Have we done our last amniocentesis? Updates on cell-free DNA for Down syndrome screening

Rapid non-invasive prenatal screening test for trisomy 21 based on digital droplet PCR

Non-invasive prenatal tests for the detection of fetal aneuploidies are predominantly based on the analysis of cell-free DNA (cfDNA) from the plasma of pregnant women by next-generation sequencing. The development of alternative tests for routine genetic laboratories is therefore desirable. Multiplex digital droplet PCR was used to detect 16 amplicons from chromosome 21 and 16 amplicons from chromosome 18 as the reference. Two fluorescently labeled lock nucleic acid probes were used for the detection of reaction products. The required accuracy was achieved by examining 12 chips from each patient using Stilla technology. The plasma cfDNA of 26 pregnant women with euploid pregnancies and 16 plasma samples from pregnancies with trisomy 21 were analyzed to determine the cutoff value for sample classification. The test was validated in a blind study on 30 plasma samples from pregnant patients with a risk for trisomy 21 ranging from 1:4 to 1:801. The results were in complete agreement with the results of the invasive diagnostic procedure (sensitivity, specificity, PPV, and NPV of 100%). Low cost, and speed of analysis make it a potential screening method for implementation into the clinical workflow to support the combined biochemical and ultrasound results indicating a high risk for trisomy 21.

The effectiveness of non-invasive prenatal test technology and the prenatal screening algorithm based on various methods for determining foetal aneuploidy

Objective

The purpose was to evaluate the effectiveness of a non-invasive prenatal test (NIPT) using mass parallel sequencing (MPS) to detect trisomy 13, 18, 21 and fetal sex chromosome abnormalities in maternal blood samples by isolating freely circulating foetal extracellular DNA (eDNA), and to develop an algorithm for prenatal screening.

Material and Methods

The research methods used included blood sampling from patients, isolation of eDNA, determination of DNA concentration and quality, library preparation for sequencing, MPS using an Illumina HiSeq2000, positive and negative control samples, monitoring, and analysis of results using the distributed algorithms platform based on calculations of z-value and the average absolute deviation. Pregnant women were divided into two groups based on gestational age at sampling, group 1; 9-14 weeks and group 2; 15-27 weeks.

Results

A total of 377 pregnant women were included with a mean (range) age of 33 (23-44) years. The mean gestational age at the time of blood sampling in group 1 was 11 (9-14) weeks, and in group 2 was 21 (15-27) weeks. In the first group, three cases of trisomy 18 chromosomes were detected in patients aged 43 years old, and female children were subsequently born with Edwards syndrome. In the second group, one case of trisomy 21 was detected in a patient aged 36 years and the pregnancy was terminated at 25 weeks.

Conclusion

The analysis of freely circulating foetal eDNA was a sensitive method for detecting chromosomal abnormalities. The study has a practical significance, since the NIPT for frequent aneuploidy considerably exceeds the effectiveness of traditional screening methods and allows identifying chromosomal disorders starting from the 9th week of the gestation period.

Incidental finding of maternal malignancy in an unusual non-invasive prenatal test and a review of similar cases

We present a clinical case where a complex abnormal non-invasive prenatal test (NIPT) result in a research project revealed carcinoma of the breast in the pregnant woman. Furthermore, the NIPT result did not demonstrate the same fetal chromosomal aberration as the chorion villus sample. A literature search for similar cases was performed identifying 43 unique cases, where abnormal NIPT results were related to maternal malignancy. Malignancy is a rare but important cause of complex abnormal non-invasive prenatal test (NIPT) results and should be considered when fetal karyotype and abnormal NIPT results are discordant. Furthermore, a follow-up invasive sample is essential for correct fetal diagnosis when abnormal NIPT results are found.

