Committee Opinion No. 640: Cell-Free Dna Screening For Fetal Aneuploidy

Should vanishing twin pregnancies be systematically excluded from cell-free fetal DNA testing?

OBJECTIVE

To demonstrate the feasibility of cell-free DNA (cfDNA) testing in vanishing twin (VT) pregnancies in routine clinical practice.

METHODS

Our study included 24 874 singleton and 206 VT consecutive pregnancies. Cell-free DNA was analyzed by massively parallel sequencing. Both aneuploidy analysis (chromosomes 13,18, 21, X, and Y) and fetal fraction estimation were performed according to an Illumina algorithm. Contaminant DNA contribution from the demised co-twin was studied in detail.

RESULTS

VT pregnancies exhibited a higher prevalence of screen-positive cases (5.8% vs 2.5%), sex discrepancies (10.2% vs 0.05%), and false positive rates (FPR) (2.6% vs 0.3%) than singleton pregnancies. However, their incidence was significantly lower in tests performed after the 14th week (screen-positive cases: 3.1%; sex discrepancies: 7.8%; and FPR: 0.8%). Among the 12 cases in which cfDNA was performed at two time points, fading of contaminating cfDNA was observed in four cases with a sex discrepancy and in one false positive for trisomy 18, resulting in a final correct result.

CONCLUSIONS

Our data suggest VT pregnancies could be included in cfDNA testing as long as it is applied after the 14th week of pregnancy. However, future studies to validate our findings are needed before including VT cases in routine clinical practice. Once established, unnecessary invasive procedures could be avoided, mitigating negative emotional impact on future mothers.

Impact of cell-free DNA screening on parental knowledge of fetal sex and disorders of sex development

OBJECTIVE

Discrepancies between cfDNA and ultrasound predicted fetal sex occur, possibly indicating disorders/differences of sex development (DSDs). Among expectant/recent parents, this study assessed cfDNA knowledge/use, fetal sex determination attitudes/behaviors, general knowledge of DSD, and possible psychological impact of discrepancy between fetal sex on cfDNA and ultrasound.

METHOD

Parents were surveyed about fetal sex determination methods, knowledge of cfDNA and DSD, distress related to possible cfDNA inaccuracy.

RESULTS

Of 916 respondents, 44% were aware of possible discrepancy between cfDNA and ultrasound, 22% were aware of DSD. 78% and 75% would be upset and worried, respectively, with results showing fetal sex discrepancy. Most (67%) revealed predicted fetal sex before delivery. 38% were offered cfDNA. Of those revealing fetal sex, 24% used cfDNA results, 71% ultrasound, and 7% both. cfDNA users were more frequently aware of possible discrepancy between cfDNA and ultrasound (76% vs 41%, P < .0001), but not of DSD (29% vs 23%, P = .29).

CONCLUSION

Fetal sex determination is favored, and cfDNA is frequently used for predicting fetal chromosomal sex. Many parents are unaware of possible discrepancies between cfDNA and ultrasound, and potential for DSD. Most would be distressed by discordant results. Accurate counseling regarding limitations cfDNA for fetal sex determination is needed.

A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center

OBJECTIVE

To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center.

METHODS

A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings.

RESULTS

Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs.

CONCLUSIONS

NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.

Update on noninvasive prenatal testing: A review based on current worldwide research

Eight years have passed since noninvasive prenatal testing (NIPT) was clinically evaluated and data on NIPT for trisomy 21, 18 and 13 were collected. The data revealed that NIPT is more accurate than conventional first-trimester screening. However, there is still insufficient data regarding the clinical use of NIPT results in detecting sex chromosome aneuploidies or whole-genome regions. NIPT is already being used as a clinical screening method globally. However, it is an unconfirmed diagnostic test and the results must be interpreted with caution as they may yield false negatives, false positives or inconclusive results. Therefore, the aim of this review is to highlight the current status of information, including the different methodologies, shortcomings and implications, regarding NIPT after its adoption worldwide. It is important to include genetic counseling when implementing NIPT. Going forward, the knowledge obtained to date, including the associated shortcomings, must be considered in evaluating the effectiveness of NIPT in detecting genetic abnormalities.

Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing

OBJECTIVE

Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT.

STUDY DESIGN

We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up.

RESULTS

A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality.

CONCLUSION

When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.

Pregnancy-associated changes in cervical noncoding RNA

Aim: To identify pregnancy-associated changes in cervical noncoding RNA (ncRNA), including miRNA and long noncoding RNA (lncRNA), and their potential effects on biologic processes. Materials & methods: We enrolled 21 pregnant women with term deliveries (≥37 weeks' gestation) in a prospective cohort and collected cervical swabs before 28 weeks' gestation. We enrolled 21 nonpregnant controls. We analyzed miRNA, lncRNA and mRNA expression, applying a Bonferroni correction. Results: Five miRNA and three lncRNA were significantly differentially (>twofold change) expressed. Putative miRNA targets are enriched in genes mediating organogenesis, glucocorticoid signaling, cell adhesion and ncRNA machinery. Conclusion: Differential cervical ncRNA expression occurs in the setting of pregnancy. Gene ontology classification reveals biological pathways through which miRNA may play a biologic role in normal pregnancy physiology.

Comparison of indications and results of prenatal invasive diagnostic tests before and after the implementation of the use of cell-free fetal DNA: a tertiary referral center experience

PURPOSE

In this study, we aimed to compare the changes in the number, yield, and the percentage of karyotyping indications of the invasive prenatal diagnostic tests between the periods before and after cell-free fetal DNA was introduced to clinical use.

METHOD

The number of invasive prenatal diagnostic procedures such as amniocentesis and chorionic villus sampling, indication percentages and karyotype results in the periods before (January 1, 2009-December 31, 2010), (n = 1412) and after (January 1, 2016-December 31, 2017), and (n = 593) the introduction of cell-free fetal DNA was retrospectively evaluated.

RESULTS

When compared with the period before cell-free fetal DNA came into clinical use, the number of invasive prenatal diagnostic tests decreased by 58% while their yield was found to have increased (4.4% vs. 10.3%) in the period after cell-free DNA began to be used (p < 0.001). While there was a decrease in the indications due to advanced maternal age, an increase was found in ultrasonography indications for structural anomaly and the risk of a single-gene disorder (p < 0.001). Amniocentesis rate was found to have decreased in invasive prenatal diagnostic procedure types, while an increase was reported in CVS rates (p < 0.001).

CONCLUSIONS

Invasive prenatal diagnosis gradually decreases over the years, but the yield of invasive prenatal diagnostic tests increases. In parallel with the rapid development of modern molecular technologies and cheaper and easier access to the tests, we think that the number of invasive prenatal diagnostic tests will experience a more dramatic decrease in the following years.

