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

Anticoagulation use is associated with lower fetal fraction and more indeterminate results

BACKGROUND

Maternal anticoagulation use may increase indeterminate result rates on cell-free DNA-based screening, but existing studies are confounded by inclusion of individuals with autoimmune disease, which alone is associated with indeterminate results. Changes in chromosome level Z-scores are proposed by others as a reason for indeterminate results, but the etiology of this is uncertain.

OBJECTIVE

This study aimed to evaluate differences in fetal fraction, indeterminate result rate, and total cell-free DNA concentration in individuals on anticoagulation without autoimmune disease compared with controls undergoing noninvasive prenatal screening. Secondly, using a nested case-control design, we evaluated differences in fragment size, GC-content, and Z-scores to evaluate laboratory-level test characteristics.

STUDY DESIGN

This was a retrospective single-institution study of pregnant individuals undergoing cell-free DNA-based noninvasive prenatal screening using low-pass whole-genome sequencing between 2017 and 2021. Individuals with autoimmune disease, suspected aneuploidy, and cases where fetal fraction was not reported were excluded. Anticoagulation included heparin-derived products (unfractionated heparin, low-molecular-weight heparin), clopidogrel, and fondaparinux, with a separate group for those on aspirin alone. An indeterminate result was defined as fetal fraction <4%. We evaluated the association between maternal anticoagulation or aspirin use, and fetal fraction, indeterminate results, and total cell-free DNA concentration using univariate and multivariate analyses, controlling for body mass index, gestational age at sample collection, and fetal sex. For the anticoagulation cohort, we compared laboratory-level test characteristics among cases (on anticoagulation) and a subset of controls. Lastly, we evaluated for differences in chromosome level Z-scores among those on anticoagulation with and without indeterminate results.

RESULTS

A total of 1707 pregnant individuals met the inclusion criteria. Of those, 29 were on anticoagulation and 81 were on aspirin alone. For those on anticoagulation, the fetal fraction was significantly lower (9.3% vs 11.7%; P<.01), the indeterminate result rate was significantly higher (17.2% vs 2.7%; P<.001), and the total cell-free DNA concentration was significantly higher (218 pg/μL vs 83.7 pg/μL; P<.001). Among those on aspirin alone, the fetal fraction was lower (10.6% vs 11.8%; P=.04); however, there were no differences in the rate of indeterminate results (3.7% vs 2.7%; P=.57) or total cell-free DNA concentration (90.1 pg/μL vs 83.8 pg/μL; P=.31). After controlling for maternal body mass index, gestational age at sample collection, and fetal sex, anticoagulation was associated with an >8-fold increase in the likelihood of an indeterminate result (adjusted odds ratio, 8.7; 95% confidence interval, 3.1-24.9; P<.001), but not aspirin (adjusted odds ratio, 1.2; 95% confidence interval, 0.3-4.1; P=.8). Anticoagulation was not associated with appreciable differences in cell-free DNA fragment size or GC-content. Although differences in chromosome 13 Z-scores were observed, none were observed for chromosomes 18 or 21, and this difference did not contribute to the indeterminate result call.

CONCLUSION

In the absence of autoimmune disease, anticoagulation use, but not aspirin, is associated with lower fetal fraction, higher total cell-free DNA concentration, and higher rates of indeterminate results. Anticoagulation use was not accompanied by differences in cell-free DNA fragment size or GC-content. Statistical differences in chromosome level Z-scores did not clinically affect aneuploidy detection. This suggests a likely dilutional effect by anticoagulation on cell-free DNA-based noninvasive prenatal screening assays contributing to low fetal fraction and indeterminate results, and not laboratory or sequencing-level changes.

Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing

Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.

Analysis of retest reliability for pregnant women undergoing cfDNA testing with a no-call result

BACKGROUND

Determining the reasons for unreportable or no-call cell-free DNA (cfDNA) test results has been an ongoing issue, and a consensus on subsequent management is still lacking. This study aimed to explore potential factors related to no-call cfDNA test results and to discuss whether retest results are reliable.

