Non-Invasive Prenatal Testing: Current Perspectives and Future Challenges

Fetal aneuploidies are among the most common causes of miscarriages, perinatal mortality and neurodevelopmental impairment. During the last 70 years, many efforts have been made in order to improve prenatal diagnosis and prenatal screening of these conditions. Recently, the use of cell-free fetal DNA (cff-DNA) testing has been increasingly used in different countries, representing an opportunity for non-invasive prenatal screening of pregnant women. The aim of this narrative review is to describe the state of the art and the main strengths and limitations of this test for prenatal screening of fetal aneuploidies.

Fetal Tachycardia Is an Independent Risk Factor for Chromosomal Anomalies in First-Trimester Genetic Screening

OBJECTIVES

The association of an abnormal fetal heart rate (FHR) and chromosomal anomalies in the first trimester of pregnancy remains unclear, probably because of the lack of control for known confounding factors. This study was designed to determine whether an increased FHR is an independent risk factor for chromosomal anomalies between 11 and 14 weeks' gestation.

METHODS

This cohort study included women who underwent first-trimester genetic screening between 2011 and 2014 at a single institution. A multivariable logistic regression analysis was performed to determine whether an FHR of 170 beats per minute (bpm) or higher, derived from a receiver operating characteristic curve, is an independent risk factor for all chromosomal anomalies while controlling for known confounding factors. P < .05 was considered significant.

RESULTS

An FHR of 170 bpm or higher was observed in 7% (228 of 3254), and chromosomal anomalies were present in 1.0% (31 of 3254) of the population. A higher proportion of fetuses with an FHR of 170 bpm or higher had chromosomal anomalies compared to those with an FHR lower than 170 bpm. An FHR of 170 bpm or higher was an independent risk factor for chromosomal anomalies after controlling for known confounding factors. Of note, in the group of fetuses with a nuchal translucency above the 95th percentile, the frequency of chromosomal anomalies was significantly higher among fetuses with an FHR of 170 bpm or higher compared to those with an FHR lower than 170 bpm.

CONCLUSIONS

Fetal tachycardia is a risk factor for chromosomal anomalies during first-trimester genetic screening, independent of increased nuchal translucency, nuchal septations, and maternal age.

Cell-free DNA and contingent screening: Our first year

INTRODUCTION

Analysis of cell-free DNA (cfDNA) from maternal blood has showed a great potential as a screening method for fetal aneuploidies. cfDNA can be used as a first line screening tool or in a contingent model, after the combined test.

METHODS

Prospective study of women attending for first trimester combined screening in our Hospital, in the first year of contingent cfDNA screening. According to the combined screening test result patients were divided in high-risk (offered invasive test or routine follow-up), intermediate-risk (counselled for cfDNA, invasive or routine follow-up) or low-risk (routine ultrasound follow-up). Pregnancy outcomes and performance of screening were evaluated. A cost-effectiveness analysis was also done.

RESULTS

The majority of the 1272 enrolled participants were Caucasian (82,6%), multiparous (51,7%) and the median maternal age was 30 years old. Thirty women screened high-risk and 83,3% of them opted for an invasive test. Forty-nine patients had an intermediate risk and 75,5% of them choose cfDNA testing. Our rate of invasive tests decreased from 3.5% to 2.4%.

DISCUSSION

The cut-offs used to determine high and intermediate-risk are based on a compromise between detection rate, pregnancy lost rate and cost. Above a determined cut-off in the intermediate-risk group, the cost for each additional detected trisomy case is very high. One major benefit of this contingent model was the decrease in invasive testing.

CONCLUSION

The contingent cfDNA screening model can be easily implemented in a public hospital with a low-risk population. Since cost/benefit is an important issue, further studies are needed to determine the ideal cut-off for our country.

Evaluation of Noninvasive Prenatal Testing (NIPT) guidelines using the AGREE II instrument

Objective: The rapid increase of cell-free fetal DNA analysis for Down syndrome screening requires evidence-based clinical practice guidelines for noninvasive prenatal testing (NIPT). Several studies show that the quality of many guidelines is low and there are still many health areas where this quality is not systematically evaluated. Given the absence of research, in the NIPT field, we used an internationally validated tool to evaluate a set of three NIPT practice guidelines and to look at dimensions that can be improved.Methods: Four appraisers, experts in prenatal screening, evaluated three main NIPT guidelines published in the last 2 years using the AGREE II (Appraisal of Guidelines for Research and Evaluation II), a tool specifically designed for guideline quality appraisal.Results: Guidelines scored higher in domains related with scope, purpose, and clarity of presentation, and lower in stakeholder involvement and rigor of development. Intradomain items evaluation showed asymmetries between guidelines. The UK-NSC was the guideline with the best scores.Discussion: Several areas of NIPT guidelines, such as stakeholders involvement, selection of supporting evidence, external reviews, updating processes, and competing interests disclosure, can be improved. Appraisers recommend modifications to all NIPT guidelines that can lead to substantial improvements in their methodological quality and subsequently make a contribution to prenatal screening improvement.