The rate of undetectable genetic causes by Cell-free DNA test in congenital heart defects

Objective: The study aimed to estimate the rate of genetic causes that were undetectable by Cell-free DNA (cfDNA) test in prenatally diagnosed congenital heart defect (CHD) cases based on an assumption that cfDNA would accurately detect common aneuploidies including trisomy 21/18/13/45X, and del22q11.2.Methods: This study included prenatally diagnosed CHD cases with diagnostic genetic results. The possibility of false-positive/negative results from cfDNA testing was discarded. Thus, cfDNA results would be positive in common aneuploidies or del22q11.2 and negative in normal diagnostic genetic testing results or other genetic conditions. The rate of genetic causes that were undetectable by cfDNA test was estimated for all cases as well as for CHD subgroups.Results: Of 302 cases, 98 (34.8%) had a type of genetic abnormalities, with 67 having common aneuploidies or del22q11.2 and 31 having other genetic conditions. The rate of genetic causes that were undetectable by cfDNA test in CHD cases was 13.2% among those with assumingly negative cfDNA screen results and 10.3% among the entire study population. These rates were similar between CHD subgroups (p > .05). The rate of genetic causes that were undetectable by cfDNA test was higher in the non-isolated cases than in the isolated ones among those with assumingly negative-screen results (20.5% and 9.9%, respectively, p = .025).Conclusion: In prenatally diagnosed CDH cases, a significant number of chromosomal abnormalities are still identified after diagnostic testing even if cfDNA screen is negative, and thus it is important to extensively counsel patients with negative cfDNA screen carrying a CHD-affected fetus.

Status of medical genomics and genetics education in maternal-fetal medicine: survey of program directors and clinical fellows in the USA

Objective: The study aimed to assess the current state of medical genetics and genomics (MGG) education amongst maternal-fetal medicine (MFM) program directors (PDs) and clinical fellows.Methods: An online questionnaire was generated and distributed to all current program directors and fellows in ACGME-accredited MFM fellowships across the USA in 2018.Results: A total of 13 program directors and 54 MFM fellows responded to our survey. Of the respondents, 73% of the MFM fellows mentioned having dedicated structured MGG rotations as part of their training. Only 12% of fellows reported a high level of satisfaction with their programs' structured MGG rotations and almost 40% reported dissatisfaction, compared to 56% of PDs who reported very high satisfaction. Furthermore, 84% of PDs reported high levels of satisfaction with MGG didactics currently in place compared to only 24% of fellows sharing the same opinion. When compared to PDs, fellows reported a significantly lower satisfaction score toward their MGG rotations (p < .05) and didactic sessions (p < .05). More than 62% of PDs were satisfied with the number of MGG-faculty in their division compared to 80% of fellows who thought more faculty is needed. Thirty-eight percent of PDs quoted curricular overload and lack of time as the most important obstacles to MGG education, compared to 43% of fellows citing a limited number of genetics services providers as the most important obstacles to their MGG education.Conclusion: MFM fellows and PDs differ in their satisfaction with the current state of MGG didactics and rotations in their programs, the number of MGG faculty in their divisions, and the perceived obstacles to MGG education . Our study illustrates the need for MGG curriculum development in MFM fellowships as this subspecialty relies heavily on the use of genetics and genomics services.

A two-year experience of non-invasive prenatal testing (NIPT) at an urban tertiary medical center in South Korea

OBJECTIVE

To report our experience of implementing non-invasive prenatal testing (NIPT) in a tertiary urban academic medical center in South Korea.

MATERIALS AND METHODS

An observational retrospective study of singleton and twin pregnancies that underwent prenatal screening for fetal aneuploidy from July 2016 to April 2018 was conducted. Demographics of the study population electing NIPT versus those opting the integrated test were compared. We also assessed clinical significant factors influencing cfDNA fetal fraction in NIPT.

RESULTS

Among the 817 women who underwent serum screening tests during the study period, 490 women (60.0%) chose the integrated test while 327 women (40.0%) chose NIPT. Compared to the integrated test group, women in the NIPT group were older (mean age 34.7 ± 3.7 vs. 32.6 ± 3.4; p-value < 0.01), multiparous (47.1% vs. 39.8%; p-value = 0.046), and had higher rate of previous abortion history (28.4% vs. 21.6%; p-value = 0.033). A significant decrease in the number of invasive diagnostic tests was observed since the adoption of NIPT. The screen negative and positive rates of the integrated test group for fetal aneuploidy were 95.3% and 4.7%, respectively while those of the NIPT group were 95.9% and 1.2%, respectively. The rate of inadequate cfDNA fetal fraction was 3.0%. Low fetal fraction was associated with higher maternal age, body weight and BMI.

CONCLUSIONS

The implementation of NIPT has significantly affected the practice pattern of prenatal aneuploidy screening by replacing the integrated test and decreasing invasive diagnostic tests.

Evidence of compliance with and effectiveness of guidelines for noninvasive prenatal testing in China: a retrospective study of 189,809 cases

In China, the medical guidelines recommend performing noninvasive prenatal testing (NIPT) with caution for pregnant women aged 35 years or older. However, the Mother and Child Health Care Law suggests that all primiparous women whose age is older than 35 years undergo prenatal diagnosis. These two inconsistent suggestions/recommendations have made obstetricians confused about whether to offer NIPT to these older pregnant women. To face this issue and find out the solution we performed a retrospective study of 189,809 NIPT samples collected from 28 provincial-leveled administrative units in China. Of 1,564 women with high-risk pregnancies who underwent NIPT, 459 (29.3%) did not participate in follow-up. The compound sensitivity and specificity of NIPT for trisomies 21, 18 and 13 detection was 99.1% (95% CI, 98.0%-99.6%) and 99.9% (95% CI, 98.8%-99.9%), respectively. In secundiparous women, NIPT showed high sensitivity and specificity similar to that in primiparous women. The observed risk for trisomies 21 and 18 significantly increased when the maternal age was 39 and older. After the publication of the current NIPT policy, the follow-up rate at our center was 91.9%; however, a large number of women are not in maternal and infant care networks nationwide, and that makes the follow-up rate outside our center relatively low. Our study shows that to balance the prevention of major aneuploidies and the limited resources for prenatal diagnosis, the cut-off age of 35 for invasive prenatal diagnosis might be unnecessary. Although the NIPT guidelines are well written, how to practice it effectively, especially in less industrialized areas, is worth discussing.

Liquid biopsies in myeloid malignancies

Hematologic malignancies are the most common type of cancer affecting children and young adults, and encompass diseases, such as leukemia, lymphoma, and myeloma, all of which impact blood associated tissues such as the bone marrow, lymphatic system, and blood cells. Clinical diagnostics of these malignancies relies heavily on the use of bone marrow samples, which is painful, debilitating, and not free from risks for leukemia patients. Liquid biopsies are based on minimally invasive assessment of markers in the blood (and other fluids) and have the potential to improve the efficacy of diagnostic/therapeutic strategies in leukemia patients, providing a useful tool for the real time molecular profiling of patients. The most promising noninvasive biomarkers are circulating tumor cells, circulating tumor DNA, microRNAs, and exosomes. Herein, we discuss the role of assessing these circulating biomarkers for the understanding of tumor progression and metastasis, tumor progression dynamics through treatment and for follow-up.

