Common Aneuploidies Research Articles

Clinical Selection of Prenatal Diagnostic Techniques Following Positive Noninvasive Prenatal Screening Results in Southwest China.

Background: This study aims to evaluate prenatal diagnosis methods following positive noninvasive prenatal screening (NIPS) results. Methods: According to the positive noninvasive prenatal screening results, 926 pregnant women were divided into three groups: main target disease group (high risk for trisomy 21, trisomy 18, or trisomy 13), sex chromosome aneuploidy (SCA) group, and other chromosomal abnormalities group [abnormal Z-scores for chromosomes other than trisomy (T)21/T18/T13 or SCAs]. The verification methods and results were then retrospectively analysed. Results: In the main target disease group, the positive rate of chromosomal abnormalities confirmed by quantitative fluorescence polymerase chain reaction (QF-PCR) was 75.18% (212/282), which was not significantly different from that by karyotyping (79.36%, 173/218) and copy number variation (CNV) detection methods (71.43%, 65/91). The positive rate of additional findings confirmed by karyotyping and copy number variation detection methods in main target disease group was 0.46% (1/218) and 8.79% (8/91), respectively. The positive rate of chromosomal abnormalities confirmed by karyotyping and CNV detection methods were 27.11% (45/166) and 38.46% (95/247) in the SCA group and 4.17% (1/24) and 20% (36/180) in the other chromosomal abnormalities group, respectively. Fetal sex chromosome mosaicism was detected in 16.13% (20/124) of the confirmed SCA cases. There were no significant differences in the detection rates of chromosomal microarray analysis (CMA) and CNV sequencing (CNVseq) among the three groups (p > 0.05). Conclusion: QF-PCR can quickly and accurately identify aneuploidies following NIPS-positive results for common aneuploidy, and in combination with karyotyping and CNV detection techniques can provide more comprehensive results. With the NIPS-positive results for SCA or other abnormalities, CMA and CNVseq may have the same effect on increasing the detection rate. The addition of fluorescence in situ hybridization assay may help to identify true fetal mosaicism.

Identification of differentially methylated genes in first-trimester placentas with trisomy 16

The presence of an extra chromosome in the embryo karyotype often dramatically affects the fate of pregnancy. Trisomy 16 is the most common aneuploidy in first-trimester miscarriages. The present study identified changes in DNA methylation in chorionic villi of miscarriages with trisomy 16. Ninety-seven differentially methylated sites in 91 genes were identified (false discovery rate (FDR) < 0.05 and Δβ > 0.15) using DNA methylation arrays. Most of the differentially methylated genes encoded secreted proteins, signaling peptides, and receptors with disulfide bonds. Subsequent analysis using targeted bisulfite massive parallel sequencing showed hypermethylation of the promoters of specific genes in miscarriages with trisomy 16 but not miscarriages with other aneuploidies. Some of the genes were responsible for the development of the placenta and embryo (GATA3-AS1, TRPV6, SCL13A4, and CALCB) and the formation of the mitotic spindle (ANKRD53). Hypermethylation of GATA3-AS1 was associated with reduced expression of GATA3 protein in chorionic villi of miscarriages with trisomy 16. Aberrant hypermethylation of genes may lead to a decrease in expression, impaired trophoblast differentiation and invasion, mitotic disorders, chromosomal mosaicism and karyotype self-correction via trisomy rescue mechanisms.

Simple and rapid detection of common fetal aneuploidies using peptide nucleic acid probe-based real-time polymerase chain reaction

To examine the detection performance of a peptide nucleic acid (PNA) probe-based real-time time polymerase chain reaction (PCR) assay to detect common aneuploidies. Using amniotic fluid samples, PNA probe based real-time PCR (Patio DEP Detection Kit; SeaSun Biomaterials, Korea) assay was performed. PNA probe was designed to hybridize to similar sequences located on different segments of target chromosomes (21, 18, and 13) and a reference chromosome. Amplification of target sequences and melting curve analysis was performed. When analyzing the melting curve, the ratio of the peak height of the target and reference chromosome was calculated and determined as aneuploidy if the ratio of peak height was abnormal. All the results from the PNA probe-based real-time PCR and melting curve analyses were compared to those from conventional karyotyping. Forty-two cases with common aneuploidies (24 of trisomy 21, 12 of trisomy 18, and 6 of trisomy 13) and 131 cases with normal karyotype were analyzed. When comparing the karyotyping results, the sensitivity and specificity of the PNA probe-based real-time PCR assay were both 100%. The level of agreement was almost perfect (k = 1.00). PNA real-time PCR assay is a rapid and easy method for detecting common aneuploidies.

