Non-invasive prenatal test findings in 41,819 pregnant women: results from a clinical laboratory in southern China

Prenatal diagnosis of imprinted associated chromosome abnormalities identified by noninvasive prenatal testing (NIPT)

To explore the clinical value of noninvasive prenatal testing (NIPT) combined with chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), and fluorescence in situ hybridization (FISH) in the early screening of imprinted chromosome abnormalities. We retrospectively studied the prenatal diagnosis and pregnancy outcomes of 9 pregnant women with imprinted associated chromosome abnormalities via NIPT. All pregnant women received detailed genetic counselling and prenatal diagnosis. Karyotyping analysis, CNV-seq, CMA, FISH or MS-MLPA were performed on the amniotic fluid samples. We collected the intrauterine phenotypes via ultrasound and followed them up until the induction of labor or one year after birth. Six fetuses (6 out of 9) were diagnosed with regional abnormalities of Imprinting Disease. The most commonly diagnosed syndrome was 15q11-q13 duplication syndrome ( 3 out of 6), followed by mosaic trisomy 7 (2 out of 6) and Temple syndrome (1 out of 6). The other three fetuses (3 out of 9) were diagnosed with absence of heterozygosity (AOH). After genetic counselling, 4 pregnant women (4 out of 9) chose induced labor, 3 pregnant women (3 out of 9) chose spontaneous labor, and 2 pregnant women (2 out of 9) chose cesarean section. The widespread use of NIPT in prenatal screening provides more opportunities to detect rare chromosome aneuploidies (RCAs) and microdeletion/microduplication syndromes (MMSs) in mid-pregnancy. The combination of NIPT and other prenatal diagnostic technologies can help increase the possibility of detecting imprinting-related diseases with no phenotype or a late phenotype in utero.

Prenatal Detection of Silver-Russell Syndrome: A First Trimester Suspicion and Diagnostic Approach

Background and Objectives: Silver-Russell Syndrome (SRS) is a rare genetic disorder characterized by prenatal and postnatal growth restriction, distinctive facial features, and body asymmetry. Early suspicion during the first trimester remains challenging but crucial for optimizing clinical outcomes. This study aims to highlight a diagnostic approach to the early suspicion of SRS. Materials and Methods: A 28-year-old primigravida presented for routine first-trimester prenatal care. An ultrasound revealed asymmetric growth restriction with normal anatomical findings. The first-trimester biochemical markers, including PAPP-A and β-hCG, were within the normal range. A further evaluation, including amniocentesis and genetic testing, was performed. Results: Genetic testing identified hypomethylation at the 11p15 imprinting control region, confirming the diagnosis of SRS. Parental testing excluded the maternal uniparental disomy of chromosome 7, suggesting an epigenetic mechanism. The findings were consistent with a clinical diagnosis of SRS, and appropriate counseling and multidisciplinary management were initiated. Conclusions: This case underscores the importance of the early recognition of atypical growth patterns, the integration of advanced genetic testing, and multidisciplinary counseling to guide parental decision-making and improve outcomes.

Discrepancies Between Sex Prediction and Fetal Sex After Prenatal Noninvasive Cell-Free DNA Screening

In the last 10 years the field of prenatal diagnosis has been significantly reshaped followed by the implementation of noninvasive prenatal cell-free DNA (cfDNA) testing methodologies in clinical practice. Based on a superior performance and higher sensitivity and specificity than the former practice of biochemical markers screening, the American College of Obstetricians and Gynecologists and American College of Medical Genetics and Genomics recommend noninvasive prenatal cfDNA screening for trisomy 21, 18, 13, and sex chromosome aneuploidy to all pregnant people. While cfDNA screening is helpful in risk assessment for the most common autosomal trisomies, cfDNA also provides information about fetal sex chromosomes. Prediction of fetal sex is highly desired by the parents and also useful to healthcare providers for management of pregnancies that are at-risk for X-linked conditions. In fact, utilization of cfDNA screening has resulted in a significant number of referrals to evaluate discordant results for cfDNA sex prediction and appearance of fetal genitalia by prenatal ultrasound scan or at birth raising concerns about the fetus/infant atypical sex development known as a difference in sex development (DSD). In this mini-review, we outline principles and limitations of cfDNA technology, summarize recent findings related to cfDNA test performance in prediction of sex chromosome abnormalities and DSD conditions, define the technical and biological causes of discrepant results, provide recommendations to consolidate efforts by prenatal and clinical management teams in challenging situations, and discuss ethical considerations associated with fetal sex prediction and prenatal DSD diagnosis.

