Fetal Aneuploidy Research Articles

Non-Invasive Prenatal Screening from a Genetic Counseling Prospective: Pre and Post-Genetic Counseling Regarding Rare Chromosomal Abnormalities and Incidental Finding.

Arising in the late 1990s, when a promising role in prenatal diagnostics was first delineated for circulating fetal DNA, non-invasive prenatal tests (NIPTs) have been increasingly used with more frequency and popularity. These exams have been used as a prenatal screening tests for genetic diseases. Initially, they were developed for the investigation of the main fetal chromosomal aneuploidies, but lately they have also been used to rule out genomic microrearrangements and monogenic conditions. However, along with great opportunities and potential, the tests can show inconclusive or unexpected results. Several studies have shown that the current pre-test counseling is often insufficient, and more oriented at providing pieces of information about the identifiable diseases rather than providing extensive information on all possible scenarios which may affect both the fetus and the pregnant mother, especially in the case of an invasive test for the pregnant mother. We have gathered from the literature on NIPT the main pitfalls, imperfections, and particular cases associated with this innovative diagnostic procedure. In view of further improvements in the methods that can limit the inconclusive or unexpected results, this paper aims to reinforce the importance of more accurate pre-test counseling with comprehensive information about the above-mentioned questions, as well as ultrasound use and also the creation of an international consensus statement concerning these topics.

Expert consensus on the clinical application strategy of NIPT2.0, a new-generation non-invasive prenatal screening technology

The new-generation non-invasive prenatal screening technology (NIPT2.0) is a new method successfully realized in recent years based on high-throughput sequencing to synchronously and accurately detect fetal chromosomal aneuploidies, microdeletion/microduplication syndromes and dominantly inherited monogenic disorders. NIPT2.0 can circumvent the shortcomings of previous non-invasive prenatal screening techniques (NIPT and NIPT Plus) including incapability to detect fetal monogenic disorders, insufficient accuracy of detection and low positive predictive values for certain chromosomal abnormalities (in particular trisomy 13, sex chromosomal abnormalities, and small-segment microdeletions and microduplication syndromes). How to apply NIPT2.0 reasonably and normatively to maximize its clinical value has become an issue which requires clarification. The Reproductive Health Branch of the Chinese Maternal and Child Health Care Association and the Genetic Diagnosis Branch of the Genetics Society of China have organized experts to fully discuss and jointly drafted this consensus, which has put forwards suggestions over the clinical application strategy for NIPT2.0, including the scope of application, target disease, pre-test consultation, clinical application pathway, post-test genetic counseling and intervention, quality control and limitations, for the reference by peers, with a view to standardize its application and provide better clinical service.

12333 46 XX/XY Chimerism - Positive NIPT And Post-natal Karyotype Is It Real?

Abstract Disclosure: K.L. Del Rosario: None. N. Sheriden: None. N. Vijayakanthi: None. Introduction: Non-Invasive Prenatal Testing(NIPT) using cell free fetal DNA in plasma of pregnant women has become a routine part of prenatal care in screening for fetal aneuploidies including sex chromosome abnormalities in most regions around the world. False positive results are increasingly imposing challenges in pre-natal as well as post-natal care. Case Discussion: We report a neonate born at 32+2 weeks gestation to a 42-year-old G2 P2 mother. Pregnancy was complicated by insulin dependent maternal type 2 diabetes mellitus, maternal chronic hypertension and a positive NIPT for high-risk monosomy X. Prenatal ultrasound showed male anatomy. Interestingly on physical exam after birth, the neonate had typical male external genitalia with bilateral normal male gonads. Chromosome analysis done immediately after birth revealed the presence of two cell lines: 40 of the 50 cells (80%) had a normal female 46 XX karyotype and 10 of the 50 cells (20%) had a normal male 46 XY karyotype. These findings could be due to reabsorbed twin, Klinefelter syndrome with two trisomy rescue events, maternal cell contamination or true chimerism. In addition, fluorescence in situ hybridization (FISH) analysis for X and Y probes revealed the presence of two cell lines. The first cell line (70% of the cells) had two hybridization signals for chromosome X and the second cell line (∼25% of the cells) had one hybridization signal for chromosome X and one for chromosome Y. Postnatal ultrasound showed normal testicles with no evidence of Mullerian structures. Newborn screening was negative for congenital adrenal hyperplasia (CAH). Genetics was consulted and recommended repeat chromosomal analysis, parental testing to determine sex chromosome segregation, and follow-up with pediatric endocrinology. Repeat cytogenetic testing at 2 weeks of life resulted in a normal male chromosome complement of 46,XY. Previous abnormal cytogenetics were thought to be due to maternal cell contamination. Further endocrine labs showed LH(1.16 uIU/ml) and testosterone levels ( 87 ng/dL), appropriate levels for age indicating normal Hypothalamic Pituitary Gonadal (HPG) axis and testicular Leydig cell function. Since the family was previously counseled regarding the concept of maternal cell contamination, they expressed understanding and were happy with the update of the normal karyotype result. Conclusion: False-positive results concerning for rare chimerism on NIPT can occur and should prompt a thorough history, physical exam, ultrasound studies and repeat testing to confirm its presence. Careful consideration should be taken when counseling family about the implications of these results, especially communication about gender assignment of the infant. Presentation: 6/3/2024