What's missing in sex chromosome aneuploidies? Representation and inclusion

What's missing in sex chromosome aneuploidies? Representation and inclusion

Pubertal induction in girls with Turner Syndrome.

Turner Syndrome (TS) is the most common female sex chromosome aneuploidy in females, and patients may present with hypergonadotropic hypogonadism due to gonadal dysgenesis. Timing and modalities of pubertal induction in these patients is still a matter of debate. Aim of this review was to focus on the latest update on pubertal induction in TS. Based on literature data, the following practical approach to this issue is recommended. Pubertal induction should begin between 11 and 12 years of age, starting with low doses of estradiol to preserve height potential. Transdermal 17β-Estradiol (17β-E2) could represent the first-choice induction regimen as it is more physiologic compared to an oral regimen and avoids the first-pass mechanism in the liver. In the case of poor compliance, administration of oral 17β-E2 or ethinyl estradiol could be offered. Incremental dose increases, approximately every 6 months, can contribute to mimic normal pubertal progression until adult dosing is reached over a 2- to 3-year period. Progestin should be added once breakthrough bleeding occurs or after 2 to 3 years of estrogen therapy or if ultrasound shows a mature uterus with thick endometrium. Treatment needs to be individualized and monitored by clinical assessment in relation to patient compliance and satisfaction. Well-designed prospective randomized clinical trials aimed to identify the best estrogen regimen for pubertal induction in TS girls are needed.

Prevalence of common aneuploidy in twin pregnancies

The incidence of chromosomal abnormalities in twin pregnancies is not well-studied. In this retrospective study, we investigated the frequency of chromosomal abnormalities in twin pregnancies and compared the incidence of chromosomal abnormalities in dichorionic diamniotic (DD) and monochorionic diamniotic (MD) twins. We used data from 57 clinical facilities across Japan. Twin pregnancies of more than 12 weeks of gestation managed between January 2016 and December 2018 were included in the study. A total of 2899 and 1908 cases of DD and MD twins, respectively, were reported, and the incidence of chromosomal abnormalities in one or both fetuses was 0.9% (25/2899) and 0.2% (4/1908) in each group (p = 0.004). In this study, the most common chromosomal abnormality was trisomy 21 (51.7% [15/29]), followed by trisomy 18 (13.8% [4/29]) and trisomy 13 (6.9% [2/29]). The incidence of trisomy 21 in MD twins was lower than that in DD twins (0.05% vs. 0.5%, p = 0.007). Trisomy 21 was less common in MD twins, even when compared with the expected incidence in singletons (0.05% vs. 0.3%, RR 0.15 [95% CI 0.04–0.68]). The risk of chromosomal abnormality decreases in twin pregnancies, especially in MD twins.

Noninvasive detection of fetal genetic variations through polymorphic site sequencing of maternal plasma DNA.

Noninvasive prenatal testing (NIPT) for common fetal aneuploidies has been widely adopted in clinical practice for its sensitivity and accuracy. However, detection of pathogenic copy number variations (pCNVs) or monogenic disorders (MDs) is inaccurate and not cost effective. Here we developed an assay, the noninvasive prenatal testing based on goodness-of-fit and graphical analysis of polymorphic sites (GGAP-NIPT), to simultaneously detect fetal aneuploidies, pCNVs, and MDs. Polymorphic sites were amplicon sequenced, followed by fetal fraction estimation using allelic reads counts and a robust linear regression model. The genotype of each polymorphic site or MD variant was then determined by allelic goodness-of-fit test or graphical analysis of its different alleles. Finally, aneuploidies and pCNVs were detected using collective goodness-of-fit test to select each best fit from all possible chromosomal models. Of the simulated 1,692 chromosomes and 1,895 pCNVs, all normals and variants were correctly identified (accuracy 100%, sensitivity 100%, specificity 100%). Of the 713,320 simulated MD variants, more than 90% of the genotypes were determined correctly (accuracy: 98.3 ± 1.0%; sensitivity: 98.7 ± 1.96%; specificity: 99.7 ± 0.6%). The detection accuracies of three public MD datasets were 95.70%, 93.43%, and 96.83%. For an MD validation dataset, 75% detection accuracy was observed when a site with sample replicates was analyzed individually, and 100% accuracy was achieved when analyzed collectively. Fetal aneuploidies, pCNVs, and MDs could be detected simultaneously and with high accuracy through amplicon sequencing of polymorphic and target sites, which showed the potential of extending NIPT to an expanded panel of genetic disorders.