METHODS AND RESULTS

This was a retrospective study of women with singleton pregnancies undergoing cfDNA testing in 2021. Of the 9871 pregnant patients undergoing cfDNA testing, 111 had a no-call result, and their results were compared to those of 170 control patients. The no-call rate was 1.12% (111/9871), and the primary cause for no-call results was data fluctuation (88.29%, 98/111). Medical conditions were significantly more frequent in the no-call group than in the reportable results group (P < 0.001). After retesting, 107 (107/111, 96.40%) patients had a result, and the false-positive rate (FPR) of retesting was 10.09% (10.09%, 11/109). In addition, placental lesions were more frequent in the no-call group than in the reportable results group (P = 0.037), and 4 patients, all in the no-call group, experienced pregnancy loss.

CONCLUSIONS

Pregnant women with medical conditions are more likely to have a no-call result. A retest is suggested for patients with a no-call result, but retests have a high FPR. In addition, pregnant women with a no-call result are at increased risk of adverse pregnancy outcomes. In conclusion, more attention should be given to pregnant women for whom a no-call cfDNA result is obtained.

Maternal, neonatal, pregnancy outcome characteristics of pregnant women with high plasma cell-free DNA concentration in non-invasive prenatal screening: a retrospective analysis

Objective

Cell-free DNA (cfDNA) is a useful biomarker in various clinical contexts. Herein, we aimed to identify maternal characteristics and pregnancy outcomes associated with a failed NIPS test due to high cfDNA concentrations.

Methods

A retrospective study of cases with high plasma cfDNA concentration in pregnant women in which NIPS test was performed (from 174,318 cases). We reported the detection of 126 cases (118 with complete clinical information) in which the high amount of cfDNA did not allow the performance of NIPS and study the possible causes of this result.

Results

622 (0.35%) of 174,318 pregnant women had failed the NIPS test, including 126 (20.3%) cases with high plasma cfDNA concentrations. The failed NIPS due to high plasma cfDNA concentrations was associated with maternal diseases and treatment with low-molecular-weight heparin (LMWH). Further follow-up of the 118 pregnant women in the case group revealed that the pregnancy outcomes included 31 premature deliveries, 21 abortions. The cfDNA concentrations of pregnant women with preterm deliveries were 1.15 (0.89, 1.84), which differed significantly from those who had full-term deliveries.

Conclusions

Among pregnant women with high cfDNA concentrations, systemic autoimmune diseases, pregnancy complications and LMWH were associated with increased incidence of failed NIPS test. High maternal cfDNA concentrations may not be associated with chromosomal abnormalities in the fetus. However, they should be alerted to the possibility of preterm births and stillbirths. Further clinical studies on pregnant women with high cfDNA concentrations are required.

The effects of heparin, aspirin, and maternal clinical factors on the rate of nonreportable cell-free DNA results: a retrospective cohort study

BACKGROUND

Technological advances in the analysis of cell-free DNA in maternal serum have allowed expanded prenatal screening possibilities for fetal aneuploidies. The sensitivity and positive predictive value of the assay are partly dependent on the amount of cell-free DNA present in maternal circulation. Thus, it is important to know what fetal and maternal factors influence the level of cell-free DNA in maternal circulation. Maternal heparin use has been associated with an increase in nonreportable cell-free DNA results because of a low fetal fraction in some, but not all, previous studies. In addition, there are likely additional factors that affect cell-free DNA that remain uncharacterized.

OBJECTIVE

This study aimed to determine whether heparins, low-dose aspirin, and maternal clinical factors affect the rate of nonreportable cell-free DNA testing results.