Progress in fetal fraction prediction of placental diseases

Placental diseases may affect the outcome of pregnancy and long-term health of the mother and fetus. Fetal fraction is a key indicator for the success of non-invasive prenatal testing, and has been associated with gestational age, body mass index and fetal chromosomal aneuploidies. Many studies have found that fetal fraction is also related to placenta-derived diseases and may become a new predictor for such diseases. This article has summarized the association between the two, with an aim to provide new ideas for the prediction of placental diseases.

Unusual Maternal and Fetal Findings With Cell-Free DNA Screening.

With advances in prenatal cell-free DNA (cfDNA) technology, the information available with cfDNA continues to expand beyond the common fetal aneuploidies such as trisomies 21, 18, and 13. Due to the admixture of maternal and fetal/placental DNA, prenatal cfDNA remains a screening test with the possibility of false-positive and false-negative results. This review aims to summarize unusual incidental maternal and fetal genomic abnormalities detectable by cfDNA and to provide anticipatory guidance regarding management. Of 140 articles identified with keywords such as "incidental" and "discordant" cfDNA, 55 original research articles, review articles, case series, and societal guidelines were reviewed. Prenatal cfDNA may incidentally identify a spectrum of maternal genomic abnormalities such as malignancy, mosaicism, and copy number variants. When discordant with fetal diagnosis, these cases require additional investigation with maternal genetic testing and follow-up evaluation. Such incidental fetal/placental abnormalities may include rare autosomal trisomies, uniparental disomy, and triploidy. Further evaluation of fetal/placental abnormalities can be pursued with a combination of ultrasound and prenatal diagnosis with chorionic villous sampling and/or amniocentesis. Societal guidelines do not currently recommend cfDNA screening for rare autosomal trisomies, microdeletions, or copy number variants, and some experts suggest that sex chromosome screening should be opted in after counseling. Knowledge about possible incidental findings with prenatal cfDNA is needed to inform pretest and posttest counseling with appropriate follow-up evaluation. As cfDNA technology has advanced to include genome-wide findings, it is important for clinicians, genetic counselors, and societal guidelines to acknowledge the spectrum of possible results outside of the traditional and sex chromosome aneuploidies.

The Effect of Self-Reported Race on Noninvasive Prenatal Screening Test Characteristics.