Methods of detection and isolation of trophoblast cells from trans-cervical specimens – a historical overview

Abstract Trophoblast cells can be detected and isolated from the cervical epithelial cells obtained via various techniques of trans-cervical samples collection such as a mucus aspiration, endocervical lavage, or standard cervical brushing in the early first trimester, even from the 5 weeks’ gestation. Isolated fetal cells can be used in the early prediction of fetal sex, prenatal diagnostics of the most common aneuploidies, and any other genetic abnormalities. Nevertheless, the collection of trophoblastic cells has limited efficacy compared to currently used methods of detection of free fetal DNA in maternal circulation or other protocols of invasive prenatal diagnostics available at later stages of pregnancy. In the past years, trans-cervical cell samples were collected mainly in women before planned pregnancy termination. The early trophoblastic cells isolation from women in ongoing pregnancies opens new perspectives for further studies focused on the elucidation of pathophysiology of numerous pregnancy-related complications.

Analysis of the effect of expanded non-invasive prenatal testing in prenatal screening population during pregnancy

To explore the clinical effect of expanded non-invasive prenatal testing (NIPT-plus) for prenatal screening. The screening result, prenatal diagnosis and pregnancy outcome of 3700 pregnant women who volunteered NIPT-plus screening at our center from September 2018 to December 2019 were reviewed. Among the 3700 pregnant women, 74(2.0%) were scored positive for clinically significant fetal chromosomal abnormalities and underwent NIPT-plus screening. Sixty three women with a high risk underwent invasive prenatal diagnosis, among whom 19 were diagnosed, which yielded a positive predictive value (PPVs) of 30.2% (19/63). Statistical analysis showed that NIPT-plus has higher PPVs for common aneuploidies and low-to-medium PPVs for sex chromosome aneuploidies and microdeletion/microduplication syndromes. As a screening technique, NIPT-plus has broader applications compared with conventional techniques, and has reference value for clinicians and pregnant women during pregnancy.

The ethical landscape(s) of non-invasive prenatal testing in England, France and Germany: findings from a comparative literature review.

Since 2019, England, France and Germany have started offering NIPT as a publicly funded second-tier test for common chromosomal aneuploidies (trisomy 21, 18 and/or 13). Despite these benefits, the introduction of NIPT into routine prenatal care also raises a number of ethical concerns. In this paper, we analyse how these issues are discussed differently across countries, echoing the different socio-political particularities and value-systems that shape the use and regulation of NIPT in a specific country. The international comparison between England, France and Germany shows how each country defines the principle of reproductive autonomy and weighs it against other principles and values, such as, human dignity, disability rights and the duty of care of health professionals. In terms of methodology, our literature review focuses on arguments and regulations of prenatal testing and reproductive choices (specifically on NIPT), through the investigation of regulatory, parliamentary, scientific, medical, association, institutional and media sources. The comparative review helps to better understand ethical questions discussed with regard to NIPT, and, more broadly, to prenatal genomic testing, and the limits associated with reproductive autonomy in the three countries studied. Whereas reproductive autonomy is valued in each country, it is understood and implemented differently depending on the socio-cultural context, and on what other principles are evoked and how they are defined.

Performance capabilities of prenatal diagnosis of chromosomal anomalies: what changed with the introduction of non-invasive prenatal test (NIPT)?

This review systematizes scientific data on the possibilities and limitations of combined prenatal screening for detecting common chromosomal abnormalities (CA) in the first trimester of pregnancy, as well as an innovative technology – non-invasive prenatal test (NIPT) based on free fetal DNA fraction. A review of current clinical guidelines on the place of NIPT in models of prenatal screening, the experience of various countries on the implementation of NIPT in national programs for prenatal screening of CA was carried out. Also, a synthesis of evidence and expert opinions on the controversial issues of the feasibility of using the extended options of NIPT (beyond the identification of common aneuploidies as trisomy 21, 13, 18) was carried out, a review of current data on the possibilities and limitations of various NIPT techniques was carried out.Despite the general increase in the sensitivity of prenatal screening for CA due to the combination of clinical, biochemical and ultrasound indicators, its main disadvantage is insufficient specificity (the frequency of false positive results of 5%). One of the ways to increase the effectiveness of prenatal screening for CA is the study of free fraction of fetal DNA (NIPT). According to a 2017 meta-analysis, the sensitivity of NIPT is more than 99% for trisomy 21, 98% for trisomy 18, and 99% for trisomy 13 with a specificity of 99%. This high efficacy has been confirmed in subsequent studies, making NIPT the best screening test for the most common trisomies – Down syndrome (trisomy 21), Edwards syndrome (trisomy 18) and Patau syndrome (trisomy 13). NIPT can be used as the first line of prenatal screening or as a second line after combined first trimester screening.Since 2015, NIPT has been included in the clinical guidelines of international and national professional societies. Common to the 11 reviewed documents is the recognition of NIPT as an important tool for increasing the efficiency of prenatal detection of CA, information about which should be provided to all pregnant women.In order for the pregnant woman to receive the maximum benefit from NIPT, pre- and post-test counseling with an explanation of the possibilities and limitations of the method in general and in the given clinical situation is crucial.

