Clinical Utility of Noninvasive Prenatal Screening for Rare Chromosome Abnormalities in Singleton Pregnancies

Objective: To systematically investigate the clinical utility of noninvasive prenatal screening (NIPS) commercially used for the common fetal aneuploidies as a prenatal screening tool for rare chromosome abnormalities (RCAs). Design: Prospective study. Setting: Hospital-based. Population or Sample: 528 gravidas with positive NIPS results for RCAs. Methods: Gravidas with positive NIPS results for RCAs subsequently underwent amniocentesis for single nucleotide polymorphism array (SNP-array) were recruit. The degrees of concordance between NIPS and SNP-array were classified into full concordance, partial concordance, discordance related and discordance. Main Outcome Measures: The positive predictive values (PPVs) for rare aneuploidies and segmental imbalances, while incidental findings for regions of homozygosity/uniparental disomy (ROH/UPD), were used to evaluate the performance of NIPS. Results: Of the 528 gravidas with positive NIPS results, 29.2% were confirmed with positive prenatal SNP-array results (154/528). The PPVs for rare aneuploidies and segmental imbalances were 6.1% (7/115) and 21.1% (87/413), respectively. ROH/UPDs, as incidental findings, have been identified in 9.5% (50/528) of gravidas with positive NIPS results. The PPV for clinical significant findings was 8.9% (47/528), including 7 cases with mosaic rare aneuploidies, 35 with pathogenic/likely pathogenic copy number variants, and 5 with imprinting disorders. Conclusions: NIPS commercially used for the common fetal aneuploidies yielded low PPV for rare aneuploidies, moderate PPV for segmental imbalances, and incidental findings for ROH/UPD. For the low PPV for clinical significant findings, NIPS has limited clinical utility for RCAs. Prenatal SNP-array should be regarded as the first-tier test for positive NIPS, particularly for those involved imprinted chromosomes.

The Influence of Maternal Cell Contamination on Fetal Aneuploidy Detection Using Chip-Based Digital PCR Testing

Prenatal samples obtained by amniocentesis or chorionic villus sampling are at risk of maternal cell contamination (MCC). In traditional prenatal analysis, MCC is recommended to be assayed by special tests, such as the short tandem repeat analysis and, if detected at a high level, may result in failed analysis report. The objective of this study was to test the ability of chip-based digital PCR to detect fetal aneuploidies in the presence of MCC. To determine the level of accuracy of MCC detection, an aneuploid male sample was subjected to serial dilution with an euploid female sample. DNA was extracted from prenatal samples and analyzed with QuantStudio 3D Digital PCR. Digital PCR analysis allowed the detection of trisomy 21, trisomy 18, and X monosomy accurately in samples with 90%, 85%, and 92% of MCC, respectively. Moreover, our results indicated that digital PCR was able to accurately confirm the presence of Y chromosome at up to 95% contamination. The amniotic fluid and chorionic villus sampling (CVS) received in our clinical laboratory was subjected to further analysis of MCC based on the aneuploidy assessment algorithm, resulting in the identification of 10 contaminated samples and four cases of true fetal mosaicism. We conclude that chip-based digital PCR analysis enables the detection of fetal aneuploidy with high levels of accuracy, even in cases of significant MCC. Importantly, the algorithm eliminates the need for maternal DNA and additional MCC tests, which reduces costs and simplifies the diagnostic procedure. The method is easy to set up and suitable for routine clinical practice.

Assessment and Clinical Utility of a Non-Next-Generation Sequencing-Based Non-Invasive Prenatal Testing Technology

Background: Rolling-circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus, and 25 synthetic samples, were analyzed for the fetal risk of trisomy 21 (T21), trisomy 18 (T18) and trisomy 13 (T13), by three laboratories on three continents. All the screen-positive pregnancies were provided post-test genetic counseling and confirmatory diagnostic invasive testing (e.g., amniocentesis). The screen-negative pregnancies were routinely evaluated at birth for fetal aneuploidies, using newborn examinations, and any suspected aneuploidies would have been offered diagnostic testing or confirmed with karyotyping. Results: The study found rolling-circle replication to be a highly viable technology for the clinical assessment of fetal aneuploidies, with 100% sensitivity for T21 (95% CI: 82.35–100.00%); 100.00% sensitivity for T18 (71.51–100.00%); and 100.00% sensitivity for T13 analyses (66.37–100.00%). The specificities were >99% for each trisomy (99.7% (99.01–99.97%) for T21; 99.5% (98.62–99.85%) for T18; 99.7% (99.03–99.97%) for T13), along with a first-pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling-circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening, and it would provide comparable results to other reported cfDNA methodologies.