STUDY DESIGN

A retrospective cohort study was conducted using pregnant people receiving cell-free fetal DNA testing from January 1, 2014, to June 30, 2018. Data were collected on patient demographics, medical comorbidities, medication use, and cell-free DNA test results. Univariate and multivariate analyses were performed to determine which factors were independently associated with the rate of nonreportable results.

RESULTS

From an original sample of 1117 pregnant people, 743 met the inclusion criteria. Maternal weight (odds ratio, 1.02), heparin use (odds ratio, 12.06), aspirin use (odds ratio, 4.70), chronic hypertension (odds ratio, 5.26), pregestational diabetes mellitus (odds ratio, 2.46), and autoimmune disease (odds ratio, 3.59) were significantly associated with an increased rate of nonreportable results in the univariate analysis. Moreover, the association was present for maternal weight (odds ratio, 1.02), heparin use (odds ratio, 21.87),and aspirin use (odds ratio, 2.85) in the multivariate analysis.

CONCLUSION

The previously seen association between maternal heparin use and an increase in nonreportable cell-free DNA results was confirmed. Furthermore, there seems to be an increase in nonreportable results in pregnant people taking low-dose aspirin. Providers should consider the effect of these medications when counseling patients on prenatal genetic screening options.

Factors affecting low fetal fraction in fetal screening with cell-free DNA in pregnant women: a systematic review and meta-analysis

BACKGROUND

Cell-Free DNA (cfDNA) is a non-invasive perinatal test (NIPT) used to assess fetal anomalies. The ability to detect fetal chromosomal aneuploidies is directly related to a sample's fetal to total DNA fraction, known as the fetal fraction (FF). The minimum FF is considered 4%, and the test result below 4% is uncertain due to low fetal fraction (LFF). This study aimed to conduct a systematic review and a meta-analysis to determine the possible factors affecting LFF in cfDNA testing for fetal screening.

METHODS

PubMed, Web of Science, Google Scholar, Since Direct, Scopus, CINHAL, Cochrane Library, and Persian databases, including Scientific Information Database, Irandoc, and Magiran were searched for studies investigating factors affecting LFF in cfDNA testing from 2000 until the end of 2021. Gathered data were analyzed using Comprehensive Meta-Analysis (CMA) software version 3.3.070. The quality of the included studies was assessed using the Joanna Briggs Institute Critical Appraisal of Cohort Studies tool.

RESULTS

Thirteen articles related to the topic were included, and seven related articles were reviewed for meta-analysis. The other six were reviewed qualitatively. Four factors were identified that might have a potential effect on the LFF, of which only gestational age had a significant association with LFF (Pooled mean difference= -1.111, SE = 0.515, 95% CI= -2.121, -0.101, (P-value < 0.05)). Maternal age (P-value = 0.573), maternal weight (P-value = 0.113), and Body Mass Index (P-value = 0.104) had no statically significant effect. The effect size was pooled by mean difference and 95% confidence interval.

CONCLUSION

Lower gestational age is significantly associated with LFF. Thus, this factor can be considered when interpreting prenatal cfDNA screening tests.

Machine learning-based detection of immune-mediated diseases from genome-wide cell-free DNA sequencing datasets

The early detection of tissue and organ damage associated with autoimmune diseases (AID) has been identified as key to improve long-term survival, but non-invasive biomarkers are lacking. Elevated cell-free DNA (cfDNA) levels have been observed in AID and inflammatory bowel disease (IBD), prompting interest to use cfDNA as a potential non-invasive diagnostic and prognostic biomarker. Despite these known disease-related changes in concentration, it remains impossible to identify AID and IBD patients through cfDNA analysis alone. By using unsupervised clustering on large sets of shallow whole-genome sequencing (sWGS) cfDNA data, we uncover AID- and IBD-specific genome-wide patterns in plasma cfDNA in both the obstetric and general AID and IBD populations. We demonstrate that pregnant women with AID and IBD have higher odds of receiving inconclusive non-invasive prenatal screening (NIPS) results. Supervised learning of the genome-wide patterns allows AID prediction with 50% sensitivity at 95% specificity. Importantly, the method has the potential to identify pregnant women with AID during routine NIPS. Since AID pregnancies have an increased risk of severe complications, early recognition or detection of new-onset AID can redirect pregnancy management and limit potential adverse events. This method opens up new avenues for screening, diagnosis and monitoring of AID and IBD.