Non-invasive prenatal detection of dominant single-gene disorders in fetal structural abnormalities: a clinical feasibility study

OBJECTIVE

This study evaluated the accuracy of non-invasive prenatal testing (NIPT-SGDs) for dominant monogenic genetic diseases associated with fetal structural abnormalities and to assess the feasibility of clinical application.

METHODS

Pregnant women requiring prenatal diagnosis due to fetal structural abnormalities were enrolled. Maternal peripheral blood was analyzed for cell-free DNA (cfDNA) using coordinative allele-aware target enrichment sequencing (COATE-seq). This assessed fetal allele depth distribution, fraction and variation ratio. The variation's origin was then determined to obtain fetal variation information. Finally, NIPT-SGDs results were confirmed via invasive prenatal diagnosis (IPD).

RESULTS

Upon examination of 113 samples using NIPT-SGDs, COATE-seq successfully analyzed 112 for fetal variation, excluding one due to hemolysis. The study detected six positive cases, yielding a 5.36% detection rate. These disorders included tuberous sclerosis complex (TSC1 and TSC2 being its causative genes), Noonan syndrome (PTPN11), polycystic kidney disease (PKD1), and Kabuki syndrome (KMT2D), occurring twice each, except for Noonan and polycystic kidney disease. Two false positives were due to the mother being a genetic mosaicism. Compared to invasive whole-exome sequencing (WES), NIPT-SGDs did not detect nine positive cases of IPD dominant monogenic diseases, accurately identifying 90.18% (101/112) of the actual positive and negative cases.

CONCLUSION

Our findings demonstrate the clinical utility of NIPT-SGDs using COATE-seq in effectively identifying fetuses with dominant single-gene disorders. Furthermore, this method can be applied to all fetuses.

Evaluation of the clinical utility of NIPT-plus and analysis of adverse pregnancy outcomes

PURPOSE

To evaluate the performance of NIPT-plus in detecting fetal aneuploidies and CNVs and analyze the factors influencing adverse pregnancy outcomes.

METHODS

The retrospectively analyzed 8726 pregnant women who underwent NIPT-plus for fetal screening were classified into low- (who tested voluntarily) and high-risk (women with advanced age, abnormal ultrasound, abnormal serological screening, or a combination of indications) groups. Basic maternal information, prenatal findings, and pregnancy outcomes were recorded. NIPT-plus performance was assessed for various chromosomal abnormalities and the association between the fetal fraction and adverse pregnancy outcomes.

RESULTS

Thirty-six (0.4%) patients had failed tests; 144 (1.65%) positive cases were detected, of which, 107 (74.31%) opted for invasive testing, and 51 were verified as true positives. The total positive predictive value was 45.45% and 48.65% in the low- and high-risk groups, respectively, and the difference was not significant. Among the subsequent cases with abnormal ultrasound monitoring, two false-negative cases were identified, and pathogenic CNV diagnosis was confirmed through amniocentesis, resulting in pregnancy termination. Fetal fraction was not associated with an increased adverse pregnancy outcome risk; however, ethnic differences may affect pregnancy outcomes.

CONCLUSION

NIPT-plus technology use is no longer restricted to high-risk pregnant women, and it may produce false-positive results. The stakeholders should be aware of this limitation. The uncertainties and potential risks of the test results should be explained to the test takers to enable informed decision making and to minimize unnecessary anxiety and concerns. Ethnicity may influence adverse pregnancy outcomes in local multiracial settings.

Noninvasive prenatal testing (NIPT) results are less accurate the later applied during pregnancy

OBJECTIVE

Noninvasive prenatal testing (NIPT) has been introduced in prenatal genetics, recently. Even though it is connected with biological, technical, medical and ethical issues also reviewed here, it is meanwhile applied as a standard screening test. One of the obvious, but yet not further reviewed peculiarities of NIPT is that the reported false positives rates are variant, specifically in European, compared with Chinese publications.