Diagnosis of Sepsis with Cell-free DNA by Next-Generation Sequencing Technology in ICU Patients

BACKGROUND AND AIMS

Bacteremia is a common serious manifestation of disease in the intensive care unit (ICU), which requires quick and accurate determinations of pathogens to select the appropriate antibiotic treatment. To overcome the shortcomings of traditional bacterial culture (BC), we have adapted next-generation sequencing (NGS) technology to identify pathogens from cell-free plasma DNA.

METHODS

In this study, 78 plasma samples from ICU patients were analyzed by both NGS and BC methods and verified by PCR amplification/Sanger sequencing and ten plasma samples from healthy volunteers were analyzed by NGS as negative controls to define or calibrate the threshold of the NGS methodology.

RESULTS

Overall, 1578 suspected patient samples were found to contain bacteria or fungi by NGS, whereas ten patients were diagnosed by BC. Seven samples were diagnosed with bacterial or fungal infection both by NGS and BC. Among them, two samples were diagnosed with two types of bacteria by NGS, whereas one sample was diagnosed with two types of bacteria by BC, which increased the detectability of bacteria or fungi from 11 with BC to 17 with NGS. Most interestingly, 14 specimens were also diagnosed with viral infection by NGS. The overall diagnostic sensitivity was significantly increased from 12.82% (10/78) by BC alone to 30.77% (24/78) by NGS alone for ICU patients, which provides more useful information for establishing patient treatment plans.

CONCLUSION

NGS technology can be applied to detect bacteria in clinical blood samples as an emerging diagnostic tool rich in information to determine the appropriate treatment of septic patients.

A prospective clinical trial to compare the performance of dried blood spots prenatal screening for Down's syndrome with conventional non-invasive testing technology

To evaluate, side by side, the efficiency of dried blood spots (DBSs) against serum screening for Down's syndrome, and then, to construct a two-tier strategy by topping up the fetal cell-free DNA (cfDNA) secondary screening over the high-risk women marked by the primary blood testing to build a practical screening tactic to identify fetal Down's syndrome. One thousand eight hundred and thirty-seven low-risk Chinese women, with singleton pregnancy, were enrolled for the study. Alpha-fetoprotein and free beta human chorionic gonadotropin were measured for the serum as well as for the parallel DBS samples. Partial high-risk pregnant women identified by primary blood testing (n = 38) were also subject to the secondary cfDNA screening. Diagnostic amniocentesis was utilized to confirm the screening results. The true positive rate for Down's syndrome detection was 100% for both blood screening methods; however, the false-positive rate was 3.0% for DBS and 4.0% for serum screening, respectively. DBS correlated well with serum screening on Down's syndrome detection. Three out of 38 primary high-risk women displayed chromosomal abnormalities by cfDNA analysis, which were confirmed by amniocentesis. Either the true detection rate or the false-positive rate for Down's syndrome between DBS and the serum test is comparable. In addition, blood primary screening aligned with secondary cfDNA analysis, a "before and after" two-tier screening strategy, can massively decrease the false-positive rate, which, then, dramatically reduces the demand for invasive diagnostic operation. Impact statement Children born with Down's syndrome display a wide range of mental and physical disability. Currently, there is no effective treatment to ease the burden and anxiety of the Down's syndrome family and the surrounding society. This study is to evaluate the efficiency of dried blood spots against serum screening for Down's syndrome and to construct a two-tier strategy by topping up the fetal cell-free DNA (cfDNA) secondary screening over the high-risk women marked by the primary blood testing to build a practical screening tactic to identify fetal Down's syndrome. Results demonstrate that fetal cfDNA can significantly reduce false-positive rate close to none while distinguishing all true positives. Thus, we recommend that fetal cfDNA analysis to be utilized as a secondary screening tool atop of the primary blood protein screening to further minimize the capacity of undesirable invasive diagnostic operations.

Should cell-free fetal DNA be included in first trimester screening (FTS) for common trisomy? A possible scenario on 6697 women screened over 10 years

OBJECTIVE

The primary aim was to determine the performance of the first trimester screening (FTS) test in a general obstetrics population. Cost-benefit analysis of a hypothetic model based on implementation of the FTS test by cell-free fetal (cff) DNA was calculated.

