The epidemic of abnormal copy number variant cases missed because of reliance upon noninvasive prenatal screening

OBJECTIVE

To assess the implications of increasing utilization of noninvasive prenatal screening (NIPS), which may reach 50% with the concomitant decrease in diagnostic procedures (DPs) for its impact on detection of chromosomal abnormalities.

METHODS

We studied our program's statistics over 5 years for DPs and utilization of array comparative genomic hybridization (aCGH). We then modeled the implications in our program if DP had not fallen and nationally of a 50% DP and aCGH testing rate using well-vetted expectations for the diagnosis of abnormal copy number variants (CNVs).

RESULTS

Our DP fell 40% from 2013-2017. Utilization of aCGH for DP nearly tripled. We detected 28 abnormal CNVs. If DP had not fallen, we likely would have detected 60. With 4 million US births per year, 2 million DPs would detect 30 000 abnormal CNVs and 4000 standard aneuploidies. At a 1/500 complication-pregnancy loss rate, the detection/complication ratio is 8.5/1.

CONCLUSIONS

Noninvasive prenatal screening has significantly changed the practice of prenatal screening. However, while increasing the detection of Down syndrome, the concomitant decrease in DP and lack of aCGH results in missing many more abnormalities than the increase in Down syndrome and complications of DP combined. From a public health perspective, such represents a missed opportunity for overall health care delivery.

Screening and Testing in Multiples

The choice of screening or invasive procedure in twin pregnancies is a personal choice of whether the patient wishes to take a small risk of having a baby with a serious disorder versus a small risk of having a complication because she wishes to avoid that. How to interpret such risks has profound effects on the perceived value of techniques, either leading to a decision to screening or going directly to chorionic villus sampling. There are profound issues surrounding the data and the interpretation of the data. No single short review can exhaustively examine all of the issues.

Comparison of two high-throughput semiconductor chip sequencing platforms in noninvasive prenatal testing for Down syndrome in early pregnancy

Background

Noninvasive prenatal testing (NIPT) to detect fetal aneuploidy using next-generation sequencing on ion semiconductor platforms has become common. There are several sequencers that can generate sufficient DNA reads for NIPT. However, the approval criteria vary among platforms and countries. This can delay the introduction of such devices and systems to clinics. A comparison of the sensitivity and specificity of two different platforms using the same sequencing chemistry could be useful in NIPT for fetal chromosomal aneuploidies. This would improve healthcare authorities’ confidence in decision-making on sequencing-based tests.

Methods

One hundred and one pregnant women who were predicted at high risk of fetal defects using conventional prenatal screening tests, and who underwent definitive diagnosis by full karyotyping, were enrolled from three hospitals in Korea. Most of the pregnant women (69.79 %) received NIPT during weeks 11–13 of gestation and 30.21 % during weeks 14–18. We used Ion Torrent PGM and Proton semi-conductor-based sequencers with 0.3× sequencing coverage depth. The average total reads of 101 samples were approximately 4.5 and 7.6 M for PGM and Proton, respectively. A Burrows-Wheeler Aligner (BWA) algorithm was used for the alignment, and a z-score was used to decide fetal trisomy 21. Interactive dot diagrams from the sequencing data showed minimal z-score values of 2.07 and 2.10 to discriminate negative versus positive cases of fetal trisomy 21 for the two different sequencing systems.

Results

Our z-score-based discrimination method resulted in 100 % positive and negative prediction values for both ion semiconductor PGM and Proton sequencers, regardless of their sequencing chip and chemistry differences. Both platforms performed well at an early stage (11–13 weeks of gestation) compared with previous studies.

Conclusions

These results suggested that, using two different sequencers, NIPT to detect fetal trisomy 21 in early pregnancy is accurate and platform-independent. The data suggested that the amount of sequencing and the application of common, simple, and robust statistical analyses are more important than sequencing chemistry and platform types. This result has practical implications in countries where PGM is approved for NIPT but the Proton system is not.

The feasibility study of non-invasive fetal trisomy 18 and 21 detection with semiconductor sequencing platform

OBJECTIVE

Recent non-invasive prenatal testing (NIPT) technologies are based on next-generation sequencing (NGS). NGS allows rapid and effective clinical diagnoses to be determined with two common sequencing systems: Illumina and Ion Torrent platforms. The majority of NIPT technology is associated with Illumina platform. We investigated whether fetal trisomy 18 and 21 were sensitively and specifically detectable by semiconductor sequencer: Ion Proton.