MATERIALS AND METHODS

Here the only 15 suited studies on >600,000 cases were identified in which at least average pregnancy age was reported for the time NIPT was done.

RESULTS AND CONCLUSION

It could be shown, that NIPT is done in China in later weeks of gestation, than in other countries. Besides, here for the first time it is highlighted that false positive NIPT results are less frequent, the earlier the screening is performed. Most likely this is related to two biological phenomena: loss of trisomic pregnancies and preferential survival of fetuses which underwent trisomic rescue, however, with major trisomic populations in placenta. This yet not considered aspect needs to be kept in mind especially in late stage high risk pregnancies.

Comparison of the performance of NIPT and NIPT-plus for fetal chromosomal aneuploidy and high Z-score increases the positive predictive value

OBJECTIVE

To evaluate non-invasive prenatal testing (NIPT) and expanded non-invasive prenatal testing (NIPT-plus) for detecting aneuploidies at different sequencing depths and assess Z-score accuracy in predicting trisomies 21, 18, 13, 45X, and 47XXX.

METHODS

Pregnancies with positive NIPT or NIPT-plus results detected at the prenatal diagnosis center of Nanfang Hospital were included in this retrospective study, between January 2017 and December 2022. Invasive prenatal diagnostic results were collected. Logistic regression analyses were used to study the relationship between Z-score and positive predictive value (PPV). Optimal cut-off values were obtained based on receiver operating characteristic analysis, and PPVs were calculated in different groups.

RESULTS

We evaluated 1348 pregnant women with positive results, including 930 reported by NIPT and 418 reported by NIPT-plus. NIPT reported significantly more rare chromosomal aneuploidies (RCAs), and NIPT-plus had a significantly higher PPV for trisomy 21 (T21). Logistic regression analyses showed a significant association (P < 0.001) between Z-score and PPVs for T21 and trisomy 18 (T18). A linear relationship was observed between fetal fraction (FF) and Z-values in the true positive cases of T21 and T18.The high Z-score group had significantly higher PPVs than the low Z-score group for T21, T18, trisomy 13, and 47XXX, but not for 45X.

CONCLUSION

The Z-score is helpful in assessing NIPT or NIPT-plus results. Therefore, we suggest including the Z-score and FF in the results. By combining the Z-score, FF, and maternal age, clinicians can interpret NIPT results more accurately and improve personal counsel to reduce patients' anxiety.

Performance Evaluation of Noninvasive Prenatal Testing in Screening Chromosome Disorders: A Single-Center Observational Study of 15,304 Consecutive Cases in China

Objective

This study was to evaluate the performance of noninvasive prenatal testing (NIPT) in detecting fetal chromosome disorders in pregnant women.

Methods

From October 1st, 2017, to December 31th, 2022, a total of 15,304 plasma cell free DNA-NIPT samples were collected for fetal chromosome disorders screening. The results of NIPT were validated by confirmatory invasive testing or clinical outcome follow-up. Further, NIPT performance between low-risk and high-risk groups, as well as singleton pregnancy and twin pregnancy groups was compared. Besides, analysis of 111 false-positive cases was performed.

Results

Totally, NIPT was performed on 15,086 eligible venous blood samples, of which 179 (1.19%) showed positive NIPT results and 68 were further validated to be true positive samples via confirmatory invasive testing or follow-up of clinical outcomes. For common chromosome aneuploidies, sex chromosome abnormalities (SCA) and other chromosomal aneuploidies, the detection sensitivities of NIPT were all 100%, the specificities were 99.87%, 99.70%, and 99.68% and the positive predictive values (PPVs) were 65.45%, 31.82%, and 10.91%, respectively. No statistically significant variance in detection performance was observed among 2987 high-risk and 12,099 low-risk subjects, as well as singleton and twin pregnancy subjects. The concentration of cell-free fetal DNA of 111 false-positive cases ranged from 5.5% to 33.7%, which was higher than the minimum requirement of NIPT.