Low fetal fraction (FF) on cell-free DNA (cfDNA)-based noninvasive prenatal screening (NIPS) is a common etiology for indeterminate results. As maternal Black race is implicated as a risk factor for low FF and more indeterminate results, we sought to evaluate this association. This was a single-institution, retrospective cohort study of cfDNA-based NIPS performed between May 2017 and May 2022 with complete clinical data abstraction. We compared FF, indeterminate rates, and total cfDNA concentration among self-reported Black, White, and Other groups from NIPS results from 2017 to 2022 with full clinical data abstraction. Using linear regression and interaction testing, we evaluated associations between self-reported race, FF, indeterminate rate, and total cfDNA concentration. In total, 1,591 participants met the inclusion criteria; 70.8% (n = 1,126) self-identified as White, 6.9% (n = 110) as Black, and 22.3% (n = 355) self-identified with another race. Mean FF was not different between the White, Black, or Other groups (11.8 vs. 11.2 vs. 11.7%, respectively, p = 0.52). This remained true after adjusting for body mass index (BMI), gestational age (GA) at draw, and fetal sex (all p > 0.17). Interaction testing for FF and total cfDNA by race with BMI, GA at draw, and fetal sex demonstrated no effect modification. In our population, maternal self-identified race, particularly Black race, does not affect FF. Biological plausibility for race-based differences on clinical tests requires ongoing thoughtful consideration. · NIPS is widely used to screen for fetal aneuploidy.. · FF is an important test metric, and low FF is associated with adverse outcomes, like aneuploidy.. · In existing studies, Black race is implicated as a risk factor for lower FF.. · Our study found no differences in FF between groups by self-reported race.. · Biological plausibility for race-based differences on clinical tests requires ongoing consideration..

Mainstreaming genetics into Italian prenatal care: exploring the future implementation of non-invasive prenatal testing (NIPT) in the Italian National Healthcare System using stakeholder interviews

IntroductionNon-invasive prenatal testing (NIPT) has revolutionised the way prenatal testing is performed globally. Italy is one of the European countries considering incorporating NIPT nationwide into the publicly funded healthcare system....

Prenatal diagnosis and genetic counseling of a de novo 10q11.21q11.23 duplication associated with a normal phenotype.

Copy number variants (CNVs) are an important source of normal and pathogenic genome variations. Unbalanced chromosome abnormalities are either gains or losses of large genomic regions that do not or only minimally clinically affect the individual. Noninvasive prenatal testing (NIPT) is widely used in the screening of common fetal chromosome aneuploidy. One example is the duplication of 10q11.21q11.23, which includes the 10q11.2 region. This region contains a complex set of low-copy repeats that may lead to various genomic alterations through non-allelic homologous recombination. In this report, we present a case of a de novo 10q11.21q11.23 duplication with a normal phenotype. This case may be helpful for prenatal diagnosis and genetic counseling. A combination of NIPT, prenatal ultrasound, karyotype analysis, copy number variation sequencing, and genetic counseling is helpful for the prenatal diagnosis of CNVs.

Perspectives of pregnant women on broadening the scope of noninvasive prenatal testing from screening for foetal aneuploidies to prediction of adverse pregnancy outcomes: Aqualitative study.

To explore the perspectives of pregnant women on broadening the scope of noninvasive prenatal testing (NIPT) from screening for foetal aneuploidies to prediction of adverse pregnancy outcomes. Four online focus groups (n=23 participants) and 14 individual semi-structured interviews were conducted. Participants included pregnant women with and without a history of adverse pregnancy outcomes. Both women at low and high risk of adverse pregnancy outcomes had a positive attitude towards using NIPT to predict adverse pregnancy outcomes. Perceived benefits included the possibility to potentially improve maternal and foetal outcomes by taking risk-reducing measures and/or intensified monitoring during pregnancy and the ability to mentally prepare for the potential adverse outcome. Perceived concerns included anxiety and stress caused by a high-risk test result, a false sense of control over pregnancy, and potential false reassurance. Additionally, women reasoned that broadening the scope of NIPT could increase the complexity of prenatal screening and raised concerns on the combined screening aims in one test (prediction of adverse pregnancy outcomes to improve foetal and maternal health vs. screening for foetal aneuploidies to increase reproductive autonomy). On a societal level, considerations on the risk of medicalising pregnancy and overall pressure to opt for NIPT were mentioned. In general, pregnant women have a positive attitude towards broadening the scope of NIPT to the prediction of pregnancy outcomes, although some concerns are acknowledged.

Clinical Applications of Fetal Cell-Free DNA: State of the Science.

Advances in technology have correlated with expanding prenatal genetic testing options for pregnant people. Leading medical organizations recommend cell-free DNA as the most sensitive screening test for trisomies 13, 18, and 21, as well as for fetal sex chromosome aneuploidies. The commercially available testing options go beyond these recommended tests, and prenatal care professionals should be familiar with the tests that their patients may choose despite being beyond the scope of current medical recommendations. This article explains updates in cell-free DNA technology and clinical considerations for prenatal care professionals, recognizing that this is a rapidly changing field of science and health care.