Application of Combined Ultrasound and Maternal Serum Biochemical Indexes in the Detection of Fetal Structural Abnormalities and Chromosomal Abnormalities

By exploring different prenatal diagnosis indications of fetal chromosomal abnormalities, it can provide a theoretical basis and reference value for clinical consultation of pregnant women with similar high-risk factors. In this paper, 1800 pregnant women undergoing amniotic fluid aspiration chromosomal examination in the prenatal diagnosis center were selected as the object of this study. Amniocentesis, fetal cell culture, and karyotype analysis were performed on pregnant women who were 14-20 weeks pregnant and had signed an informed consent. After amniocentesis fetal chromosome analysis, the type of fetal chromosomal abnormality was determined, and the detection rate of chromosomal abnormality was statistically described. Chi-square test was used for comparison between groups, P < 0.05. This study shows that the use of ultrasound screening combined with maternal serum indicators is effective in screening fetal structural abnormalities and chromosomal abnormalities in early pregnancy, and significantly improves the detection rate of chromosomal abnormalities. The detection of fetal structural malformations is also very high, but it should be combined with ultrasound screening of mid-to-late pregnancy. The tricuspid regurgitation and umbilical vein a-wave reversal in the soft ultrasound index can be used as predictors of fetal congenital heart disease in early pregnancy.

Risk stratification for early-onset fetal growth restriction in women with abnormal serum biomarkers: a retrospective cohort study

Abnormal maternal serum biomarkers (AMSB), identified through the aneuploidy screening programme, are frequent incidental findings in pregnancy. They are associated with fetal growth restriction (FGR), but previous studies have not examined whether this association is with early-onset (< 34 weeks) or late-onset (> 34 weeks) FGR; as a result there is no consensus on management. The aims of this study were to determine the prevalence and phenotype of FGR in women with AMSB and test the predictive value of placental sonographic screening to predict early-onset FGR. 1196 pregnant women with AMSB underwent a 21-24 week "placental screen" comprising fetal and placental size, and uterine artery Doppler. Multivariable regression was used to calculate a predictive model for early-onset FGR (birthweight centile < 3rd/< 10th with absent umbilical end-diastolic flow, < 34 weeks). FGR prevalence was high (10.3%), however early-onset FGR was uncommon (2.3%). Placental screening effectively identified early-onset (area under the curve (AUC) 0.93, 95% confidence interval (CI) 0.87-1.00), but not late-onset FGR (AUC 0.70, 95% CI 0.64-0.75). Internal validation demonstrated robust performance for detection/exclusion of early-onset FGR. In this cohort, utilisation of our proposed algorithm with targeted fetal growth and Doppler surveillance, compared with universal comprehensive surveillance would have avoided 1044 scans, potentiating significant cost-saving for maternity services.

The Level of Free Fetal DNA as Precise Noninvasive Marker for Chromosomal Aneuploidies: First Results from BALTIC Region

Background and objectives: Noninvasive prenatal testing (NIPT), which has been introduced clinically since 2011, uses the circulating cell-free fetal DNA in the maternal blood to evaluate the risk of a chromosomal anomaly. The aim of this study was to examine the effectiveness of NIPT using a single nucleotide polymorphism method. Materials and Methods: A retrospective study was conducted between 2013 and 2019. The Natera Panorama test was used to analyze the risk of trisomies 21, 18, 13, X monosomy, trisomy, and other sex chromosome abnormalities. A positive result of NIPT for aneuploidy was confirmed by invasive testing. Results: 850 women with a singleton pregnancy participated in the study. The median fetal fraction was 9.0%. The fetal fraction was lower in the no-call group (3.1%) compared with the group that received a call (9.1%) (p < 0.001). A positive correlation was determined between the gestational age and the fetal fraction (r = 0.180, p < 0.001). The overall positive predictive value (PPV) of NIPT for trisomy 21 (n = 9), trisomy 18 (n = 3) and XYY syndrome (n = 1) was 100%. Conclusions: The results of present study showed 100% PPV effectiveness of NIPT Panorama test detecting trisomies of 21 and 18 chromosomes, as well as XYY syndrome in the studied cohort. Therefore, NIPT due to its high PPV, significantly reduces the need for invasive testing, thereby reducing the risk of miscarriage and stillbirth.