Conclusion

With stringent protocol, NIPT shows high sensitivity and specificity for detecting fetal chromosome disorders in a large-scale clinical service, helping improving overall pregnancy management.

Clinical Potential of Expanded Noninvasive Prenatal Testing for Detection of Aneuploidies and Microdeletion/Microduplication Syndromes

OBJECTIVE

We aimed to evaluate the clinical performance of expanded noninvasive prenatal testing (NIPT-Plus) for the detection of aneuploidies and microdeletion/microduplication syndromes.

METHODS

A total of 7177 pregnant women were enrolled in the study from June 2020 to March 2022 at Xijing Hospital, China. Cases with NIPT-Plus-positive results were further confirmed by chromosomal karyotyping and a chromosomal microarray analysis.

RESULTS

A total of 112 positive cases (1.56%) were identified by NIPT-Plus, including 60 chromosome aneuploidies and 52 microdeletion/microduplication syndromes. Ninety-five cases were validated by amniocentesis, and 57 were confirmed with true-positive results, comprising 18 trisomy 21, 4 trisomy 18, 1 trisomy 13, 17 sex chromosome aneuploidies, 1 other aneuploidy, and 16 microdeletion/microduplication syndromes. The positive predictive value of total chromosomal abnormalities was 60% (57/95). For trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidies, other aneuploidies and microdeletion/microduplication syndromes, the sensitivity was all 100%, the specificity was 100, 99.986, 100, 99.888, 99.958, and 99.636%, and the positive predictive value was 100, 80, 100, 68, 25, and 38.10%, respectively. For all clinical characteristics, the abnormal maternal serum screening group was found to have the highest prevalence of chromosomal abnormalities (1.54%), and the ultrasound abnormality group presented the highest positive predictive value (73.33%).

CONCLUSIONS

NIPT-Plus has great potential for the detection of aneuploidies and microdeletion/microduplication syndromes owing to its high sensitivity, safety, and specificity, which greatly reduces unnecessary invasive procedures and the risk of miscarriage and allows informed maternal choice.

Prenatal Detection of Trisomy 2: Considerations for Genetic Counseling and Testing

We report on the case of prenatal detection of trisomy 2 in placental biopsy and further algorithm of genetic counseling and testing. A 29-year-old woman with first-trimester biochemical markers refused chorionic villus sampling and preferred targeted non-invasive prenatal testing (NIPT), which showed low risk for aneuploidies 13, 18, 21, and X. A series of ultrasound examinations revealed increased chorion thickness at 13/14 weeks of gestation and fetal growth retardation, a hyperechoic bowel, challenging visualization of the kidneys, dolichocephaly, ventriculomegaly, increase in placental thickness, and pronounced oligohydramnios at 16/17 weeks of gestation. The patient was referred to our center for an invasive prenatal diagnosis. The patient's blood and placenta were sampled for whole-genome sequencing-based NIPT and array comparative genomic hybridization (aCGH), respectively. Both investigations revealed trisomy 2. Further prenatal genetic testing in order to confirm trisomy 2 in amniocytes and/or fetal blood was highly questionable because oligohydramnios and fetal growth retardation made amniocentesis and cordocentesis technically unfeasible. The patient opted to terminate the pregnancy. Pathological examination of the fetus revealed internal hydrocephalus, atrophy of brain structure, and craniofacial dysmorphism. Conventional cytogenetic analysis and fluorescence in situ hybridization revealed chromosome 2 mosaicism with a prevalence of trisomic clone in the placenta (83.2% vs. 16.8%) and a low frequency of trisomy 2, which did not exceed 0.6% in fetal tissues, advocating for low-level true fetal mosaicism. To conclude, in pregnancies at risk of fetal chromosomal abnormalities that refuse invasive prenatal diagnosis, whole-genome sequencing-based NIPT, but not targeted NIPT, should be considered. In prenatal cases of trisomy 2, true mosaicism should be distinguished from placental-confined mosaicism using cytogenetic analysis of amniotic fluid cells or fetal blood cells. However, if material sampling is impossible due to oligohydramnios and/or fetal growth retardation, further decisions should be based on a series of high-resolution fetal ultrasound examinations. Genetic counseling for the risk of uniparental disomy in a fetus is also required.