Cell-Free DNA Analysis of Fetal Aneuploidies in Early Pregnancy Loss.

Background: Products of conception samples are often collected and analyzed to try to determine the cause of an early pregnancy loss. However, sample collection may not always be possible, and maternal cell contamination and culture failure can affect the analysis. Cell-free DNA-based analysis of a blood sample could be used as an alternative method in early pregnancy loss cases to detect if aneuploidies were present in the fetus. Methods: In this prospective study, blood samples from early pregnancy loss patients were analyzed for the presence of fetal aneuploidies using a modified version of a noninvasive prenatal testing assay for cell-free DNA analysis. Results from cell-free DNA analysis were compared against the gold standard, microarray analysis of products of conception samples. This study was registered with ClinicalTrials.gov, identifier: NCT04935138. Results: Of the 76 patient samples included in the final study cohort, 11 were excluded from performance calculations. The 65 patient samples included in the final analysis included 49 with an abnormal microarray result and 16 with a normal microarray result. Based on results from these 65 samples, the study found that genome-wide cell-free DNA analysis had a sensitivity of 73.5% with a specificity of 100% for the detection of fetal aneuploidies in early pregnancy loss cases. Conclusions: This prospective study provides further support for the utility of cell-free DNA analysis in detecting fetal aneuploidies in early pregnancy loss cases. This approach could allow for a noninvasive method of investigating the etiology of miscarriages to be made available clinically.

Potential efficacy of digital polymerase chain reaction for non-invasive prenatal screening of autosomal aneuploidies: a systematic review and meta-analysis

BackgroundDigital Polymerase Chain Reaction (dPCR) presents a promising approach for quantifying DNA and analyzing copy number variants, particularly in non-invasive prenatal testing. This method offers a streamlined and time-efficient procedure in contrast to the widely used next-generation sequencing for non-invasive prenatal testing. Studies have reported encouraging results for dPCR in detecting fetal autosomal aneuploidies. Consequently, this systematic review aimed to evaluate the effectiveness of dPCR in screening for trisomy 21, 18, and 13.MethodsA systematic search was conducted in PubMed, Web of Sciences, and Embase for relevant articles published up to December 30, 2023. The Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) was utilized for the quality assessment of the included articles. Furthermore, a bivariate random-effect regression model was used to conduct a meta-analysis on the utility of dPCR for trisomy 21 screening.ResultsA total of 9 articles were included in this review, with all of them assessing the utility of dPCR in trisomy 21 screening, and 2 and 1 studies conducting additional analysis on the screening abilities of dPCR for trisomy 18 and 13, respectively. A bivariate random-effects model calculated pooled sensitivity and specificity with a 95% confidence interval (CI). Meta-analysis of 6 studies comparing trisomy-21 screening with karyotyping demonstrated dPCR's pooled sensitivity of 98% [95% CI: 94 -100] and specificity of 99% [95% CI: 99 -100]. While conducting a meta-analysis for trisomy 13 and 18 proved impractical, reported values for sensitivity and specificity were favorable.ConclusionsThese findings suggest that dPCR holds promise as an effective tool for non-invasive prenatal testing, presenting a less time-consuming and intricate alternative to next-generation sequencing. However, further research is necessary to evaluate dPCR's applicability in clinical settings and to delineate its specific advantages over next-generation sequencing. This study contributes valuable insights into the potential of dPCR for enhancing prenatal screening methodologies.Trial registrationThe protocol of this study was registered in the International Prospective Register of Systematic Reviews (PROSPERO) on 7/3/2024, with a registration code of CRD42024517523.

Accuracy of fetal fraction measurements in a single-nucleotide polymorphism-based noninvasive prenatal test.