CRISPR/cas systems redefine nucleic acid detection: Principles and methods

Methods that enable rapid, sensitive and specific analyses of nucleic acid sequences have positive effects on precise disease diagnostics and effective clinical treatments by providing direct insight into clinically relevant genetic information. Thus far, many CRISPR/Cas systems have been repurposed for diagnostic functions and are revolutionizing the accessibility of robust diagnostic tools due to their high flexibility, sensitivity and specificity. As RNA-guided targeted recognition effectors, Cas9 variants have been utilized for a variety of diagnostic applications, including biosensing assays, imaging assays and target enrichment for next-generation sequencing (NGS), thereby enabling the development of flexible and cost-effective tests. In addition, the ensuing discovery of Cas proteins (Cas12 and Cas13) with collateral cleavage activities has facilitated the development of numerous diagnostic tools for rapid and portable detection, and these tools have great potential for point-of-care settings. However, representative reviews proposed on this topic are mainly confined to classical biosensing applications; thus, a comprehensive and systematic description of this fast-developing field is required. In this review, based on the detection principle, we provide a detailed classification and comprehensive discussion of recent works that harness these CRISPR-based diagnostic tools from a new perspective. Furthermore, current challenges and future perspectives of CRISPR-based diagnostics are outlined.

Direct comparison of QIAamp DSP Virus Kit and QIAamp Circulating Nucleic Acid Kit regarding cell-free fetal DNA isolation from maternal peripheral blood

BACKGROUND

Blood of pregnant women contains cell-free fetal DNA (cffDNA), which is widely used in non-invasive prenatal diagnosis. The modern laboratory equipment market provides huge variety of commercial kits for isolation of circulating nucleic acids, but unfortunately none of them are standardized for isolation of cffDNA, which is a crucial step for success of subsequent analysis.

AIM

To compare DSPVK and CNAK in terms of cffDNA, cell-free total DNA (cftDNA) yield and resulting cffDNA fraction, as well as to try to explain the possible difference between the efficacy of these kits.

METHODS

Peripheral blood samples were collected from 18 healthy pregnant women (6^th-14th week of pregnancy) and from 12 healthy unpregnant subjects. cftDNA was isolated using QIAamp Circulating Nucleic Acid Kit (CNAK) (Qiagen, Germany) and QIAamp DSP Virus Kit (DSPVK) (Qiagen, Germany) from 1 ml of plasma of each sample. Methylation-sensitive restriction was carried out to isolate cffDNA. Yield of cffDNA and cftDNA was quantified using digital PCR. To explain the difference in resulting efficacy of these two kits PCR inhibitors analysis was performed, as well as the optimal plasma input for DSPVK was investigated.

RESULTS

Yield of cffDNA using CNAK was statistically significantly higher than using DSPVK (167.62 (125.34-192.47) vs 52.88 (35.48-125.42) GEq/mL, p < 0.001). The same applies to cftDNA yield, CNAK appears to be statistically significantly superior to DSPVK (743.42 (455.02-898.33) vs 371.07 (294.37-509.89) GEq/mL, p < 0.001). cffDNA fraction using CNAK was also higher than using DSVPK (24.75 (14.5-31.53) vs 14.20 (6.88-25.83) %, p = 0.586), although the difference was not statistically significant due to inconsistency of DSPVK results from sample to sample. PCR inhibitors analysis uncovered increased amount of PCR inhibitors in CNAK cftDNA solution, compared to DSPVK (p = 0.002). Usage of 0.5 mL of plasma for cftDNA extraction with DSPVK over 1 mL demonstrates almost 1.8 times higher cftDNA output (p = 0.028), which suggests that this kit is not so viable for volumes of plasma larger than 0.5 mL.

CONCLUSIONS

We recommend CNAK over DSPVK for quantitative analysis of cffDNA. Nevertheless, DSPVK is definitely suitable for qualitative analysis as well as for research with limited budget, since it is almost 3 times cheaper than CNAK.