Development of a new methylation-based fetal fraction estimation assay using multiplex ddPCR

Background

Non‐invasive prenatal testing (NIPT) for fetal aneuploidies has rapidly been incorporated into clinical practice. Current NGS‐based methods can reliably detect fetal aneuploidies non‐invasively with fetal fraction of at least 4%. Inaccurate fetal fraction assessment can compromise the accuracy of the test as affected samples with low fetal fraction have an increased risk for misdiagnosis. Using a novel set of fetal‐specific differentially methylated regions (DMRs) and methylation sensitive restriction digestion (MSRD), we developed a multiplex ddPCR assay for accurate detection of fetal fraction in maternal plasma.

Methods

We initially performed MSRD followed by methylation DNA immunoprecipitation (MeDIP) and NGS on fetal and non‐pregnant female tissues to identify fetal‐specific DMRs. DMRs with the highest methylation difference between the two tissues were selected for fetal fraction estimation employing MSRD and multiplex ddPCR. Chromosome Y multiplex ddPCR assay (YMM) was used as a reference standard, to develop our fetal fraction estimation model in male pregnancy samples. Additional 123 samples were tested to examine whether the model is sex dependent and/or ploidy dependent.

Results

In all, 93 DMRs were identified of which seven were selected for fetal fraction estimation. Statistical analysis resulted in the final model which included four DMRs (FFMM). High correlation with YMM‐based fetal fractions was observed using 85 male pregnancies (r = 0.86 95% CI: 0.80–0.91). The model was confirmed using an independent set of 53 male pregnancies.

Conclusion

By employing a set of well‐characterized DMRs, we developed a SNP‐, sex‐ and ploidy‐independent methylation‐based multiplex ddPCR assay for accurate fetal fraction estimation.

Implementation of maternal blood cell-free DNA testing in early screening for aneuploidies

Several externally blinded validation and implementation studies in the last 9 years have shown that it is now possible, through analysis of cell-free (cf) DNA in maternal blood, to effectively detect a high proportion of fetuses affected by trisomies 21, 18, and 13 at a much lower false-positive rate (FPR) than all other existing screening methods. This article is aimed at reviewing technical and clinical considerations for implementing cfDNA testing in routine practice, including methods of analysis, performance of the test, models for clinical implementation, and interpretation of results.

Targeted capture enrichment followed by NGS: development and validation of a single comprehensive NIPT for chromosomal aneuploidies, microdeletion syndromes and monogenic diseases

BACKGROUND

Non-invasive prenatal testing (NIPT) has been widely adopted for the detection of fetal aneuploidies and microdeletion syndromes, nevertheless, limited clinical utilization has been reported for the non-invasive prenatal screening of monogenic diseases. In this study, we present the development and validation of a single comprehensive NIPT for prenatal screening of chromosomal aneuploidies, microdeletions and 50 autosomal recessive disorders associated with severe or moderate clinical phenotype.

RESULTS

We employed a targeted capture enrichment technology powered by custom TArget Capture Sequences (TACS) and multi-engine bioinformatics analysis pipeline to develop and validate a novel NIPT test. This test was validated using 2033 cell-fee DNA (cfDNA) samples from maternal plasma of pregnant women referred for NIPT and paternal genomic DNA. Additionally, 200 amniotic fluid and CVS samples were used for validation purposes. All NIPT samples were correctly classified exhibiting 100% sensitivity (CI 89.7-100%) and 100% specificity (CI 99.8-100%) for chromosomal aneuploidies and microdeletions. Furthermore, 613 targeted causative mutations, of which 87 were unique, corresponding to 21 monogenic diseases, were identified. For the validation of the assay for prenatal diagnosis purposes, all aneuploidies, microdeletions and point mutations were correctly detected in all 200 amniotic fluid and CVS samples.

CONCLUSIONS

We present a NIPT for aneuploidies, microdeletions, and monogenic disorders. To our knowledge this is the first time that such a comprehensive NIPT is available for clinical implementation.

Creating basis for introducing non‐invasive prenatal testing in the Estonian public health setting

OBJECTIVE

The study aimed to validate a whole-genome sequencing-based NIPT laboratory method and our recently developed NIPTmer aneuploidy detection software with the potential to integrate the pipeline into prenatal clinical care in Estonia.

METHOD

In total, 424 maternal blood samples were included. Analysis pipeline involved cell-free DNA extraction, library preparation and massively parallel sequencing on Illumina platform. Aneuploidies were determined with NIPTmer software, which is based on counting pre-defined per-chromosome sets of unique k-mers from sequencing raw data. SeqFF was implemented to estimate cell-free fetal DNA (cffDNA) fraction.

RESULTS

NIPTmer identified correctly all samples of non-mosaic trisomy 21 (T21, 15/15), T18 (9/9), T13 (4/4) and monosomy X (4/4) cases, with the 100% sensitivity. However, one mosaic T18 remained undetected. Six false-positive (FP) results were observed (FP rate of 1.5%, 6/398), including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). The level of cffDNA of <4% was estimated in eight samples, including one sample with T13 and T18. Despite low cffDNA level, these two samples were determined as aneuploid.

CONCLUSION

We believe that the developed NIPT method can successfully be used as a universal primary screening test in combination with ultrasound scan for the first trimester fetal examination.

Chromosomal microarray vs. NIPS: analysis of 5541 low-risk pregnancies

PURPOSE

To evaluate the diagnostic yield of chromosomal microarray (CMA) in pregnancies with normal ultrasound.

METHODS

This retrospective cohort analysis included all pregnancies with normal ultrasound undergoing CMA testing between the years 2010 and 2016. We calculated the rate of detection of clinically significant CMA findings in the whole cohort and according to various indications.

RESULTS

Of 5541 CMA analyses, clinically significant findings were yielded in 78 cases (1.4%). Of these, 31 (39.7%) variants could have theoretically been detected by karyotyping (e.g., sized above 10 Mb), and 28 (35.9%) by noninvasive prenatal screening aimed at five common aneuploidies. Of the 47 submicroscopic findings detectable by CMA only, the majority (37 cases, 78.7%) represented known recurrent syndromes. Detection of clinically significant CMA findings in women with no indication for invasive testing was 0.76% (21/2752), which was significantly lower compared with 1.8% in advanced maternal age group (41/2336), 2.8% in abnormal biochemical serum screening (6/211), and 4.1% (10/242) in fetuses with sonographic soft markers.

CONCLUSION

Clinically significant CMA aberrations are detected in 1 of 71 pregnancies with normal ultrasound, and in 1 of 131 women with no indication for invasive testing. Thus, CMA might be recommended a first-tier test in pregnancies with normal ultrasound.

Fetal sex discordance between noninvasive prenatal screening results and sonography: A single institution's experience and review of the literature

BACKGROUND

With the increasing availability of noninvasive prenatal screening (NIPS) and high-resolution ultrasound, more cases of sex discordance are being identified in routine clinical practice. This can be a source of much concern for families and clinicians. Knowledge about the limitations of NIPS and reasons for discordant results are critical for counseling parents.

AIMS

Here, we present three cases from a single tertiary care referral center. We also review the literature to address potential limitations of NIPS in correctly identifying fetal sex chromosomes.

MATERIALS AND METHODS

After Institutional Review Board approval, cases of discordant fetal sex were identified using ICD-9 and ICD-10 codes. In addition, departmental counseling database and cytogenetics laboratory logbooks were reviewed.