Noninvasive prenatal testing (NIPT) for fetal aneuploidy relies on the analysis of fetoplacental cell-free DNA (cfDNA) found in maternal plasma. A minimum cfDNA fetal fraction (FF) is required for reliable test performance, but some methods may have suboptimal accuracy for FF measurement. This study investigated the accuracy of a single-nucleotide polymorphism- (SNP-) based NIPT method to assess FF. FF measurements using SNP-based NIPT in consecutive samples from singleton male pregnancies were compared with FF measured using a "gold standard" Y-chromosome method. In a cohort of 106,846 samples, the SNP-based FF method showed a standard deviation (SD) of 0.42%. Compared to the Y chromosome FF method, a correlation coefficient, r, of 0.995, and bias of 0.17% were observed. The SD was not substantially different across specific FF ranges or for samples with high-risk NIPT results. The SNP-based NIPT method estimates FF with good accuracy, with a SD three to eight times better than other NIPT methods (0.42% vs. 1.3%-3.4%). FF is an important quality control parameter and should be routinely reported as part of NIPT.

P-387 The use of cell-free DNA analysis to identify fetal aneuploidies in early pregnancy loss

Abstract Study question Can cell-free (cf) DNA-based analysis of a maternal blood sample be used to identify presence of fetal aneuploidies in early pregnancy loss (EPL) cases? Summary answer CfDNA analysis was able to detect fetal aneuploidies in EPL cases with 73.5% sensitivity and 100% specificity. What is known already Miscarriages occur in about 10%–20% of pregnancies, and the majority occur in the first trimester. About 50% of EPL cases result from the presence of fetal aneuploidy. Knowing the etiology of a miscarriage can be helpful for future reproductive planning along with providing a psychological benefit for patients. Although products of conception (POC) samples can be collected and assessed for presence of fetal aneuploidies, this is not always possible. Recent studies have shown that a noninvasive approach using cfDNA analysis of a blood sample can identify fetal aneuploidies in patients that experience EPL. Study design, size, duration In this prospective study, samples were collected from 78 patients across the United States from June 2021–December 2022. Blood specimens were collected for cfDNA analysis and maternal cell contamination analysis, and POC samples were collected following surgical evacuation for microarray analysis. Performance of the cfDNA assay was determined by comparing results from the cfDNA analysis against the gold standard of microarray results. Participants/materials, setting, methods Patients were recruited from six reproductive endocrinology/infertility practices. Eligible participants were between 5–20 weeks of gestation with miscarriage of a singleton pregnancy diagnosed by ultrasound and presence of pregnancy tissue in utero. Limited clinical information was collected, including demographics and expected clinical gestational age (GA) at sample collection. Blood samples underwent cfDNA analysis using an adapted version of a noninvasive prenatal test, which included establishment and use of pregnancy loss-specific log likelihood ratio thresholds. Main results and the role of chance Seventy-eight patients were recruited, of which two were excluded due to blood sample collection issues. Eleven of the 76 patients that underwent cfDNA analysis were excluded from performance calculations for several reasons including maternal cell contamination of POC samples and detection of triploidy by microarray. The final 65 samples included 49 affected and 16 unaffected samples based on POC microarray results; this included 42 with one fetal aneuploidy, six with two fetal aneuploidies, and one with three fetal aneuploidies. Average fetal fraction of these 65 samples was 4.9% (range: 0.6%–13.9%) and average expected clinical GA at time of sample collection was 8.7 weeks (range: 5.9–12.1 weeks). Performance of the cfDNA assay was determined by comparing cfDNA analysis results with POC microarray results using either a full concordance approach (correct classification of all affected chromosomes in an affected sample) or a partial concordance approach (correct classification of at least one affected chromosome in an affected sample). Based on the full concordance approach, sensitivity of the cfDNA assay was 69.4% and specificity was 100%. For the partial concordance approach, sensitivity of the cfDNA assay increased to 73.5% whilst specificity remained at 100%. The cfDNA assay failure rate was 0%. Limitations, reasons for caution Study limitations include a small study cohort, the inability of the cfDNA assay to detect triploidy or partial deletions/duplications <7 Mb and possibly mosaicism, and that this cfDNA analysis approach can only be used for EPL cases that are identified before complete expulsion of the products of conception. Wider implications of the findings This study provides further evidence of the ability of cfDNA analysis to detect fetal aneuploidies in EPL cases. A clinically available cost-effective noninvasive approach to determine the etiology of a miscarriage could help inform medical management of patients for future reproductive planning and could provide psychological benefits to patients. Trial registration number NCT04935138

P-238 Evaluating the role of blastocyst quality in blighted ovum: a propensity score matching analysis