Association of fetal fraction with hypertensive disorders of pregnancy incidence and disease severity

BACKGROUND

Hypertensive disorders of pregnancy contribute to maternal and offspring morbidity and mortality. Studies suggest that a lower early pregnancy fetal fraction is associated with an increased risk of hypertensive disorders of pregnancy. However, maternal obesity significantly affects fetal fraction and is a risk factor for hypertensive disorders of pregnancy.

OBJECTIVE

We determined the association between fetal fraction (using a standardized single-institution platform, including male and female fetuses) and hypertensive disorders of pregnancy, stratified by obesity status. Second, we evaluated differences in total cell-free DNA concentration and correlation of fetal fraction with clinical markers of hypertensive disorders of pregnancy severity.

STUDY DESIGN

This was a retrospective, single-institution study of a previously validated cell-free DNA-based noninvasive prenatal screening assay of 1058 samples. Maternal body mass index at the time of noninvasive prenatal screening was assessed, and hypertensive disorders of pregnancy were confirmed by a detailed medical record review. Differences in fetal fraction and total cell-free DNA concentration between the groups were assessed with univariate analyses. Multivariable regression was used to evaluate the association between fetal fraction and hypertensive disorders of pregnancy, adjusted for body mass index, maternal age, gestational age at noninvasive prenatal screening, and fetal sex. The association between fetal fraction and hypertensive disorders of pregnancy among individuals with obesity (body mass index, ≥30 kg/m2) and individuals without obesity (body mass index, <30 kg/m2) was investigated while controlling for the aforementioned covariates. Lastly, multivariable linear regression was used to evaluate the association between fetal fraction and clinical markers of hypertensive disorders of pregnancy severity.

RESULTS

We identified individuals with (n=117) and without (n=941) hypertensive disorders of pregnancy with noninvasive prenatal screening drawn before 20 weeks of gestation and with fetal fraction and body mass index data available. Those with hypertensive disorders of pregnancy had a lower fetal fraction (10.2%±4.2% vs 11.6%±4.7%; P<.01), without differences in total cell-free DNA concentration (P=.14). When groups were stratified by obesity status, this relationship was only valid for individuals without obesity (P=.02). Only when logistic regression analysis was restricted to individuals without obesity did the likelihood of hypertensive disorders of pregnancy rise with decreasing fetal fraction (odds ratio, 0.93; 95% confidence interval, 0.88-0.99; P=.02). In addition, fetal fraction was inversely associated with maximum systolic blood pressure at the time of hypertensive disorders of pregnancy only in the population without obesity (β, -0.08; 95% confidence interval, -0.147 to -0.01; P=.02).

CONCLUSION

Although a lower fetal fraction is associated with the development of hypertensive disorders of pregnancy, the use of this parameter for the prediction may be problematic in individuals with obesity, as obesity has such a profound effect on fetal fraction. However, we uniquely noted that among individuals without obesity, fetal fraction is lower for those that develop hypertensive disorders of pregnancy and lower fetal fraction increases the odds of hypertensive disorders of pregnancy development. Lastly, low fetal fraction in the population without obesity that developed hypertensive disorders of pregnancy was associated with higher systolic blood pressure at the time of hypertensive disorders of pregnancy, an important clinical marker of hypertensive disorders of pregnancy severity. As analytical approaches of cell-free DNA interrogation advance, the prediction of placental-mediated disorders with first-trimester sampling is likely to improve, although this may remain challenging in gravidas with obesity, a cohort at high risk of developing hypertensive disorders of pregnancy.

Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review

A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.

The impact of maternal autoimmune disease on cell-free DNA test characteristics

BACKGROUND

Maternal biologic factors can affect the fetal fraction in cell-free DNA-based prenatal screening assays, thereby limiting the effectiveness. Higher rates of indeterminate results because of a low fetal fraction have been described in cases of maternal autoimmune disease in pregnancy. Existing studies are confounded by the concomitant maternal use of anticoagulants, which may independently influence the test characteristics.

OBJECTIVE

This study aimed to evaluate the differences in fetal fraction, indeterminate results, and total cell-free DNA concentration among women with an autoimmune disease in comparison with controls, using our in-house developed, noninvasive prenatal screening platform in the absence of maternal anticoagulation use.

STUDY DESIGN

This was a retrospective, single institution cohort study of a previously validated, cell-free DNA-based, noninvasive prenatal screening assay using a low-pass whole-genome sequencing platform between 2017 and 2019. A diagnosis of an autoimmune disease included systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, and others. Immunomodulator therapies included biologics, corticosteroids, hydroxychloroquine, azathioprine, and intravenous immunoglobulin. Women who were using anticoagulants were excluded. We evaluated the association between autoimmune disease and fetal cell-free DNA fraction, indeterminate results, and total cell-free DNA concentration using univariate and multivariate analyses, stratified according to immunomodulator therapy and adjusted for body mass index, fetal sex, and gestational age at sample collection.

RESULTS

A total of 1445 patients met inclusion criteria. Of those, 43 women had a confirmed autoimmune disease, with 25 of those not on immunomodulator therapy and 18 on immunomodulator therapy. The mean fetal fraction for women with an autoimmune disease was significantly lower than for controls (9.7% vs 11.9%; P=.004). The rate of indeterminate results was significantly higher among women with an autoimmune disease than among controls (16.3% vs 3.5%; P<.001). The total cell-free DNA concentration was not statistically different between the groups (94.8 pg/µL for women with an autoimmune disease vs 83.9 pg/µL for controls; P=.06). In a logistic regression, women with an autoimmune disease had significantly higher odds of receiving an indeterminate result than controls, (adjusted odds ratio, 5.3; 95% confidence interval, 2.0-14.2). Linear regression analysis showed a significant negative association between having an autoimmune disease and the fetal cell-free DNA fraction (aβ, -2.1; 95% confidence interval, -3.4 to -0.6). When stratifying by treatment status, the mean fetal fraction was 9.8%, 9.6%, and 11.9% for women with an autoimmune disease not on immunomodulator therapy, women with an autoimmune disease on immunomodulator therapy, and the controls, respectively (P=.02). The rate of indeterminate results increased in a stepwise fashion from 3.5% to 11.1% to 20.0% for controls, women with an autoimmune disease on immunomodulator therapy, and women with an autoimmune disease not on immunomodulator therapy, respectively (P<.001). Logistic regression analysis demonstrated higher odds of an indeterminate result for women with an autoimmune disease not on immunomodulator therapy than for controls, (adjusted odds ratio, 7.3; 95% confidence interval, 2.3-22.5). There was a negative association between women with an autoimmune disease not on immunomodulator therapy and the fetal fraction when compared with controls (aβ, -2.2; 95% confidence interval, -4.2 to -0.3).

CONCLUSION

Women with an autoimmune disease have lower fetal cell-free DNA fractions and higher rates of indeterminate results than women without an autoimmune disease. There was no difference in total cell-free DNA concentration. Treatment of maternal autoimmune diseases with immunomodulator therapy may decrease the indeterminate result rate.

PGT-A: who and when? Α systematic review and network meta-analysis of RCTs

PURPOSE

Wide controversy is still ongoing regarding efficiency of preimplantation genetic testing for aneuploidy (PGT-A). This systematic review and meta-analysis, aims to identify the patient age group that benefits from PGT-A and the best day to biopsy.