Assessment and clinical utility of a non-Next Generation Sequencing based Non-Invasive Prenatal Testing technology

Background: Rolling circle replication (RCR) is a novel technology that has not been applied to cell-free DNA (cfDNA) testing until recently. Given the cost and simplicity advantages of this technology compared to other platforms currently used in cfDNA analysis, an assessment of RCR in clinical laboratories was performed. Here, we present the first validation study from clinical laboratories utilizing RCR technology. Methods: 831 samples from spontaneously pregnant women carrying a singleton fetus and 25 synthetic samples were analyzed for the fetal risk of Trisomy 21, Trisomy 18 and Trisomy 13 by three laboratories on three continents. All women who provided the samples were followed to birth, where evaluation for fetal aneuploidies was performed using newborn examinations and any suspected aneuploidies were confirmed with karyotyping. Results: The study found rolling circle replication to be a highly viable technology for clinical assessment of fetal aneuploidies with 100% sensitivity for T21 (95% CI:82.35% - 100.00%); 100.00% sensitivity for T18 (71.51% - 100.00%) and 100.00% sensitivity for T13 analyses (66.37% - 100.00%). The specificities were >99% for each trisomies [99.7% (99.01% - 99.97%) for T21; 99.5% (98.62% - 99.85%) for T18; 99.7% (99.03% - 99.97%) for T13], along with a first pass no-call rate of 0.93%. Conclusions: The study showed that using a rolling circle replication-based cfDNA system for the evaluation of the common aneuploidies would provide greater accuracy and clinical utility compared to conventional biochemical screening and comparable results to other reported cfDNA methodologies.

Quadruple Screening in the Age of Cell-Free DNA: What are We Losing?

Cell-free DNA has emerged as the most reliable, non-invasive prenatal screening tool for fetal aneuploidies. It has come to replace the previously widely used quadruple screen offered in the second trimester of pregnancy. This change comes with improved detection for aneuploidy but also presents potential gaps in prenatal diagnosis including detection of open fetal defects and emerging data on prediction of adverse pregnancy outcomes. This review article provides a historical summary of the quadruple marker screen and evaluates the intersection of this screen with cell-free DNA. Furthermore, it discusses points to consider as providers trend toward cell-free DNA testing alone and reviews potential options to remedy any disparities.

Noninvasive prenatal detection of fetal sex chromosome abnormalities using the semiconductor sequencing platform (SSP) in Southern China

Background Noninvasive prenatal testing (NIPT) has been widely used to screen for fetal aneuploidies, including fetal sex chromosome aneuploidies (SCAs). However, there is less information on the performance of NIPT in detecting SCAs. Methods A cohort of 47,800 pregnancies was recruited to review the high-risk NIPT results for SCAs. Cell-free fetal DNA (cffDNA) was extracted and sequenced. All NIPT high-risk cases were recommended to undergo invasive prenatal diagnosis for karyotyping analysis and chromosome microarray analysis (CMA). Results A total of 238 high-risk cases were detected by NIPT, including 137 cases of 45,X, 27 cases of 47,XXX, and 74 cases of 47,XYY/47,XXY. Prenatal diagnosis, including karyotyping analysis and CMA, was available in 170 cases. The positive predictive value (PPV) was 30.00% for 45,X, 70.58% for 47,XXX, and 81.13% for 47,XYY/47,XXY. In addition, 13 cases of sex chromosome mosaicism and 9 cases of sex chromosome CNVs were incidentally found in this study. Conclusion Our study showed that NIPT was reliable for screening SCAs based on a large sample, and it performed better in predicting sex chromosome trisomies than monosomy X. Our study will provide an important reference for clinical genetic counseling and further processing of the results.

Noninvasive Detection of Fetal Genetic Variations through Polymorphic Sites Sequencing of Maternal Plasma DNA

Non-invasive prenatal testing (NIPT) for common fetal aneuploidies using circulating cell free DNA in maternal plasma has been widely adopted in clinical practice for its sensitivity and accuracy. However, the detection of subchromosomal abnormalities or monogenetic variations using such a method showed no cost-effectiveness or satisfactory accuracy. Here we show that with the aid of polymorphic sites sequencing, fetal fraction of the sample and genotype of the target site were determined with high accuracy. Then genetic variations at the chromosomal, subchromosomal and nucleotide levels were detected using the overall allelic goodness-of-fit test of all target polymorphic sites to each possible genetic model. Finally, relative allelic distributions for each amplicon were visualized and genetic variations at the chromosomal, subchromosomal and nucleotide levels were determined by distinct characteristic clusters on allelic distribution plot of each possible genetic model. As no parental genetic information was required and all allelic information retained for amplicon sequencing, the reported approach has the potential to simultaneously detect genetic variations at different levels, facilitating the extension of NIPT to all common genetic conditions for general low-risk pregnancies and target variations for certain high-risk pregnancy groups.