an improved noninvasive alternative for the detection of smaller CNVs.

Ultrasound Measurements of Frontal Horns and the Cavum Septi Pellucidi in Healthy Fetuses in the Second and Third Trimesters of Pregnancy

OBJECTIVES

To assess the visualization rate and size of the frontal horns (FHs) and cavum septi pellucidi (CSP) in healthy fetuses throughout pregnancy.

METHODS

After Institutional Review Board approval, 522 consecutive uncomplicated singleton pregnancies between 15 and 39 gestational weeks were enrolled in the study. Ultrasound measurements of the anterior horn width (AHW), center from the horn distance (CFHD), distance from the FHs to the CSP, and CSP width were retrospectively performed using axial transventricular or transcerebellar planes. Available maternal body mass indices were recorded.

RESULTS

At least 1 FH was seen in 78% of the cases. The mean AHW decreased over the second trimester and plateaued in the third trimester. The CFHD plateaued in the second trimester and increased in the third trimester. Downside FHs were generally larger than upside FHs. More FHs were measured in transventricular (69%) than transcerebellar (31%) planes. Frontal horns were seen with high, low, and no confidence in 57%, 21%, and 22% of cases, respectively. No-confidence rates were 17% in the second trimester and 42% in the third trimester. The CSP was not visualized in 4% of cases; 15 of 19 cases of a nonvisualized CSP were scanned between 18 and 37 weeks. Mean body mass indices ± SDs were 27.6 ± 6.7 kg/m² for the patients in cases of a visualized CSP and 32.4 ± 9.1 kg/m² for the patients in cases of a nonvisualized CSP.

CONCLUSIONS

Normative data for the fetal FH and CSP width were established. Frontal horns are more frequently seen on transventricular views and are difficult to confidently assess in the late third trimester. This study challenges previously reported data that the CSP is seen in 100% of cases from 18 to 37 weeks.

Factors affecting cell-free DNA fetal fraction: statistical analysis of 13,661 maternal plasmas for non-invasive prenatal screening

Background

The identification of cell-free fetal DNA (cffDNA) facilitated non-invasive prenatal screening (NIPS) through analysis of cffDNA in maternal plasma. However, challenges regarding its clinical implementation become apparent. Factors affecting fetal fraction should be clarified to guide its clinical application.

Results

A total of 13,661 pregnant subjects with singleton pregnancies who undertook NIPS were included in the study. Relationship of gestational age, maternal BMI, and maternal age with the cffDNA fetal fraction in maternal plasmas for NIPS was investigated. Compared with 13 weeks (12.74%) and 14–18 weeks group (12.73%), the fetal fraction in gestational ages of 19–23 weeks, 24–28 weeks, and more than 29 weeks groups significantly increased to 13.11%, 16.14%, and 21.17%, respectively (P < 0.01). Compared with fetal fraction of 14.54% in the maternal BMI group of < 18.5 kg/m², the percentage of fetal fraction in the group of 18.5–24.9 kg/m² (13.37%), 25–29.9 kg/m² (12.20%), 30–34.9 kg/m² (11.32%), and 35–39.9 kg/m² (11.57%) decreased significantly (P < 0.01). Compared with the fetal fraction of 14.38% in the group of 18–24 years old, the fetal fraction in the maternal age group of 25–29 years old group (13.98%) (P < 0.05), 30–34 years old group (13.18%) (P < 0.01), 35–39 years old group (12.34%) (P < 0.01), and ≥ 40 years old (11.90%) group (P < 0.01) decreased significantly.

Conclusions

The percentage of fetal fraction significantly increased with increase of gestational age. Decreased fetal fraction with increasing maternal BMI was found. Maternal age was also negatively related to the fetal fraction.

Cell-free fetal DNA screening for detection of microdeletion syndromes: a cost-effectiveness analysis

OBJECTIVE

Fetuses with genetic copy number variants are poorly detected through traditional prenatal screening. Microdeletions and duplications are clearly identified with diagnostic testing through chromosomal microarray, and screening of a select number of microdeletions has become available with cell-free DNA (cfDNA). Our study compares the costs and outcomes of cfDNA for five pathogenic microdeletions and aneuploidy to cfDNA for aneuploidy alone in conjunction with ultrasound.

METHODS

A decision-analytic model was constructed using TreeAge software to compare cfDNA with microdeletions versus traditional cfDNA in a theoretical cohort of 4,000,000 pregnancies that would also be screened with ultrasound. Probabilities, costs, and utilities were derived from literature. The primary outcomes were the incremental cost per quality-adjusted life-year (QALY), terminations, and procedure-related losses. Because the microdeletion results are available, but not reported, on all cfDNA testing we set the incremental cost of the cfDNA microdeletion screening test to zero at baseline and varied the cost in sensitivity analysis.

RESULTS

Screening with cfDNA for microdeletions among all pregnant women would result in 83 fewer anomalous neonates compared to traditional cfDNA with ultrasound. This reduction is due to increased diagnosis and termination of fetuses with microdeletions in this group. Routine use of cfDNA with microdeletions resulted in more procedure-related losses. cfDNA with microdeletions would improve effectiveness by 977 QALYs and decrease costs by $90,991,784. When we varied the specificity of the screening test, we found that it remained cost-effective down to a specificity of 91%. With a threshold of $100,000/QALY, microdeletion screening is cost-effective to an incremental increase in cost over cfDNA for aneuploidy alone of $47.10.

CONCLUSION

For detection of fetal subchromosomal abnormalities, use of cfDNA with microdeletions is a cost-effective strategy compared to cfDNA for aneuploidy alone in conjunction with ultrasound. Cell-free DNA for microdeletions is not currently recommended as routine screening for low-risk obstetric populations by the American College of Obstetrics and Gynecologists or the Society for Maternal-Fetal Medicine. The test characteristics of cfDNA with microdeletions require greater examination before being routinely recommended.

Fetal cardiac abnormalities: Genetic etiologies to be considered

Congenital heart diseases are a common prenatal finding. The prenatal identification of an associated genetic syndrome or a major extracardiac anomaly helps to understand the etiopathogenic diagnosis. Besides, it also assesses the prognosis, management, and familial recurrence risk while strongly influences parental decision to choose termination of pregnancy or postnatal care. This review article describes the most common genetic diagnoses associated with a prenatal finding of a congenital heart disease and a suggested diagnostic process.

Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing

Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.

Recent trends in prenatal genetic screening and testing

Prenatal testing in recent years has been moving toward non-invasive methods to determine the fetal risk for genetic disorders without incurring the risk of miscarriage. Rapid progress of modern high-throughput molecular technologies along with the discovery of cell-free fetal DNA in maternal plasma led to novel screening methods for fetal chromosomal aneuploidies. Such tests are referred to as non-invasive prenatal tests (NIPTs), non-invasive prenatal screening, or prenatal cell-free DNA screening. Owing to many advantages, the adoption of NIPT in routine clinical practice was very rapid and global. As an example, NIPT has recently become a standard screening procedure for all pregnant women in the Netherlands. On the other hand, invasive sampling procedures remain important, especially for their diagnostic value in the confirmation of NIPT-positive findings and the detection of Mendelian disorders. In this review, we focus on current trends in the field of NIPT and discuss their benefits, drawbacks, and consequences in regard to routine diagnostics.

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.