METHODS

A systematic search of the literature was performed on MEDLINE/PubMed, Embase and Cochrane Central Library up to May 2020. Eleven randomized controlled trials employing PGT-A with comprehensive chromosomal screening (CCS) on Day-3 or Day-5 were eligible.

RESULTS

PGT-A did not improve live-birth rates (LBR) per patient in the general population (RR:1.11; 95%CI:0.87-1.42; n=1513; I2=75%). However, PGT-A lowered miscarriage rate in the general population (RR:0.45; 95%CI:0.25-0.80; n=912; I2=49%). Interestingly, the cumulative LBR per patient was improved by PGT-A (RR:1.36; 95%CI:1.13-1.64; n=580; I2=12%). When performing an age-subgroup analysis PGT-A improved LBR in women over the age of 35 (RR:1.29; 95%CI:1.05-1.60; n=692; I2=0%), whereas it appeared to be ineffective in younger women (RR:0.92; 95%CI:0.62-1.39; n=666; I2=75%). Regarding optimal timing, only day-5 biopsy practice presented with improved LBR per ET (RR: 1.37; 95% CI: 1.03-1.82; I2=72%).

CONCLUSION

PGT-A did not improve clinical outcomes for the general population, however PGT-A improved live-birth rates strictly when performed on blastocyst stage embryos of women over the 35-year-old mark.

Low fetal fraction in obese women at first trimester cell-free DNA based prenatal screening is not accompanied by differences in total cell-free DNA

OBJECTIVE

Reasons for first trimester noninvasive prenatal screening (NIPS) test failure in obese women remain elusive. As dilution from maternal sources may be explanatory, we determined the relationship between obesity, fetal fraction (FF), and total cell-free DNA (cfDNA) using our NIPS platform.

METHODS

We assessed differences in first trimester (≤14 weeks) FF, indeterminate rate, and total cfDNA between obese (n = 518) and normal-weight women (n = 237) after exclusion of confounders (anticoagulation, autoimmunity, aneuploidy) and controlling for covariates.

RESULTS

Fetal fraction was lower, and the indeterminate rate higher, in obese compared to controls (9.2% ± 4.4 vs. 12.5% ± 4.5, p < 0.001 and 8.4 vs. 1.7%, p < 0.001, respectively), but total cfDNA was not different (92.0 vs. 82.1 pg/µl, p = 0.10). For each week, the FF remained lower in obese women (all p < 0.01) but did not increase across the first trimester for either group. Obesity increased the likelihood of indeterminate result (OR 6.1, 95% CI 2.5, 14.8; p < 0.001) and maternal body mass index correlated with FF (β -0.27, 95% CI -0.3, -0.22; p < 0.001), but not with total cfDNA (β 0.49, 95% CI -0.55, 1.53; p = 0.3).

CONCLUSIONS

First trimester obese women have persistently low FF and higher indeterminate rates, without differences in total cfDNA, suggesting placental-specific mechanisms versus dilution from maternal sources as a potential etiology.

Impact of Emerging Technologies in Prenatal Genetic Counseling

For decades, prenatal testing has been offered to evaluate pregnancies for genetic conditions. In recent years, the number of testing options and range of testing capabilities has dramatically increased. Because of the risks associated with invasive diagnostic testing, research has focused on the detection of genetic conditions through screening technologies such as cell-free DNA. Screening for aneuploidy, copy number variants, and monogenic disorders is clinically available using a sample of maternal blood, but limited data exist on the accuracy of some of these testing options. Additional research is needed to examine the accuracy and utility of screening for increasingly rare conditions. As the breadth of prenatal genetic testing options continues to expand, patients, clinical providers, laboratories, and researchers need to find collaborative means to validate and introduce new testing technologies responsibly. Adequate validation of prenatal tests and effective integration of emerging technologies into prenatal care will become even more important once prenatal treatments for genetic conditions become available.