Bladder outlet obstruction

Bladder outlet obstruction

Multicystic dysplastic kidney

Multicystic dysplastic kidney

Hydroureter

Hydroureter

Renal agenesis

Renal agenesis

CLINICAL UTILITY OF HUMAN REVIEW: EXPERIENCE WITH PREVIOUSLY UNKNOWN REARRANGEMENT CARRIERS USING FAST-SEQS, A NEXT-GENERATION SEQUENCING PGT ASSAY

To report clinical preimplantation genetic testing (PGT) experience identifying previously unknown balanced rearrangement carriers using the FAST-SeqS NGS-based PGT assay. Trophectoderm biopsies were analyzed using our modified FAST-SeqS NGS-based PGT method and bioinformatics pipeline, which detects whole chromosome and segmental aneuploidies (≥10Mb), most types of polyploidy, and many instances of single chromosome uniparental isodisomy. A retrospective analysis of all embryos from patients where we suspected a parental balanced rearrangement (PBR) based on PGT-A results was performed, as identified by a recommendation for follow-up testing, either by traditional karyotyping or fluorescent in situ hybridization (FISH), on their PGT-A report. We analyzed ∼244,700 embryos from ∼39,750 patients undergoing PGT testing. Of those patients, 170 (0.43%) specifically ordered PGT-SR testing due to a known PBR. In addition, based on the PGT-A results, we suspected a previously unidentified PBR in 181 patients (0.46%). The vast majority (151/181) of patients received a recommendation on their first PGT-A cycle, with a range of 2-15 biopsies; however, 30 patients were not identified until subsequent cycles. This was due to a combination of low number of biopsies per cycle, common whole-chromosome aneuploidies, and identification of only one translocation segment. We received follow-up test results for 88 couples; all but ten (88.6%) were found to carry a PBR. Among identified PBRs, balanced reciprocal translocations were the most common (72/78); of note, due to size, three patients required FISH to demonstrate the PBR. The remaining PBRs were Robertsonian translocations and pericentric inversions (three each). The putative PBRs in the remaining ten patients may require higher resolution testing (FISH) or may be restricted to the gonads; alternatively, the pattern of abnormalities seen in the biopsies was due to random chance. Most PBR carriers are unaware of their rearrangement until karyotype analyses are performed, typically as part of an infertility workup or after an unbalanced rearrangement is detected in a pregnancy, products of conception, or child. Many IVF centers only recommend karyotype analysis after two or more miscarriages or in cases of an abnormal semen analysis. Therefore, there are patients undergoing IVF who unknowingly carry a PBR, some of whom may choose to pursue PGT-A to help increase their chances of a successful pregnancy. Astute analysis of their PGT-A results may lead to detection of the PBR. With the advances of PGT-A technology allowing for routine detection of segmental aneuploidy, more PBR carriers will be picked up through routine PGT-A testing, providing couples with an answer to their “unexplained” infertility.

Rapid Detection of Aneuploidies in Spontaneous Aborted Fetal Samples by Quantitative Fluorescence-PCR: A Descriptive Study

Chromosomal aneuploidies are the most chromosomal abnormalities at birth due to maternal meiosis I errors. Pregnancies with autosomal chromosomal aneuploidies that survive are namely trisomies 13 (Patau syndrome), 18 (Edward syndrome), and 21 (Down syndrome), account for 89% of chromosome abnormalities. Quantitative fluorescent polymerase chain reaction (QF-PCR) which amplifies specific DNA sequences called short tandem repeats (STRs), by using fluorescently labeled primers is a rapid technique for prenatal diagnosis of common aneuploidies. In this study, DNA extraction was performed from 100 samples isolated from muscle tissue of aborted fetuses. The analysis was performed by multiplex QF-PCR using a panel of 25 STRs markers for chromosomes X, Y, 13, 18, and 21. Our results showed that 20% of abortions were due to aneuploidy. 53% of mothers who had abortions were aged 26-35 years old and 32% of them were aged 36-45 years old. The analysis of muscle samples of aborted fetuses indicated that 20 samples showed chromosomal aneuploidy. Of the abnormal cases, 10 cases (~50 %) showed trisomy 21 followed by trisomy 18 (7 cases, ~35%), Klinefelter syndrome (2 cases, ~10 %), and showed trisomy X (1 case, ~5 %). Our results indicated that the D21S1414 marker showed the highest rate of heterozygosity in the study population. Besides some limitations of this study such as sample size, these results suggest that one of the causes of these abortions could be maternal age. We concluded that QF-PCR could be a rapid and reliable method to screen prenatal chromosomal aneuploidy and allow appropriate counseling.