METHODS

From March 2012 to October 2013, we enrolled 155 pregnant women with fetuses who were diagnosed as high risk of fetal defects at Xiamen Maternal & Child Health Care Hospital (Xiamen, Fujian, China). Adapter-ligated DNA libraries were analyzed by the Ion Proton™ System (Life Technologies, Grand Island, NY, USA) with an average 0.3× sequencing coverage per nucleotide. Average total raw reads per sample was 6.5 million and mean rate of uniquely mapped reads was 59.0%. The results of this study were derived from BWA mapping. Z-score was used for fetal trisomy 18 and 21 detection.

RESULTS

Interactive dot diagrams showed the minimal z-score values to discriminate negative versus positive cases of fetal trisomy 18 and 21. For fetal trisomy 18, the minimal z-score value of 2.459 showed 100% positive predictive and negative predictive values. The minimal z-score of 2.566 was used to classify negative versus positive cases of fetal trisomy 21.

CONCLUSION

These results provide the evidence that fetal trisomy 18 and 21 detection can be performed with semiconductor sequencer. Our data also suggest that a prospective study should be performed with a larger cohort of clinically diverse obstetrics patients.

Maternal age-specific rates of fetal chromosomal abnormalities in Korean pregnant women of advanced maternal age

Objective

To evaluate the association of maternal age with occurrence of fetal chromosomal abnormalities in Korean pregnant women of advanced maternal age (AMA).

Methods

A retrospective review of the amniocentesis or chorionic villous sampling (CVS) database at Gangnam and Bundang CHA Medical Centers, between January 2001 and February 2012, was conducted. This study analyzed the incidence of fetal chromosomal abnormalities according to maternal age and the correlation between maternal age and fetal chromosomal abnormalities in Korean pregnant women ≥35 years of age. In addition, we compared the prevalence of fetal chromosomal abnormalities between women of AMA only and the others as the indication for amniocentesis or CVS.

Results

A total of 15,381 pregnant women were selected for this study. The incidence of aneuploidies increased exponentially with maternal age (P<0.0001). In particular, the risk of trisomy 21 (standard error [SE], 0.0378; odds ratio, 1.177; P<0.001) and trisomy 18 (SE, 0.0583; odds ratio, 1.182; P=0.0040) showed significant correlation with maternal age. Comparison between women of AMA only and the others as the indication for amniocentesis or CVS showed a significantly lower rate of fetal chromosomal abnormalities only in the AMA group, compared with the others (P<0.0001).

Conclusion

This study demonstrates that AMA is no longer used as a threshold for determination of who is offered prenatal diagnosis, but is a common risk factor for fetal chromosomal abnormalities.

Cell-free fetal DNA and maternal serum analytes for monitoring embryonic and fetal status

Biomarkers can be employed for screening for fetal genetic disorders, identifying individuals at sufficiently high risk for a confirmatory invasive procedure. In this article we discuss prenatal genetic aneuploidy screening. Maternal serum analytes and ultrasound have long been routinely offered, providing detection rates of 80% to 93% for trisomy 21; however, an invasive procedure (false-positive) must be performed in 5% of pregnancies screened. Recovering fetal cells from maternal blood initially proved inconsistent, but new methods recovering trophoblasts offer promise for detecting disorders using a single fetal cell, analogous to preimplantation genetic diagnosis. Current emphasis is focused predominantly on cell-free fetal DNA, which accounts for 5% to 10% of total cell-free DNA in maternal blood. Analysis of maternal blood results in detection rates of over 99% for fetal trisomy 21, and also very high rates for trisomy 18 and sex chromosomal abnormalities. Such detection rates are substantively higher than with maternal serum analytes, and are accompanied by a much lower (<1%) false-positive rate.

First-trimester screening and its impact on uptake of diagnostic testing

OBJECTIVE

To determine the influence of first-trimester screening (FTS) on a patient's decision regarding prenatal diagnostic testing (PDT) and if the uptake rate of PDT has changed among women with advanced maternal age (AMA) following the January 2007 American College of Obstetricians and Gynecologists statement regarding FTS.