Abstract Study question What is the impact of blastocyst stage and inner cell mass (ICM) grade on the formation of blighted ovum in in vitro fertilization? Summary answer Analysis indicates blastocyst stage influences gestational sac formation, while ICM grade significantly predicts blighted ovum occurrence, highlighting potential predictive markers What is known already It is well known that the blastocyst grading, encompassing stage, ICM and trophectoderm (TE) is correlated with the pregnancy outcome. Although Gardner criteria is widely used for blastocyst grading, the significance and clinical implications of each component remain challenging to assess. A blight ovum, a presence of GSAC without advancement to FHT, commonly results from fetal aneuploidy. The quality of ICM, evolving into the fetus, is thought to reflect fetal euploidy, whereas TE develops into the placenta. However, the specific influence of these blastocyst grading components on blighted ovum incidence remains underexplored. Study design, size, duration This study analyzed 897 patient clinical data from 2011 to 2022, collected from three IVF clinics. It included maternal age, embryo transfer method (fresh or frozen), and outcomes (GSAC, FHT). Day 5 embryos were graded for blastocyst stage, ICM, and TE using Gardner criteria. Participants/materials, setting, methods Of 897 IVF cycles, 416 led to GSAC formation and 379 to FHT. Thirty-seven cycles resulted in blighted ovum. Logistic regression analyzed blastocyst stage, ICM, and TE grades’ effects on GSAC and FHT, accounting for confounding factors. Due to the small sample size, propensity score matching (PSM) was performed at 1:3 and 1:4 ratios matched blighted ovum cases with controls based on age and embryo status. Main results and the role of chance As anticipated, ANOVA and logistic regression analyses identified blastocyst stage, ICM, and TE as significant predictors of GSAC and FHT development, underscoring the relevance of Gardner criteria. However, the limited number of blighted ovum cases necessitated further analysis. Propensity score matching (PSM) was thus applied to 37 blighted ovum cases, compared against non-blighted ovum cases at ratios of 1:3 and 1:4, selected randomly from the dataset. The standardized mean differences pre- and post-PSM were 0.14 and 0, indicating well-balanced group characteristics. GSAC formation probability increased with advanced blastocyst stages (5,6) compared to earlier stages (3,4), with ICM and TE grades showing no significant impact. Conversely, FHT advancement from GSAC was unaffected by blastocyst stage, but the likelihood of FHT occurrence was 3.618 and 3.476 times higher for ICM grades A or B compared to C, at 1:3 and 1:4 ratios respectively. Limitations, reasons for caution The study accounted for age and cycle type (fresh or thawed) as confounding factors affecting pregnancy outcomes. To further minimize potential biases, controlling additional factors is crucial. Moreover, with data derived from three clinics, external validation is vital to substantiate the findings. Wider implications of the findings Blighted ovum, an early form of miscarriage, is deeply distressing for patients. This study highlights the potential role of ICM grades in predicting blighted ovum occurrences. Such insights could be invaluable for embryo selection and patient counseling. Trial registration number not applicable

O-236 Why one is not enough when studying pregnancy loss - a European perspective