Can the Cell-free DNA Test Predict Placenta Accreta Spectrum or Placenta Previa Totalis?

Following the discovery that fetal DNA originates from the trophoblastic cells of the placenta, the contribution of the cell-free DNA test in placenta-related obstetric complications has begun to be investigated. Compared to uncomplicated pregnancies, higher fetal fractions were detected in placenta accreta spectrum and placenta previa, which are among placenta-related obstetric complications. However, this data applies only to advanced gestational weeks. To investigate the possible predictive value of fetal fraction in cell-free DNA tests in pregnancies with placenta previa and placenta accreta spectrum in early gestational ages. This study was conducted in women who were screened via cell-free DNA tests for common aneuploidies in the first and second trimester and subsequently diagnosed with placenta previa or placenta accreta spectrum. After the diagnosis was confirmed with a C-section, fetal fractions were retrospectively compared to a control group with a history of an uncomplicated C-section who were also previously screened by cell-free DNA test. The median and interquartile range (IQR) of fetal fractions for placenta previa (n=19), placenta accreta spectrum (n=7), and control groups (n=85) were 8.1 (6-10), 6.8 (6.7-10.7), and 7.1 (4.7-9.65), respectively. No statistically significant difference was observed among the three groups in terms of fetal fractions (p=0.587). According to our data, we did not observe any relationship between placental invasion abnormalities vs. control group or placenta previa vs. control group using the fetal fractions of the cell-free DNA test. Furthermore, we could not confirm a predictive role and/or any additional clinical contribution. We believe that future studies focusing on placental mRNA might be more helpful than cell-free fetal DNA testing.

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.

Performance of a universal prenatal screening program incorporating cell-free fetal DNA analysis in Ontario, Canada.

BACKGROUND:The emergence of cell-free fetal DNA (cfDNA) testing technology has disrupted the landscape of prenatal screening for trisomies 21 (T21) and 18 (T18). Publicly funded systems around the world are grappling with how to best integrate this more accurate but costly technology, as there is limited evidence about its incremental value in real-world conditions. The objectives of this study were to describe the population-based performance of Ontario’s prenatal screening program, which incorporates publicly funded cfDNA screening for specific indications, and the effect of cfDNA testing on the screening and diagnostic choices made by pregnant people.METHODS:We conducted a retrospective, descriptive cohort study using routinely collected data from Better Outcomes & Registry Network (BORN) Ontario, which captures linked population data for prenatal and neonatal health encounters across Ontario. We included all singleton pregnancies with an estimated due date between Sept. 1, 2016, and Mar. 31, 2019, that underwent publicly funded prenatal screening in Ontario, and a comparison cohort from Apr. 1, 2012, and Mar. 31, 2013. We assessed performance of the screening program for the detection of T21 or T18 by calculating sensitivity, specificity, positive predictive value and negative predictive value against diagnostic cytogenetic results or birth outcomes. We assessed the impact of the program by calculating the proportion of T21 screen-positive pregnancies undergoing subsequent cfDNA screening and invasive prenatal diagnostic testing.RESULTS:The study cohort included 373 682 pregnancies. The prenatal screening program had an uptake of 69.9%, a screen-positive rate and sensitivity of 1.6% and 89.9% for T21, and 0.2% and 80.5% for T18, respectively. The test failure rate for cfDNA screening was 2.2%. Invasive prenatal diagnostic testing decreased from 4.4% in 2012–2013 to 2.4% over the study period; 65.2% of pregnant people who received a screen-positive result from cfDNA testing went on to have invasive prenatal diagnostic testing.INTERPRETATION:This publicly funded screening program, incorporating cfDNA analysis for common aneuploidies, showed robust performance, a substantial reduction in invasive prenatal diagnostic testing and that pregnant people exercise autonomy in their choices about prenatal screening and diagnosis.