RESULTS

In our first case, a 37-year-old G4 P2012 underwent NIPS at 11 weeks gestation and Monosomy X (associated with Turner syndrome) was identified. Morphological sonographic assessment at 20 weeks gestation was consistent with a female fetus following an amniocentesis at 16 weeks that revealed normal 46, XX karyotype. During the third trimester, the patient was diagnosed with Stage IV invasive ductal carcinoma of the breast. Postnatal follow-up of the neonate was consistent with a phenotypic female. In the second case, a 22-year-old G2 P1001 obese female underwent NIPS at 14 weeks gestation and normal 46, XY karyotype was identified. Morphological sonographic assessment at 20 weeks was not consistent with a male fetus. The patient declined invasive testing. Postnatally, the karyotype was 46, XX and the neonate was phenotypically female. The reason for the discordant results was not identified. In the third case, a 25-year-old G1 P0 obese female underwent NIPS at 13 weeks gestation and normal 46, XY karyotype was identified. Morphological sonographic assessment at 20 weeks was indeterminate; however, follow-up at 24 weeks was consistent with a female fetus. The patient declined invasive prenatal testing. Postnatally, the karyotype was 46, XX, and the neonate was phenotypically female with uterus present on ultrasound. The reason for the discordant results was not identified.

DISCUSSION

Our cases demonstrate possible limitations of NIPS in correctly identifying sex chromosomes.

CONCLUSIONS

Providers and patients need to be aware of these limitations, and invasive diagnostic prenatal testing should be offered in cases of discordance between NIPS and sonographic sex assessment.

Cell-Free Fetal DNA in the Early and Late First Trimester

OBJECTIVE

The aim of this work was to investigate the association between maternal and fetal characteristics and the fetal fraction at 8-14 weeks' gestation, with emphasis on the change in the fetal fraction upon repeat sampling.

METHOD

One sample for cell-free DNA (cfDNA) testing was collected at the same time as the biochemical markers for combined first trimester screening (visit 1) and another at the nuchal translucency scan (visit 2). Chromosome-selective cfDNA analysis was performed on frozen plasma.

RESULTS

Overall, 321 women were included at visit 1, and 307 had a repeat blood sampling. A fetal fraction was obtained in 532 samples (238 samples with repeat fetal fraction). The fetal fraction decreased with maternal BMI (p < 0.001), was lower in Asian women (p = 0.03), and increased with β-hCG levels (p < 0.001) and gestational age (p = 0.04). Before 10 weeks' gestation, the fetal fraction was lower (p = 0.02), as was the probability of a sufficient fetal fraction (p = 0.03) after adjustment for maternal BMI. Asian women had a higher increase in fetal fraction upon repeat sampling (p < 0.001).

CONCLUSION

Before 10 weeks' gestation, the fetal fraction is significantly lower but seems to increase more rapidly compared to later gestations. Presently, combined first trimester screening with cfDNA testing should not include samples before 10 weeks' gestation.

Evaluation of a novel screening method for fetal aneuploidy using cell-free DNA in maternal plasma

Objective

To evaluate the test performance of a novel sequencing technology using molecular inversion probes applied to cell-free DNA screening for fetal aneuploidy.

Methods

Two cohorts were included in the evaluation; a risk-based cohort of women receiving diagnostic testing in the first and second trimesters was combined with stored samples from pregnancies with fetuses known to be aneuploid or euploid. All samples were blinded to testing personnel before being analyzed, and validation occurred after the study closed and results were merged.

Results

Using the new sequencing technology, 1414 samples were analyzed. The findings showed sensitivities and specificities for the common trisomies and the sex chromosome aneuploidies at >99% (Trisomy 21 sensitivity 99.2 CI 95.6–99.2; specificity 99.9 CI 99.6–99.9). Positive predictive values among the trisomies varied from 85.2% (Trisomy 18) to 99.0% (Trisomy 21), reflecting their prevalence rates in the study. Comparisons with a meta-analysis of recent cell-free DNA screening publications demonstrated equivalent test performance.

Conclusion

This new technology demonstrates equivalent test performance compared with alternative sequencing approaches, and demonstrates that each chromosome can be successfully interrogated using a single probe.

Prenatal detection of 1p36 deletion syndrome: ultrasound findings and microarray testing results

OBJECTIVE

Only a small number of reports have been made on the prenatal ultrasound findings observed in 1p36 deletion syndrome. We explored prenatal diagnosis of 1p36 deletion by ultrasound as well as chromosomal microarray (CMA), and delineated the fetal presentation of this syndrome.

STUDY DESIGN

This was a retrospective analysis of 10 new prenatal cases of 1p36 deletion identified by CMA at a single Chinese medical center. Clinical data were reviewed for these cases, including maternal demographics, indications for invasive testing, sonographic findings, CMA results and pregnancy outcomes.

RESULTS

One case was diagnosed because of a positive cell-free DNA (cfDNA) testing result for terminal 1p deletion, and the remaining nine cases were identified because of an abnormal ultrasound findings, including early miscarriage, structural abnormalities and fetal growth restriction. CMA revealed 1p36 deletions to be terminal in six cases, and interstitial in four cases. Deletion sizes ranged from 1.7 to 42.7 Mb.

CONCLUSIONS

Prenatal findings such as cardiac malformations, especially Ebstein anomaly, and fetal growth retardation should warrant the diagnosis of 1p36 deletion and invasive genetic testing using CMA.

Expanded Prenatal Genetic and Newborn Screening: One Family's Wild Ride

The exponential rate at which genetic testing has been integrated into routine and high-risk obstetric care has been exciting to watch. With this technical explosion, however, the knowledge surrounding the benefits and limitations of prenatal genetic and newborn screening can be overlooked by both parents and providers. The following case exemplifies how a couple with infertility who underwent comprehensive prenatal expanded genetic carrier screening and parental karyotype experienced the benefits and limitations of such testing. It guides the reader through diagnostic testing for an infant, born to a father with a balanced translocation, who presented with an abnormal newborn screening result for an inherited metabolic disorder of fatty acid oxidation metabolism, very-long-chain acyl-coenzyme dehydrogenase deficiency, for which the prenatal expanded carrier screening result was negative.

Cell-Free Fetal DNA: A Novel Biomarker for Early Prediction of Pre-eclampsia and Other Obstetric Complications

Hypertensive disorder of pregnancy, especially Pre-eclampsia is one of the major causes of increased maternal and perinatal morbidity and mortality all over the world. Early prediction of pre-eclampsia is the need of modern obstetrics, as this can timely prevent the progress of disease as well as related fetal and maternal morbidity and mortality. In addition to the screening of fetal aneuploidies, Rhesus-D status, fetal sex, single gene disorders, the cell-free fetal Deoxyribonucleic acid (DNA) quantification has emerged as a promising biomarker for the prediction of pre-eclampsia. Hence, its use can help in the early prediction of hypertensive disorders of pregnancy, especially pre-eclampsia even before the appearance of symptoms. Furthermore, in future, it can also help in the determination of the complete DNA sequence of every gene of the fetus. The present review focuses on recent literature concerning the use of cell-free fetal DNA in early prediction of preeclampsia as well as for non-invasive prenatal genetic screening of fetus for various disorders. Methods: The recent literature related to cell-free fetal DNA was searched from numerous English language journals and published peer-reviewed articles on Pubmed, Google Scholar, MEDLINE and various government agencies till 2016.