METHODS

A total of 6697 women were screened using FTS test. A two-step strategy based upon nuchal translucency, serum screening and ultrasound assessment of nasal bone (NB) was applied. Three groups were identified (high-risk: >1:250; intermediate-risk: 1:251-1:999 and low-risk group: <1:1000). Women at intermediate-risk (1:251-1:999) underwent NB assessment and recalculation of individual risk. All women at high-risk were offered fetal karyotyping.

RESULTS

A total of 321 women (4.8%) resulted at high-risk while 480 women (7.1%) with intermediate-risk underwent assessment of the NB, which was absent in 15 fetuses. Overall, 54 aneuploidies were detected for a 96.4% sensitivity, a 96.1% specificity, a 99.9% negative predictive value and a false positive rate of 4.8%. Audit was conducted on a yearly basis and lost to follow up was 0.47% (32 cases).

CONCLUSIONS

Public health system would not be able to cover the cost of including cff DNA in women undergoing first trimester screening on universal basis. However, assuming a possible scenario based on implementation of FTS by cff DNA in women at high-risk would result in a 6-fold reduction in the number of invasive procedures while avoiding two false negative results (trisomy 21) that were diagnosed in women with intermediate-risk using current screening strategy by combined test.

Down syndrome-A narrative review with a focus on anatomical features

Down syndrome (DS) is the most common aneuploidy of chromosome 21, characterized by the presence of an extra copy of that chromosome (trisomy 21). Children with DS present with an abnormal phenotype, which is attributed to a loss of genetic balance or an excess dose of chromosome 21 genes. In recent years, advances in prenatal screening and diagnostic tests have aided in the early diagnosis and appropriate management of fetuses with DS. A myriad of clinical symptoms resulting from cognitive, physical, and physiological impairments caused by aberrations in various systems of the body occur in DS. However, despite these impairments, which range from trivial to fatal manifestations, the survival rate of individuals with DS has increased dramatically from less than 50% during the mid-1990s to 95% in the early 2000s, with a median life expectancy of 60 years reported recently. The aim of this narrative review is to review and summarize the etiopathology, prenatal screening and diagnostic tests, prognosis, clinical manifestations in various body systems, and comorbidities associated with DS. Clin. Anat. 29:568-577, 2016. © 2015 Wiley Periodicals, Inc.

Pre- and post-test genetic counseling for chromosomal and Mendelian disorders

Genetic carrier screening, prenatal screening for aneuploidy, and prenatal diagnostic testing have expanded dramatically over the past 2 decades. Driven in part by powerful market forces, new complex testing modalities have become available after limited clinical research. The responsibility for offering these tests lies primarily on the obstetrical care provider and has become more burdensome as the number of testing options expands. Genetic testing in pregnancy is optional, and decisions about undergoing tests, as well as follow-up testing, should be informed and based on individual patients' values and needs. Careful pre- and post-test counseling is central to supporting informed decision-making. This article explores three areas of technical expansion in genetic testing: expanded carrier screening, non-invasive prenatal screening for fetal aneuploidies using cell-free DNA, and diagnostic testing using fetal chromosomal microarray testing, and provides insights aimed at enabling the obstetrical practitioner to better support patients considering these tests.

Cell-Free Fetal DNA Testing for Prenatal Diagnosis

Prenatal diagnosis and screening have undergone rapid development in recent years, with advances in molecular technology driving the change. Noninvasive prenatal testing (NIPT) for Down syndrome as a highly sensitive screening test is now available worldwide through the commercial sector with many countries moving toward implementation into their publically funded maternity systems. Noninvasive prenatal diagnosis (NIPD) can now be performed for definitive diagnosis of some recessive and X-linked conditions, rather than just paternally inherited dominant and de novo conditions. NIPD/T offers pregnant couples greater choice during their pregnancy as these safer methods avoid the risk of miscarriage associated with invasive testing. As the cost of sequencing falls and technology develops further, there may well be potential for whole exome and whole genome sequencing of the unborn fetus using cell-free DNA in the maternal plasma. How such assays can or should be implemented into the clinical setting remain an area of significant debate, but it is clear that the progress made to date for safer prenatal testing has been welcomed by expectant couples and their healthcare professionals.

Impact of Including or Removing Nuchal Translucency Measurement on the Detection and False-Positive Rates of First-Trimester Down Syndrome Screening

INTRODUCTION

First-trimester Down syndrome (DS) screening combining maternal age, serum markers (pregnancy-associated plasma protein-A and beta-human chorionic gonadotropin) and nuchal translucency (NT) gives an 85% detection rate for a 5% false-positive rate. These results largely depend on quality assessment of biochemical markers and of NT. In routine practice, despite an ultrasound quality control organization, NT images can be considered inadequate. The aim of the study was to evaluate the consequences for risk calculation when NT measurement is not taken into account.