Abstract Pregnancy loss is a distressing but still poorly understood condition, ending one in four pregnancies. With more than 30 million losses worldwide yearly, it is posing significant challenges to individuals, families, and healthcare systems. This presentation delves into the imperative for a multifaceted approach to studying pregnancy loss. By examining pregnancy loss through multiple lenses including fetal and parental genetics, male and female physiology, and psychosocial, lifestyle and political dimensions, we can achieve an improved understanding of the causes, impact, prevention, and treatment of pregnancy loss. Historically, pregnancy loss has been considered a part of the reproductive journey – a course of nature. And until a couple has suffered from recurrent pregnancy loss, the physiological and mental impact has been neglected. This is an outdated approach that prevents a full understanding of the consequences and underlying etiologies hindering the potential of prevention and treatment, and thereby contributes to maintaining the women’s health gap. Moreover, current practice ignores the association of euploid pregnancy loss with an increased risk of future losses and later maternal health consequences such as diabetes and cardiovascular disease. In Copenhagen, we are currently running a large-scale pregnancy loss study (Copenhagen Pregnancy Loss, COPL) involving 3000 pregnancy losses. By including the full trio (fetus, female, and male) we are gaining new insight to the mechanisms causing pregnancy loss and the consequences hereof, both in men and women. We know from previous cytogenetic investigation of lost pregnancies, that about 60% are caused by fetal aneuploidy. But the remaining part is still not well understood and leaves the opportunity of treatments and preventions if we knew the underlying mechanism. That we aim to cover by building the largest database and biobank in the field. Moreover, collected data from the COPL study will be linked to nationwide Danish registries including comprehensive information on medical history, social economic status, educational status, medication, and ancestry. We have validated the use of cell-free fetal DNA in maternal blood to separate the losses caused by fetal genetics or not. This differentiation is essential to address the heterogeneous nature of pregnancy loss, but also to provide an individual answer to the couples. In 1000 consecutive pregnancy losses between gestational age 5 and 22 weeks, we were able to provide a cffDNA based result of the fetal ploidy status in 89% of cases. When comparing the method to direct sequencing of the pregnancy tissue, the cffDNA-based testing had a higher success-rate and identified 85% of the aneuplodies (sensitivity) with a 93% specificity. These results show the potential and feasibility of the method to distinguish euploid and aneuploid pregnancy loss for improved clinical management and benefit of future research. From our close collaboration with couples that are experiencing a devastating event as pregnancy loss, we have seen the huge unmet need for better handling, but also a deep commitment and motivation from the men and women involved. We have investigated the conflicting feelings emerging in a next pregnancy and a need for closer support and care. We belief, that it takes a trio to improve the understanding and handling of pregnancy loss.

Prediction model of preeclampsia using machine learning based methods: a population based cohort study in China.

Preeclampsia is a disease with an unknown pathogenesis and is one of the leading causes of maternal and perinatal morbidity. At present, early identification of high-risk groups for preeclampsia and timely intervention with aspirin is an effective preventive method against preeclampsia. This study aims to develop a robust and effective preeclampsia prediction model with good performance by machine learning algorithms based on maternal characteristics, biophysical and biochemical markers at 11-13+6 weeks' gestation, providing an effective tool for early screening and prediction of preeclampsia. This study included 5116 singleton pregnant women who underwent PE screening and fetal aneuploidy from a prospective cohort longitudinal study in China. Maternal characteristics (such as maternal age, height, pre-pregnancy weight), past medical history, mean arterial pressure, uterine artery pulsatility index, pregnancy-associated plasma protein A, and placental growth factor were collected as the covariates for the preeclampsia prediction model. Five classification algorithms including Logistic Regression, Extra Trees Classifier, Voting Classifier, Gaussian Process Classifier and Stacking Classifier were applied for the prediction model development. Five-fold cross-validation with an 8:2 train-test split was applied for model validation. We ultimately included 49 cases of preterm preeclampsia and 161 cases of term preeclampsia from the 4644 pregnant women data in the final analysis. Compared with other prediction algorithms, the AUC and detection rate at 10% FPR of the Voting Classifier algorithm showed better performance in the prediction of preterm preeclampsia (AUC=0.884, DR at 10%FPR=0.625) under all covariates included. However, its performance was similar to that of other model algorithms in all PE and term PE prediction. In the prediction of all preeclampsia, the contribution of PLGF was higher than PAPP-A (11.9% VS 8.7%), while the situation was opposite in the prediction of preterm preeclampsia (7.2% VS 16.5%). The performance for preeclampsia or preterm preeclampsia using machine learning algorithms was similar to that achieved by the fetal medicine foundation competing risk model under the same predictive factors (AUCs of 0.797 and 0.856 for PE and preterm PE, respectively). Our models provide an accessible tool for large-scale population screening and prediction of preeclampsia, which helps reduce the disease burden and improve maternal and fetal outcomes.

Implementation of an Enhanced Prenatal Checklist to Increase Rates of Counseling of Prenatal Fetal Aneuploidy Testing.