Nonreportable rates and cell-free DNA profiles in noninvasive prenatal testing among women with heparin treatment

OBJECTIVE

To evaluate the "nonreportable" rate in patients treated with heparin and to determine the effect of heparin on the results of noninvasive prenatal testing (NIPT).

METHOD

This was a single-center retrospective study of NIPT. The "nonreportable" rate of NIPT was evaluated according to presence or absence of heparin treatment. After excluding true-positive cases, a matched cohort study evaluating Z-scores, GC bias, and cell-free DNA (cfDNA) profiles was performed to investigate the effect of heparin on NIPT results.

RESULTS

Overall, 2651 singleton pregnancies with available clinical information were evaluated; 23 mothers were treated with heparin. The nonreportable rate was much higher among patients treated with heparin than among those who were not (8.70% vs 0.15%). In the matched cohort study, the Z-scores for chromosomes 13, 18, and 21, and GC bias were significantly higher in the heparin group than in the matched control group. Based on cfDNA library electrophoresis data, the proportion of short-sized cfDNA was higher in the heparin group.

CONCLUSION

Heparin use increased the nonreportable rate of NIPT results by borderline Z-scores, possibly caused by the increased proportions of shorter and GC-rich cfDNA fragments. This information will be helpful for prenatal genetic counseling for patients requiring heparin treatment.

Potential of Next-Generation Sequencing in Noninvasive Fetal Molecular Blood Group Genotyping

Hemolytic disease of the fetus and newborn and fetal and neonatal alloimmune thrombocytopenia are caused by maternal antibodies against fetal alloantigens on red blood cells or platelets that are inherited from the father. After transplacental transport to the fetal circulation, antibodies of the IgG class may cause severe fetal anemia or bleeding complications. The indication for noninvasive fetal blood group genotyping is given if a clinically relevant antibody is detected in a pregnant woman and if the father is heterozygous (or unknown) for the implicated blood group allele. This mini-review will focus on the advantages and current limitations of next-generation sequencing (NGS) for noninvasive diagnosis of fetal blood groups which is, in contrast to fetal aneuploidy screening, proposed only by some research groups. Targeted massively parallel sequencing of short DNA fragments from maternal cell-free plasma samples enables counting of fetal alleles for many single nucleotide polymorphisms in parallel. This information can be utilized for estimation of the fetal fraction of cell-free DNA (cfDNA) as well as detection of the paternal blood group allele in question. Adherence to a cut-off of ≥4% fetal fraction for reporting conclusive results is recommended to avoid false-negative results due to low fetal fraction. For screening purposes of fetal RHD in RhD-negative pregnant women, real-time PCR methods are very well established. However, for diagnostic purposes, the targeted amplicon-based NGS approach has the inherent capability to estimate the fetal fraction of cfDNA. In the future, improving the accuracy of NGS by consensus sequencing of single cfDNA molecules may enable reliable fetal blood group genotyping already in the first trimester of pregnancy.

Fetal fraction and noninvasive prenatal testing: What clinicians need to know

The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a "plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.

Heparin Forms Polymers with Cell-free DNA Which Elongate Under Shear in Flowing Blood

Heparin is a widely used anticoagulant which inhibits factor Xa and thrombin through potentiation of antithrombin. We recently identified that the nucleic acid stain SYTOX reacts with platelet polyphosphate due to molecular similarities, some of which are shared by heparin. We attempted to study heparin in flowing blood by live-cell fluorescence microscopy, using SYTOX for heparin visualisation. Immunostaining was performed with monoclonal antibodies directed against various heparin-binding proteins. In addition, we studied modulation of heparin activity in coagulation assays, as well its effects on fibrin formation under flow in recalcified whole blood. We found that SYTOX-positive polymers appear in heparinised blood under flow. These polymers typically associate with platelet aggregates and their length (reversibly) increases with shear rate. Immunostaining revealed that of the heparin-binding proteins assessed, they only contain histones. In coagulation assays and flow studies on fibrin formation, we found that addition of exogenous histones reverses the anticoagulant effects of heparin. Furthermore, the polymers do not appear in the presence of DNase I, heparinase I/III, or the heparin antidote protamine. These findings suggest that heparin forms polymeric complexes with cell-free DNA in whole blood through a currently unidentified mechanism.