Cost and efficacy comparison of prenatal recall and reflex DNA screening for trisomy 21, 18 and 13

Objective

To compare costs and efficacy of reflex and recall prenatal DNA screening for trisomy 21, 18 and 13 (affected pregnancies). In both methods women have Combined test markers measured. With recall screening, women with a high Combined test risk are recalled for counselling and offered a DNA blood test or invasive diagnostic testing. With reflex screening, a DNA analysis is automatically performed on plasma collected when blood was collected for measurement of the Combined test markers.

Methods

Published data were used to estimate, for each method, using various unit costs and risk cut-offs, the cost per woman screened, cost per affected pregnancy diagnosed, and for a given number of women screened, numbers of affected pregnancies diagnosed, unaffected pregnancies with positive results, and women with unaffected pregnancies having invasive diagnostic testing.

Results

Cost per woman screened is lower with reflex v recall screening: £37 v £38, and £11,043 v £11,178 per affected pregnancy diagnosed (DNA £250, Combined test markers risk cut-off 1 in 150). Reflex screening results in similar numbers of affected pregnancies diagnosed, with 100-fold fewer false-positives and 20-fold fewer women with unaffected pregnancies having invasive diagnostic testing.

Conclusions

Reflex DNA screening is less expensive, more cost-effective, and safer than recall screening.

No. 348-Joint SOGC-CCMG Guideline: Update on Prenatal Screening for Fetal Aneuploidy, Fetal Anomalies, and Adverse Pregnancy Outcomes

OBJECTIVE

To review the available prenatal screening options in light of the recent technical advances and to provide an update of previous guidelines in the field of prenatal screening.

INTENDED USERS

Health care providers involved in prenatal screening, including general practitioners, obstetricians, midwives, maternal fetal medicine specialists, geneticists, and radiologists.

TARGET POPULATION

All pregnant women receiving counselling and providing informed consent for prenatal screening.

EVIDENCE

Published literature was retrieved through searches of Medline, PubMed, and the Cochrane Library in and prior to March 2016 using an appropriate controlled vocabulary (prenatal diagnosis, amniocentesis, chorionic villi sampling, non-invasive prenatal screening) and key words (prenatal screening, prenatal genetic counselling). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies written in English and published from January 1985 to May 2016. Searches were updated on a regular basis and incorporated in the guideline. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical speciality societies.

GUIDELINE UPDATE

Evidence will be reviewed 5 years after publication to determine whether all or part of the guideline should be updated. However, if important new evidence is published prior to the 5-year cycle, the review process may be accelerated for a more rapid update of some recommendations.

Non-invasive prenatal testing of fetal chromosomal aneuploidies: validation and clinical performance of the veracity test

Introduction

Non-Invasive Prenatal Testing (NIPT) for fetal aneuploidies using cell-free DNA (cfDNA) has been widely adopted in clinical practice due to its improved accuracy. A number of NIPT tests have been developed and validated. The purpose of this study is to evaluate the performance of the Veracity NIPT test for sex chromosome aneuploidy (SCA) detection in singleton pregnancies, autosomal aneuploidy detection in twin pregnancies and evaluation of Veracity clinical performance under routine NIPT conditions in a diverse cohort.

Methods

Blinded retrospective study in singleton pregnancies (n = 305); blinded retrospective and prospective study in twin pregnancies (n = 306) and prospective evaluation of clinical performance in singleton and twin pregnancies (n = 10564).

Results

Validation study results for the detection of SCAs in singleton pregnancies exhibited 100% sensitivity and specificity and correctly classified 7 (45,X), 4 (47,XXY), 2 (47,XXX) and 1 (47,XYY) cases. Validation study results for autosomal aneuploidy detection in twin pregnancies exhibited 100% sensitivity and specificity and correctly classified 3 trisomy 21, 1 trisomy 18 and 1 trisomy 13 samples. Clinical performance evaluation of Veracity was performed in 10564 pregnancies with median gestational age of 13 weeks, median maternal age 35 years and median gestational weight of 64 kg. Based on confirmation feedback the PPV for trisomies 21, 18 and 13 was estimated at 100% (95% CI, 92–100%), 100% (95% CI, 69–100%) and 71% (95% CI, 29–96%), respectively. Estimated PPV for Monosomy X was 57% (95%CI, 18–90%), while the NPV for SCA detection was estimated at 100% (95% CI, 99.94–100%).

Conclusion

Veracity NIPT test is based on a very powerful, highly accurate methodology that can be safely applied in the clinical setting.

Electronic supplementary material

The online version of this article (10.1186/s13039-019-0446-0) contains supplementary material, which is available to authorized users.

Lower detectability of non-invasive prenatal testing compared to prenatal diagnosis in high-risk pregnant women

BACKGROUND

To investigate the detectability of non-invasive prenatal testing (NIPT) after prenatal screening to detect foetal chromosomal abnormalities in pregnant women at high risk, and the number of foetal abnormalities could be missed by NIPT.

METHODS

From January 2009 to March 2018, 3,099 pregnant women at high risk for trisomy 21 and 18 according to the results of prenatal serological screening were enrolled in this study. The women underwent amniocentesis at 18-23 weeks, as well as karyotype testing and/or chromosomal microarray analyses (CMA). We assessed the ability of NIPT to detect chromosomal abnormalities.

RESULTS

In all, 177 (5.7%, 177/3,099) chromosomal abnormalities were identified. These included 129 (72.9%) abnormal numbers of chromosomes, 6 (3.4%) chromosome structural abnormalities, and 42 (23.7%) other abnormalities, including copy number variation, inversions, and chromosome additions/deletions. Of the 177 (70.0%) chromosomal abnormalities, 124 were detected and 53 were missed by NIPT.

CONCLUSIONS

NIPT could miss 30.0% of the chromosomal abnormalities detected by amniocentesis and cytogenetic testing. This proportion will likely decrease in the future due to further development of NIPT.

Clinical features and pregnancy outcomes of women with abnormal cell-free fetal DNA test results

Background

This study was performed to examine the factors affecting attitudes regarding prenatal diagnosis and clinical treatment by analyzing the clinical data of women with positive noninvasive prenatal testing (NIPT) results.

Methods

We collected clinical data for women with positive NIPT results. The women received prenatal genetic consultation. The women with true positive results received prenatal genetic counseling again, and decided whether to continue or terminate their pregnancy.

Results

A total of 228 women received positive NIPT results. The prenatal diagnosis was accepted in 174 cases (76.3%), and 124 women were confirmed to have true positive NIPT results. The positive predictive values (PPV) of T21/T18/T13 and fetal sex chromosome aneuploidy were 88.4% and 42.9%, respectively. All (99/99, 100%) of the women with T21/T18/T13 terminated their pregnancies, while 25.0% (6/24) of women with fetal SCA continued their pregnancies. An NIPT result of Chr(9) microduplication was obtained in one woman, which was confirmed by chromosomal microarray analysis (CMA).