Aim This study aims to assess the effect of implementing an enhanced prenatal genetic checklist to guide the provider's discussion on both screening and diagnostic options for fetal aneuploidy testing at the initial prenatal visit. Methods A retrospective quality improvement (QI) project was performed at a single, large, urban academic medical center. The implementation of this project was prospective; however, data was examined retrospectively after the QI initiative was implemented for three months. Patients were included if they were less than 24 weeks gestational age with a live intrauterine gestation at their initial obstetric (OB) visit. Patients less than 18 years old at the initial OB visit were excluded. The results were analyzed using the statistical software R. Chi-squared tests were used to examine proportional differences between the pre- and post-intervention groups with respect to demographic and clinical characteristics and documented genetic counseling discussions. Results A total of 416 patients were included in the final cohort. As measured by documentation, the rate of discussion of diagnostic prenatal genetic testing increased significantly from the pre-intervention proportion of 54% to the post-intervention proportion of 72% (p < 0.001). In the subgroup analysis of patients with advanced maternal age, the rate of discussion of diagnostic prenatal genetic testing increased significantly from the pre-intervention proportion of 53% to the post-intervention proportion of 83% (p = 0.003), and the rate of genetics counseling referrals made at the initial prenatal visit increased significantly from 4% pre-intervention to 38% post-intervention (p < 0.001). Conclusions The use of an enhanced prenatal genetic checklist led to increased discussion of diagnostic fetal aneuploidy testing and increased rates of referral to genetics counseling.

NIPT-PG: empowering non-invasive prenatal testing to learn from population genomics through an incremental pan-genomic approach.

Non-invasive prenatal testing (NIPT) is a quite popular approach for detecting fetal genomic aneuploidies. However, due to the limitations on sequencing read length and coverage, NIPT suffers a bottleneck on further improving performance and conducting earlier detection. The errors mainly come from reference biases and population polymorphism. To break this bottleneck, we proposed NIPT-PG, which enables the NIPT algorithm to learn from population data. A pan-genome model is introduced to incorporate variant and polymorphic loci information from tested population. Subsequently, we proposed a sequence-to-graph alignment method, which considers the read mis-match rates during the mapping process, and an indexing method using hash indexing and adjacency lists to accelerate the read alignment process. Finally, by integrating multi-source aligned read and polymorphic sites across the pan-genome, NIPT-PG obtains a more accurate z-score, thereby improving the accuracy of chromosomal aneuploidy detection. We tested NIPT-PG on two simulated datasets and 745 real-world cell-free DNA sequencing data sets from pregnant women. Results demonstrate that NIPT-PG outperforms the standard z-score test. Furthermore, combining experimental and theoretical analyses, we demonstrate the probably approximately correct learnability of NIPT-PG. In summary, NIPT-PG provides a new perspective for fetal chromosomal aneuploidies detection. NIPT-PG may have broad applications in clinical testing, and its detection results can serve as a reference for false positive samples approaching the critical threshold.

The Association between Low Fetal Fraction of Non-Invasive Prenatal Testing and Adverse Pregnancy Outcomes for Placental Compromise

(1) Background: Non-invasive prenatal testing (NIPT) is a screening test for fetal aneuploidy using cell-free fetal DNA. The fetal fragments (FF) of cell-free DNA (cfDNA) are derived from apoptotic trophoblast of the placenta. The level of fetal cfDNA is known to be influenced by gestational age, multiple pregnancies, maternal weight, and height. (2) Methods: This study is a single-center retrospective observational study which examines the relationship between the fetal fraction (FF) of cell-free DNA in non-invasive prenatal testing (NIPT) and adverse pregnancy outcomes in singleton pregnancies. A total of 1393 samples were collected between 10 weeks and 6 days, and 25 weeks and 3 days of gestation. (3) Results: Hypertensive disease of pregnancy (HDP) occurred more frequently in the low FF group than the normal FF group (5.17% vs. 1.91%, p = 0.001). Although the rates of small for gestational age (SGA) and placental abruption did not significantly differ between groups, the composite outcome was significantly higher in the low FF group (7.76% vs. 3.64%, p = 0.002). Furthermore, women who later experienced complications such as HDP or gestational diabetes mellitus (GDM) had significantly lower plasma FF levels compared to those without complications (p &lt; 0.001). After adjustments, the low FF group exhibited a significantly higher likelihood of placental compromise (adjusted odds ratio: 1.946). (4) Conclusions: Low FF in NIPT during the first and early second trimesters is associated with adverse pregnancy outcomes, particularly HDP, suggesting its potential as a predictive marker for such outcomes.