MATERIAL AND METHOD

Comparison of detection and false-positive rates of first-trimester DS screening (PerkinElmer, Turku, Finland), with and without NT, based on a retrospective study of 117,126 patients including 274 trisomy 21-affected fetuses. NT was measured by more than 3,000 certified sonographers.

RESULTS

There was no significant difference in detection rates between the two strategies including or excluding NT measurement (86.7 vs. 81.8%). However, there was a significant difference in the false-positive rates (2.23 vs. 9.97%, p < 0.001).

DISCUSSION

Sonographers should be aware that removing NT from combined first-trimester screening would result in a 5-fold increase in false-positive rate to maintain the expected detection rates. This should be an incentive for maintaining quality in NT measurement.

Increased Umbilical Artery Pulsatility Index in Third-Trimester Fetuses with Trisomy 21

Objective: To examine the umbilical arterial Doppler flow patterns in late third-trimester fetuses with trisomy 21. Methods: This is a retrospective study on fetuses with trisomy 21 that were evaluated after 33 weeks' gestation at the Department of Obstetrics and Gynaecology of the University of Tuebingen, Germany. The umbilical and the middle cerebral artery (UA and ACM) pulsatility index (PI) measurements and the abdominal circumference were transformed into z-values. Results: Forty-two fetuses met the study criteria. The mean gestational age at the time of the first and the second visit was 35.0 and 36.6 weeks, respectively. The mean UA PI was 1.31 and 1.38, which corresponds to z-values of 2.20 and 2.70. In 24 (57.1%) cases, both PI measurements were above the 95th centile. A linear regression analysis demonstrated that the mean of both UA PI was not dependent on the abdominal circumference or on any other examined maternal and pregnancy characteristics. The mean ACM PI at the first and the second visit was 1.62 and 1.48, respectively, corresponding to mean z-values of -0.59 and -0.75, and in none of the cases was it below the 5th centile. Conclusion: In half of the third-trimester fetuses with trisomy 21, the resistance in the UA is increased - even in the absence of placental insufficiency.

Screening for trisomies 21, 18 and 13 by cell-free DNA analysis of maternal blood at 10-11 weeks' gestation and the combined test at 11-13 weeks

OBJECTIVE

To examine in a general population the performance of cell-free DNA (cfDNA) testing for trisomies 21, 18 and 13 at 10-11 weeks' gestation and compare it to that of the combined test at 11-13 weeks.

METHODS

In 2905 singleton pregnancies, prospective screening for trisomies was performed by chromosome-selective sequencing of cfDNA in maternal blood at 10-11 weeks' gestation and by the combined test at 11-13 weeks' gestation.

RESULTS

Median maternal age of the study population was 36.9 (range, 20.4-51.9) years. Results from cfDNA analysis were provided for 2851 (98.1%) cases and these were available within 14 days from sampling in 2848 (98.0%) cases. The trisomic status of the pregnancies was determined by prenatal or postnatal karyotyping or clinical examination of the neonates. Of the 2785 pregnancies with a cfDNA result and known trisomic status, cfDNA testing correctly identified all 32 cases with trisomy 21, nine of 10 with trisomy 18 and two of five with trisomy 13, with false-positive rates of 0.04%, 0.19% and 0.07%, respectively. In cases with discordant results between cfDNA testing and fetal karyotype, the median fetal fraction was lower than in those with concordant results (6% vs 11%). Using the combined test, the estimated risk for trisomy 21 was ≥ 1/100 in all trisomic cases and in 4.4% of the non-trisomic pregnancies.

CONCLUSION

The performance of first-trimester cfDNA testing for trisomies 21 and 18 in the general population is similar to that in high-risk pregnancies. Most false-positive and false-negative results from cfDNA testing could be avoided if the a priori risk from the combined test is taken into account in the interpretation of individual risk.

Noninvasive prenatal screening by next-generation sequencing

Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%. Challenging the widespread use of this technology are cost and the paradigm shift in counseling that accompanies any emerging technology. The expense of the test is expected to decrease with increased utilization, and well beyond the current NIPS technology, its components (fetal genome measurements, sequencing technology, and bioinformatics) will be utilized alone or in combinations to interrogate the fetal genome. The end goal is simple: to offer patients information early in pregnancy about fetal genomes without incurring procedural risks. This will allow patients an opportunity to make informed reproductive and pregnancy management decisions based on precise fetal genomic information.