Conclusions

NIPT exhibited good detection accuracy for T21/T18/T13, and also contributed to identifying fetal SCA and substructural chromosomal abnormalities. With a positive NIPT result, the attitudes of pregnant women regarding prenatal diagnosis and clinical treatment are related to the severity of disease, cognitive ability, and the level of prenatal genetic counseling.

Prospective head-to-head comparison of accuracy of two sequencing platforms for screening for fetal aneuploidy by cell-free DNA: the PEGASUS study

We compared clinical validity of two non-invasive prenatal screening (NIPS) methods for fetal trisomies 13, 18, 21, and monosomy X. We recruited prospectively 2203 women at high risk of fetal aneuploidy and 1807 at baseline risk. Three-hundred and twenty-nine euploid samples were randomly removed. The remaining 1933 high risk and 1660 baseline-risk plasma aliquots were assigned randomly between four laboratories and tested with two index NIPS tests, blind to maternal variables and pregnancy outcomes. The two index tests used massively parallel shotgun sequencing (semiconductor-based and optical-based). The reference standard for all fetuses was invasive cytogenetic analysis or clinical examination at birth and postnatal follow-up. For each chromosome of interest, chromosomal ratios were calculated (number of reads for chromosome/total number of reads). Euploid samples’ mean chromosomal ratio coefficients of variation were 0.48 (T21), 0.34 (T18), and 0.31 (T13). According to the reference standard, there were 155 cases of T21, 49 T18, 8 T13 and 22 45,X. Using a fetal fraction ≥4% to call results and a chromosomal ratio z-score of ≥3 to report a positive result, detection rates (DR), and false positive rates (FPR) were not statistically different between platforms: mean DR 99% (T21), 100%(T18, T13); 79%(45,X); FPR < 0.3% for T21, T18, T13, and <0.6% for 45,X. Both methods’ negative predictive values in high-risk pregnancies were >99.8%, except for 45,X(>99.6%). Threshold analysis in high-risk pregnancies with different fetal fractions and z-score cut-offs suggested that a z-score cutoff to 3.5 for positive results improved test accuracy. Both sequencing platforms showed equivalent and excellent clinical validity.

Maternal Malignancy Evaluation After Discordant Cell-Free DNA Results

Cell-free DNA screening for fetal aneuploidy is a commonly used testing strategy in pregnancies at high risk for fetal aneuploidy. The use of cell-free DNA screening is expanding to the low-risk population, because the detection rate for trisomy 21 surpasses that of traditional screening modalities. Although the sensitivity and specificity of cell-free DNA are superior to traditional screening, false-positive results do occur and may indicate an adverse maternal health condition, including maternal mosaicism or, rarely, malignancy. The risk of maternal cancer is significantly elevated when more than one aneuploidy is detected that is discordant from fetal karyotype. Given this risk as well as the rising incidence of cancer in pregnancy, patient counseling and malignancy evaluation should be considered in women when more than one aneuploidy is detected. We reviewed the published literature and developed an algorithm to evaluate women when these results are identified.

Current treatment of lymphoma in pregnancy

Introduction: Lymphoproliferative diseases occurring during pregnancy present the treating physician with unique diagnostic and therapeutic challenges, aiming to achieve maternal cure without impairing fetal health, growth, and survival. Due to the rarity of this complication, there is limited data to guide clinical decision-making, especially regarding the safety of novel emerging therapies. Areas covered: The presented review describes the current practice of treatment for Hodgkin's (HL) and non-Hodgkin's (NHL) lymphoma in the pregnant patient, according to disease stage and trimester of pregnancy. Novel agents for treatment of lymphoma in the setting of pregnancy are discussed. Therapeutic dilemmas and areas of uncertainty are illuminated. Expert opinion: HL and NHL are potentially curable diseases in the pregnant patient with generally good outcomes for the mother and the offspring, when tailoring the treatment according to the individual patient. The complexity of the situation merits shared decision-making with the patient and her family, explicitly outlining the risks and benefits. The pregnant patient is best managed by a multidisciplinary team, familiar with the intricacies of the gestational period, and providing the necessary support and sensitivity. Further studies are needed regarding the safety of novel agents in pregnancy.

Low fetal fraction of cell-free DNA predicts placental dysfunction and hypertensive disease in pregnancy

OBJECTIVE

To examine the association of low fetal fraction of cell-free DNA (cfDNA) with placental compromise and adverse perinatal outcomes.

MATERIALS AND METHODS

This was a retrospective cohort utilizing a sample of convenience including 639 women undergoing cfDNA screening at our institution from January 2013 to January 2017. Low fetal fraction was defined as less than the 25th percentile. Indicators of placental compromise were examined individually and as a composite outcome, including hypertensive disease of pregnancy, intrauterine growth restriction, abruption, and oligohydramnios. Neonatal outcomes, including preterm delivery, low Apgar scores, and small for gestational age, also were examined. We calculated risk ratios (RR) and 95% confidence intervals (CI).

RESULTS

Low fetal fraction was associated with placental compromise (RR 1.6 [CI 1.1-2.2]), hypertensive disease of pregnancy (RR 1.6 [CI 1.003-2.6]), and preeclampsia with severe features (RR 3.3 [CI 1.2-8.9]). Low fetal faction was not associated with preterm delivery, low Apgar scores, or small for gestational age.

CONCLUSIONS

Low fetal fraction of cfDNA among asymptomatic women may serve as a predictor of subsequent placental dysfunction and hypertensive disease.

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.

The consequences of implementing non-invasive prenatal testing with cell-free foetal DNA for the detection of Down syndrome in the Spanish National Health Service: a cost-effectiveness analysis

BACKGROUND

DNA-based non-invasive prenatal testing (NIPT) using maternal blood constitutes an emerging technology for the detection of Down syndrome (DS). The aim of the study was to conduct a cost-effectiveness analysis to evaluate the economic costs and health implications of the introduction of NIPT based on cell-free foetal DNA analysis through different screening strategies for the detection of DS.

METHODS

An analytical short-term decision model was developed, from the payer´s perspective (Spanish National Health Service). The main outcome measure was the number of DS cases detected. Secondary measures included associated miscarriages, women undergoing current screening, women undergoing NIPT, positive NIPT and invasive procedures performed. The study setting was the Spanish National Health Service. Three strategies were compared: (a) first- and second-trimester screening (current screening); (b) NIPT as contingent testing; and (c) NIPT as first-line testing. Modelling was based on a hypothetical cohort of 100,000 Spanish pregnant women. Population data were obtained from the database of the Basque Antenatal Screening Programme. Deterministic sensitivity analyses were performed to assess variations in the cost of NIPT, screening risk cut-off, screening uptake-rate and rate of failure of NIPT.

RESULTS

NIPT as contingent testing (strategy b) led to fewer miscarriages following invasive procedures and a slight reduction in the number of DS cases detected compared to current screening. However, lowering the screening cut-off to ≥ 1:500 would improve the overall effectiveness of NIPT as contingent testing, increasing the number of DS cases detected and decreasing foetal losses as compared to the current screening, despite there would be an extra-cost of 3.5%. When NIPT was used as first-line testing (strategy c), the screening would be more effective but also more expensive, with incremental cost-effectiveness ratios (ICERs) per additional case of DS detected of €1,299,763 and €1,232,763, compared with strategies a and b, respectively. Results were sensitive to the different parameters considered in the analysis.