METHODS

A database review was performed for the 2 years before and the 2 years after the January statement. A total of 7424 patient records were evaluated to determine the number of AMA women who obtained PDT, the number of positive and negative FTS results, and how many of those women had PDT. We then surveyed 53 patients and 23 referring physicians to determine what the patient understands about FTS, how patients utilize their FTS results, and how physicians educate their patients about FTS.

RESULTS

We determined that there was a 19.6% decrease in the uptake of PDT since that statement. Prior to their counseling session (2009-2010), 43% of those surveyed were against having PDT. After counseling, only 9% were against PDT. Overall, 91% were either open to or wanted PDT after counseling.

CONCLUSIONS

In addition to FTS results, we found that genetic counseling may be an influential factor in the patient's decision regarding PDT.

3-D ultrasound of the fetal ear and fetal autosomal trisomies: a pilot study of a new screening protocol

OBJECTIVE

We hypothesize that the rotation of the ear in fetuses with common autosomal trisomies will be markedly different from euploid fetuses and amenable to detection by 3-D ultrasound in the render mode.

METHODS

Study participants (10 weeks 4 days through 19 weeks 0 days) underwent a 3-D rendering of the fetal face and ear along with other biometric measurements prior to invasive testing.

RESULTS

Of the 348 patients who underwent chorionic villi sampling (CVS) (n = 208) or amniocentesis (n = 140), 18 were diagnosed with trisomy 21, 4 with trisomy 18, and 1 with trisomy 13. Mean gestational age was 12 weeks 6 days (range: 10 weeks 6 days to 19 weeks 0 days). Ear angles were obtained in all cases; the time to obtain this angle ranged from 5 to 25 min. Thirty-two fetuses were found to have an abnormal ear angle with 23 of the 32 characterized by one of the aforementioned trisomies.

CONCLUSIONS

These findings support the potential of this technique to provide valuable information in the identification of an increased-risk population. Prospective studies are needed to confirm the value of this screening modality as well as to assess its facility and ability to be incorporated into routine obstetrical practice.

Noninvasive prenatal diagnosis: 2010

Looking for fetal cells and now nucleic acids has been the holy grail of prenatal diagnosis for more than a century. The use of noninvasive diagnostics has potential far beyond aneuploidy; in fact, its use for Rhesus disease is already commonplace in Europe. Accurate segregation of fetal cells from maternal cells or identification of cell-free fetal (cff) DNA or RNA is critical to the development of fetal cells as a screening or diagnostic prenatal technique. The large number of approaches that have been used is testimony to the fact that none of them have been particularly successful. This article discusses the current status and challenges of noninvasive prenatal diagnosis.

Advanced maternal age as a sole indication for genetic amniocentesis; risk-benefit analysis based on a large database reflecting the current common practice

AIMS

Recent advances in prenatal screening, including first and second trimester genetic screening as well as targeted sonography, have significantly improved the detection of trisomy 21. Therefore, several investigators have questioned the validity of recommending genetic amniocentesis to all women who are 35 years or older at delivery. Thus, we sought to investigate the risks and benefits associated with performing genetic amniocentesis in women whose sole indication for testing was advanced maternal age (AMA).

METHODS

A retrospective review of a Genzyme Genetics amniocentesis database (January 2006-December 2006) was performed. All specimens obtained from women of AMA as the sole indication were eligible for analysis. The amniocentesis-related potential fetal loss was calculated based on the traditional fetal loss rate of 1/200 as well as the recently published loss rate of 1/1600 procedures. Risk-benefit analysis was performed by comparing the number of trisomy 21 fetuses identified within the AMA group to the potential number of amniocentesis-related fetal losses within this group.

RESULTS

A total of 87,241 amniocentesis specimens were processed during the study period. AMA was the sole indication for genetic amniocentesis in 43,303 cases which formed the study group. In 399 (0.92%) of these cases, a trisomy 21 was identified. Assuming an amniocentesis related fetal loss rates of 1/200 or 1/1600; 217 or 27 fetal losses would have been expected, respectively.

CONCLUSIONS

Our analysis suggests that the benefit of genetic amniocentesis for the sole indication of AMA far outweighs the potential amniocentesis-related fetal loss rate, regardless of the actual rate one considers.