Could high levels of cell-free DNA in maternal blood be associated with maternal health and perinatal outcomes?

The aim of this study was to evaluate the maternal and foetal factors affect higher cell-free DNA (cfDNA) levels and to investigate a possible relationship between high cfDNA levels and adverse perinatal outcomes. From a total of 4594 women who underwent non-invasive prenatal testing from January 2016 to March 2018 in our hospital, 112 women had high levels of cfDNA, which was not appropriate for testing. Maternal characteristics and perinatal outcomes were compared between patients with high levels of cfDNA and normal levels of cfDNA. Patients with high levels of cfDNA had greater risks than patients with normal cfDNA levels of pregnancy complications but no statistically significant difference was found. Patients with high cfDNA levels had higher foetal death rates with a statistically significant difference (9.8% versus 1.8%, p = .024). An increase in foetal death could be expected in patients with increased cfDNA levels; therefore, these patients should be carefully followed up during pregnancy.IMPACT STATEMENTWhat's already known about this topic? Most studies about cfDNA levels are focussed on the foetal fraction. There are new arguments about maternal health and cfDNA. It is known that autoimmune diseases as systemic lupus erythematosus (SLE) and maternal obesity increase cell turnover. There are also clinical studies suggesting a relationship between low molecular weight heparin therapy and the amount of cfDNA.What do the results of this study add? This is the first study evaluating the maternal and foetal biological factors affecting cfDNA concentrations and investigating the possible relationship between high cfDNA levels and adverse perinatal outcomes in patients with high levels of cfDNA compared to patients with normal levels of cfDNA. In the present study, it was found that an increase in foetal death could be expected in patients with higher cfDNA levels.What are the implications of these findings for clinical practice and/or further research? If potential effects and underlying causes of increased cfDNA could be explained, cfDNA might be used as a biomarker for adverse perinatal outcomes.

The failure of non-invasive prenatal testing due to maternal dermatomyositis

We experienced a case of a pregnant woman who failed to obtain a result from NIPT, due to the high level of total cell-free DNA. A subsequent ultrasound examination discovered that the fetus had severe intrauterine growth restriction, so the woman decided to abort the baby. At the same time, the woman developed slight swelling and tenderness of the proximal interphalangeal and meta-carpophalangeal joints. At first, these symptoms were not noticed, but, when the pregnant woman was admitted to the hospital, her laboratory tests were seriously abnormal, such as serum lactate dehydrogenase (640U/L), creatine phosphor kinase (4525U/L), kinase isoenzyme MB (170U/L), and a hydroxybutyrate dehydrogenase (398U/L). The patient had no other symptoms at this time. Misoprostol and subsequent forceps curettage were used for the induced abortion, a 167-g female fetus was aborted. Fetal skin tissue was taken for chromosomal microarray analysis (CMA) and placenta (biopsied in four places and tested as two composite samples) were taken for postnatal karyotyping to exclude a confined placental mosaicism, chromosomal microarray analysis of the fetal skin tissue revealed that the karyotype was 46, XX, karyotyping of placenta (100 cells) gave results of 46, XX, no abnormalities were detected. Ten days after induction, the patient had developed progressive symmetric muscle weakness in the proximal extremities. Physical examination revealed Gottron's sign and erythema. A manual muscle test showed weakness of the muscles (4/5) of her proximal extremities. Electromyography showed myogenic impairment. After excluding the possibility of neoplasia, the patient was diagnosed with dermatomyositis.