CONCLUSIONS

Both, as first-line testing and as contingent testing when screening cut-off was lowered ≥ 1:500, NIPT would lead to more favourable outcomes as compared to the current screening (both in terms of DS cases detected and miscarriages avoided), but at a greater cost.

Development of Reference Materials for Noninvasive Prenatal Aneuploidy Testing by Massively Parallel Sequencing: A Proof-of-Concept Study

BACKGROUND

Noninvasive prenatal aneuploidy testing (NIPT) represents the first large-scale clinical application of massively parallel sequencing technology. However, no NIPT reference material (RM) has yet been widely adopted, impeding the development of quality management systems and standardization. Developing an NIPT RM from a biological sample is complicated by the low concentration of cell-free DNA (cfDNA), which implies pooling specimens and frequent resampling.

METHODS

We tested the feasibility of using DNA from immortalized cell lines of a woman and her aneuploid offspring to spike an artificial plasma matrix. Enzymatic fragmentation of extracted DNA was optimized to achieve fragment size profiles with a mode of 150 to 200 bp, similar to biological cfDNA. This synthetic material was compared with routine biological samples from pregnant women by a targeted NIPT assay in a multiplex sequencing run on a Proton platform.

RESULTS

Sequencing statistics were similar between artificially prepared material and routine biological samples, as well as relative chromosomal representation, and no matrix effects could be detected. Estimate of fetal fraction (FF) was within the range of expected value, and aneuploidy detection statistic (z-score) was also comparable between both types of samples.

CONCLUSIONS

Artificial plasma spiked with DNA from cell lines of mother and offspring is a promising strategy for developing NIPT RM. This type of material would offer the advantage of a constant and stable composition, allowing for greater standardization of NIPT assays. Moreover, it preserves the parental relatedness used by targeted assay to estimate FF by identification of paternal alleles in single-nucleotide polymorphisms or other variable regions.

Factors associated with common and atypical chromosome abnormalities after positive combined first-trimester screening in Chinese women: a retrospective cohort study

BACKGROUND

When cell-free DNA (cfDNA) testing is used as a secondary screening tool following combined first-trimester screening (cFTS), cFTS is used to estimate the prior risk for chromosome abnormalities. This study aimed to assess the factors that are associated with common and atypical abnormalities following cFTS, including cFTS risk, advanced maternal age, increased nuchal translucency (NT) ≥3.5 mm, and abnormal levels of serum markers.

METHODS

We reviewed a historical cohort of 1855 Chinese women carrying singleton pregnancies with a positive cFTS [at a threshold of 1:250 for trisomy (T) 21 or 1:180 for T18] in one public hospital over a five-year period. All chromosome abnormalities were confirmed by invasive prenatal diagnosis (IPD) with karyotyping, with or without array comparative genomic hybridization. Using multivariable binary logistic regression analysis, we determined the parameters that were associated with common and atypical abnormalities.

RESULTS

Overall, the prevalence of common and atypical abnormalities was 6.2 and 1.2%, respectively, and the prevalence increased with the risk of T21 by cFTS. In pregnancies with a risk of T21 > 1 in 100, a high risk of both T21 and T18, an increased NT, or a pregnancy-associated plasma A (PAPP-A) level <  0.2 multiple of medians (MoM), the prevalence of common abnormalities was 12.2, 64.7, 25.5 and 33.8%, respectively, while that of atypical abnormalities was 1.6, 3.9, 4.2, and 7.4%, respectively. In the multivariable binary logistic regression analysis, out of these four factors, only two (increased NT and PAPP_A <  0.2 MoM) were significant predictors of common and atypical abnormalities, respectively. Of all positive cFTS pregnancies, 50.4% did not have any of these four factors, and the prevalence of common and atypical abnormalities was 1.1 and 0.6%, respectively. There were three atypical abnormalities, all of which were mosaicism, and they were detected among women with IPD alone. The ages of these women were ≥ 35 years. All three pregnancies were continued after proper counseling. After giving birth, only one child had mild abnormalities, while the other two were phenotypically normal.

CONCLUSIONS

Our study identified factors associated with common and atypical abnormalities after cFTS. These factors can be used to estimate the prior risk for these abnormalities to help with post-cFTS counseling in terms of choosing between cfDNA testing and IPD.

Prenatal cell-free DNA screening for fetal aneuploidy in pregnant women at average or high risk: Results from a large US clinical laboratory

BACKGROUND

We evaluated the performance of a cell-free DNA (cfDNA) prenatal screening assay for trisomies 21, 18, and 13, and sex chromosome aneuploidies (SCAs) among a population of pregnant women that included both those at average and high risk.

METHODS

Specimen collection, cfDNA extraction, massively parallel sequencing, and bioinformatics analysis were conducted per laboratory protocol. Assay results, concordance with pregnancy outcomes, and performance characteristics were evaluated.

RESULTS

A total 75,658 specimens from 72,176 individual pregnant women were received. Technical reasons accounted for 288 (0.4% of all received samples) tests not performed. In the final analysis cohort (N = 69,794), 13% of pregnancies were considered at average risk and 87% at high risk. Mean gestational age at specimen collection was 15.1 weeks. Of the 69,794 unique pregnancies, 1,359 (1.9%) had positive test results. Among the results with confirmed outcomes, PPV for trisomies 21, 18, and 13 was 98.1%, 88.2%, and 59.3%, respectively; the PPV was 69.0% for SCAs and 75.0% for microdeletions. Overall, PPV was 87.2%, sensitivity was 97.9%, and specificity was 99.9%.

CONCLUSION

This cfDNA prenatal screening assay provides highly accurate discrimination between affected and unaffected pregnancies among a population of pregnant women at average and high risk for fetal genetic abnormalities.

Abnormal nuchal translucency: residual risk with normal cell-free DNA screening

Objective: To determine the proportion of genetic abnormalities that could be identified by cell-free DNA screening in pregnancies with an abnormal nuchal translucency.Methods: From 2015-2017, pregnancies with nuchal translucency ≥ 3.0 mm on ultrasounds were identified. Pregnancies with genetic testing results were included, whether or not cell-free DNA screening was performed. Comparisons of the proportion of genetic abnormalities detectable on cell-free DNA screening versus not detectable were made based on nuchal translucency values (3.0-3.4 mm; ≥3.5 mm) and maternal age (≥35 versus <35 years). Chi-square analysis, Fisher's exact test, and Mann-Whitney U were used for statistical comparison.Results: One hundred ten patients were included, 60 had genetic abnormalities (54.5%), with 44 (73.3%) detectable on cell-free DNA screening and 16 (26.7%) not. In those with nuchal translucency ≥3.5 mm, only 40 of 56 (71.4%) of abnormalities could be detected by cell-free DNA screening. Cell-free DNA screening could identify 27 of 31 abnormalities with nuchal translucency ≥3.5 mm in women ≥35 years but could identify only 13 of 25 genetic abnormalities in younger women (87.1 versus 52.0%; p = .005).Conclusion: A significant proportion of abnormalities in those with nuchal translucency ≥3.5 mm would not be detected by cell-free DNA, especially in younger women.

Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned

OBJECTIVE

Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement.

METHODS

A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR.

RESULTS

Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism).

CONCLUSIONS

Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.

Beyond the Brochure: Innovations in Clinical Counseling Practices for Prenatal Genetic Testing Options

Remarkable advancements related to preconception and prenatal genetic screening have emerged in recent years. While technology and testing options are more numerous and complex; fundamental genetic counseling issues remain the same. It is essential that with any prenatal genetic testing, women have an opportunity to make informed and autonomous decisions that are consistent with their personal needs and values. Opportunities to discuss testing options, including potential benefits and limitations, are often limited in obstetric visits due to time constraints or lack of sufficient provider education. As genetic testing is not considered a routine component of antepartum care, review of information regarding testing options is imperative so women can decide which, if any, testing to pursue. Developing new strategies to address the growing complexity of prenatal testing while ensuring provider education is accurate is crucial in imparting evidence-based care. This article will arm providers with the knowledge needed to educate women about currently available prenatal genetic screening and diagnostic tests along with guidance on the essential elements and importance of genetic counseling.

Certified Nurse-Midwives' Experiences With Provision of Prenatal Genetic Screening: A Case for Interprofessional Collaboration

Prenatal genetic screening (GS) for the most common autosomal aneuploidies encompasses maternal serum screening (MSS) and noninvasive prenatal testing (NIPT, or cell-free fetal DNA testing). In the United States, most maternity care is provided by obstetrician-gynecologists; however, women are increasingly utilizing the services of certified nurse-midwives (CNMs). Currently, limited research exists on midwives' experiences with providing prenatal GS. Therefore, the purpose of this study was to explore CNMs' experiences in providing prenatal GS. A semistructured guide focused on MSS and NIPT was used to interview a convenience sample of 13 CNMs. Results were coded and analyzed using grounded theory to elicit overarching themes. Results were organized into 6 themes describing CNMs' prenatal GS provision: (1) clinical protocols; (2) patient education; (3) patient-CNM shared decision-making process; (4) testing initiation; (5) results delivery; and (6) follow-up coordination. Key influences on midwives' perspectives on offering prenatal GS included a noninterventionist approach to pregnancy and past experiences with false-positive MSS results. Participants had an understanding of prenatal GS that was appropriate to midwifery scope of practice. Results indicate that NIPT utilization is compatible with the midwifery philosophy of noninterventionism, although midwives had limited experiences with NIPT to date.

Counting-based cell-free DNA screening test fails to identify triploidy-A case report

Although noninvasive prenatal testing (NIPT) is a good test with high sensitivity and specificity for trisomy 21, 18, and 13, it remains a screening test and cannot be used for diagnostic purposes. It is important to consider the outcomes of this test and interpret the results and offer consultation accordingly.

Fetal fraction-based risk algorithm for non-invasive prenatal testing: screening for trisomies 13 and 18 and triploidy in women with low cell-free fetal DNA

OBJECTIVE

To identify pregnancies at increased risk for trisomy 13, trisomy 18 or triploidy attributable to low fetal fraction (FF).

METHODS

A FF-based risk (FFBR) model was built using data from more than 165 000 singleton pregnancies referred for single-nucleotide polymorphism (SNP)-based non-invasive prenatal testing (NIPT). Based on maternal weight and gestational age (GA), FF distributions for normal, trisomy 13, trisomy 18 and triploid pregnancies were constructed and used to adjust prior risks for these abnormalities. A risk cut-off of ≥ 1% was chosen to define pregnancies at high risk for trisomy 13, trisomy 18 or triploidy (high FFBR score). The model was evaluated on an independent blinded set of pregnancies for which SNP-based NIPT did not return a result, and for which pregnancy outcome information was gathered retrospectively.

RESULTS

The evaluation cohort comprised 1148 cases, of which approximately half received a high FFBR score. Compared with rates expected based on maternal age (MA) and GA, cases with a high FFBR score had a significantly increased rate of trisomy 13, trisomy 18 or triploidy combined (5.7% vs 0.7%; P < 0.001) and also of unexplained pregnancy loss (14.7% vs 10.4%; P < 0.001). For cases that did not receive a high FFBR score, the incidence of a chromosomal abnormality or pregnancy loss was not significantly different from that expected based on MA and GA. In this study cohort, the sensitivity of the FFBR model for detection of trisomy 13, trisomy 18 or triploidy was 91.4% (95% CI, 76.9-98.2%) with a positive predictive value of 5.7% (32/564; 95% CI, 3.9-7.9%).

CONCLUSIONS

For pregnancies with a FF too low to receive a result on standard NIPT, the FFBR algorithm identified a subset of cases at increased risk for trisomy 13, trisomy 18 or triploidy. For the remainder of cases, the risk of a fetal chromosomal abnormality was unchanged from that expected based on MA and GA. © 2018 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.

Autoimmune disorders but not heparin are associated with cell-free fetal DNA test failure

Background

Recent studies have suggested a possible association between heparin treatment at the time of cell-free DNA (cfDNA) testing and a non-reportable result. However, these studies lack of proper methodology and had a low level of proof to firmly incriminate heparin. Our objective was to investigate further the relationship between heparin treatment and cfDNA test results.

Methods

Two complementary approaches were used for the demonstration. First, we conducted a retrospective analysis of a cohort of patients with a singleton pregnancy, screened for aneuploidies by using cfDNA, but with a non-reportable cfDNA result. We included patients between 2013 and 2016 including the patients from the DEPOSA study as controls. CfDNA testing was performed by massive parallel sequencing by using a whole-genome approach. A multiple logistic regression was used to account for the influence of the variables included. Second, we performed in vitro experiments on mimic samples containing increased concentrations of heparin.

Results

Of 9867 singleton pregnancies tested during the inclusion period, 58 (0.59%) had a non-reportable result and were compared to 295 control patients. Fifteen (25.9%) and 20 (6.8%) patients were treated with heparin in the group with a non-reportable cfDNA result and with a successful assay, respectively. In multivariable analysis, an increased calculated risk at the first-trimester combined screening (OR 28.8 CI 9.76–85.15, p < 0.001), maternal weight (OR 1.03, CI 1.01–1.06, p = 0.01), and the presence of an autoimmune disease (OR 10.38, CI 1.62–66.53, p = 0.01) were the only characteristics associated with a non-reportable result. In vitro experiments showed that heparin had no impact on fetal fraction measurement or the final result, no matter what the dose tested.

Conclusions

Treatment by heparin had no impact on cfDNA screening test for aneuploidies, while the presence of an autoimmune disorder is an independent predictor of a non-reportable result.

Whole Exome Sequencing: Applications in Prenatal Genetics

Prenatal whole exome sequencing (WES) has the potential to increase the ability to provide more diagnostic capabilities in fetuses with sonographic abnormalities, which would then improve the ability to counsel families. It is also often the first step in improving the path toward informed diagnosis and treatment, which is especially important in the era of advancing in utero fetal therapy. This article discusses the current literature regarding prenatal WES, clinical indications for WES, challenges with interpretation/counseling (variants of unknown significance), research priorities, ethical issues, and potential future advances.